From 0bcac55da9b4e840b5c71c8c1b1c19a43a2995c6 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Sun, 7 Jul 2024 16:33:18 +0200
Subject: [PATCH 01/75] Added: Database update system and initial hashing

---
 App.R | 161 +++++++++++++++++++++++++++-------------------------------
 1 file changed, 75 insertions(+), 86 deletions(-)

diff --git a/App.R b/App.R
index 06f6e8b..ee08bfe 100644
--- a/App.R
+++ b/App.R
@@ -37,6 +37,7 @@ library(bslib)
 library(bsicons)
 library(DT)
 library(shinyBS)
+library(openssl)
 # Bioconductor Packages
 library(treeio)
 library(ggtree)
@@ -666,7 +667,6 @@ ui <- dashboardPage(
           column(1),
           column(
             width = 3,
-            align = "center",
             br(),
             br(),
             br(),
@@ -718,32 +718,27 @@ ui <- dashboardPage(
           ),
           column(
             width = 2,
-            align = "center",
             br(),
             br(),
             br(),
-            actionButton(
-              "download_cgMLST",
-              label = "Download",
-              icon = icon("download")
-            )
+            h5(textOutput("scheme_timestamp"), style = "color: white")
           ),
           column(
-            width = 6,
+            width = 2,
             br(),
             br(),
             br(),
-            align = "center",
-            conditionalPanel(
-              "input.download_cgMLST >= 1",
-              h4(p("Downloaded Loci"), style = "color:white")
+            actionButton(
+              "download_cgMLST",
+              label = "Download",
+              icon = icon("download")
             )
           )
         ),
         fluidRow(
           column(1),
           column(
-            width = 5,
+            width = 6,
             align = "center",
             br(),
             br(),
@@ -753,21 +748,6 @@ ui <- dashboardPage(
               spin = "dots",
               color = "#ffffff"
             )
-          ),
-          column(
-            width = 6,
-            align = "center",
-            br(),
-            br(),
-            br(),
-            conditionalPanel(
-              "input.download_cgMLST >= 1",
-              addSpinner(
-                dataTableOutput("cgmlst_targets"),
-                spin = "dots",
-                color = "#ffffff"
-              )
-            )
           )
         )
       ),
@@ -5489,10 +5469,11 @@ server <- function(input, output, session) {
   
   phylotraceVersion <- paste("PhyloTrace-1.4.1", Sys.Date())
   
-  # Kill server on session end
-  session$onSessionEnded( function() {
-    stopApp()
-  })
+  # TODO Enable this, or leave disabled
+  # # Kill server on session end
+  # session$onSessionEnded( function() {
+  #   stopApp()
+  # })
   
   # Disable MST variable mappings
   shinyjs::disable('mst_edge_label') 
@@ -5736,6 +5717,30 @@ server <- function(input, output, session) {
     })
   }
   
+  # Function to hash database
+  hash_database <- function(folder) {
+    loci_files <- list.files(folder)
+    loci_names <- sapply(strsplit(loci_files, "[.]"), function(x) x[1])
+    loci_paths <- file.path(folder, loci_files)
+    
+    hashes <- sapply(loci_paths, hash_locus)
+    names(hashes) <- loci_names
+    hashes
+  }
+  
+  # Function to hash a locus
+  hash_locus <- function(locus_path) {
+    locus_file <- readLines(locus_path)
+    seq_list <- locus_file[seq(2, length(locus_file), 3)]
+    seq_hash <- sha256(seq_list)
+    seq_idx <- paste0(">", seq_hash)
+    
+    locus_file[seq(1, length(locus_file), 3)] <- seq_idx
+    writeLines(locus_file, locus_path)
+    
+    seq_hash
+  }
+  
   # Function to check single typing log file
   check_new_entry <- reactive({
     
@@ -6643,11 +6648,7 @@ server <- function(input, output, session) {
             
             # Produce Loci Info table
             DB$loci_info <- read.csv(
-              paste0(
-                DB$database, "/",
-                gsub(" ", "_", DB$scheme),
-                "/targets.csv"
-              ),
+              file.path(DB$database, gsub(" ", "_", DB$scheme), "targets.csv"),
               header = TRUE,
               sep = "\t",
               row.names = NULL,
@@ -11326,65 +11327,47 @@ server <- function(input, output, session) {
     }
     
     DB$load_selected <- TRUE
-    Scheme$target_table <- NULL
+    
+    # Check if .downloaded_schemes folder exists and if not create it
+    if (!dir.exists(file.path(DB$database, ".downloaded_schemes"))) {
+      dir.create(file.path(DB$database, ".downloaded_schemes"))
+    }
     
     # Download Loci Fasta Files
     
     options(timeout = 600)
     
     tryCatch({
-      download.file(Scheme$link_cgmlst, "dataset.zip")
+      download.file(Scheme$link_cgmlst, 
+                    file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")))
       "Download successful!"
     }, error = function(e) {
       paste("Error: ", e$message)
     })
     
     unzip(
-      zipfile = "dataset.zip",
-      exdir = paste0(
-        DB$database, "/",
-        Scheme$folder_name,
-        paste0("/", Scheme$folder_name, "_alleles")
+      zipfile = file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")),
+      exdir = file.path(DB$database, 
+                        Scheme$folder_name, 
+                        paste0(Scheme$folder_name, "_alleles")
       )
     )
     
-    unlink("dataset.zip")
+    # Hash database
+    hash_database(file.path(DB$database, 
+                            Scheme$folder_name, 
+                            paste0(Scheme$folder_name, "_alleles")))
     
     # Download Scheme Info
     download(
       Scheme$link_scheme,
-      dest = paste0(DB$database, "/", Scheme$folder_name, "/scheme_info.html"),
-      mode = "wb"
-    )
-    
-    # Download Loci Info
-    download(
-      Scheme$link_targets,
-      dest = paste0(DB$database, "/", Scheme$folder_name, "/targets.csv"),
+      dest = file.path(DB$database, Scheme$folder_name, "scheme_info.html"),
       mode = "wb"
     )
     
     # Send downloaded scheme to database browser overview
     DB$available <- gsub("_", " ", basename(dir_ls(DB$database)))
     
-    Scheme$target_table <-
-      read.csv(
-        paste0(DB$database, "/", Scheme$folder_name, "/targets.csv"),
-        header = TRUE,
-        sep = "\t",
-        row.names = NULL,
-        colClasses = c(
-          "NULL",
-          "character",
-          "character",
-          "integer",
-          "integer",
-          "character",
-          "integer",
-          "NULL"
-        )
-      )
-    
     DB$exist <-
       (length(dir_ls(DB$database)) == 0)
     
@@ -11420,27 +11403,33 @@ server <- function(input, output, session) {
   
   
   # Download Target Info (CSV Table)
-  
-  
-  output$cgmlst_scheme <- renderTable({
+  observe({
+    input$download_cgMLST
+    
     scheme_overview <- read_html(Scheme$link_scheme) %>%
       html_table(header = FALSE) %>%
       as.data.frame(stringsAsFactors = FALSE)
+    
+    last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"], 
+                            format = "%B %d, %Y, %H:%M %p")
     names(scheme_overview) <- NULL
-    scheme_overview
+    
+    last_file_change <- format(
+      file.info(file.path(DB$database,
+                          ".downloaded_schemes",
+                          paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
+    
+    output$cgmlst_scheme <- renderTable({scheme_overview})
+    output$scheme_timestamp <- renderText({
+      req(last_file_change)
+      if (last_file_change < last_scheme_change) {
+        "(Newer scheme available \u274c)"
+      } else {
+        "(Scheme is up-to-date \u2705)"
+      }
+    })
   })
   
-  ### Display Target Table ----
-  
-  output$cgmlst_targets <- renderDataTable({
-    targets_overview <- Scheme$target_table
-    NULL
-  },
-  options = list(pageLength = 10,
-                 columnDefs = list(
-                   list(searchable = FALSE, targets = "_all")
-                 )))
-  
   # _______________________ ####
   
   ## Visualization ----

From 4686366c8fed9331b18c0736eb47801444fab191 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Wed, 10 Jul 2024 11:02:24 +0200
Subject: [PATCH 02/75] Adapted variant detection to hashed sequence indexes;
 minor fixes for scheme download

---
 App.R                      | 49 +++++++++++++++++++++-----------------
 execute/automatic_typing.R |  2 +-
 execute/single_typing.R    | 18 ++++++--------
 3 files changed, 35 insertions(+), 34 deletions(-)

diff --git a/App.R b/App.R
index ee08bfe..43f8b69 100644
--- a/App.R
+++ b/App.R
@@ -5482,25 +5482,6 @@ server <- function(input, output, session) {
   
   # Function to read and format FASTA sequences
   format_fasta <- function(filepath) {
-    log_message(log_file = out,
-                message = paste0("path: ", filepath),
-                append = TRUE)
-    
-    log_message(log_file = out,
-                message = paste0("db: ", DB$database),
-                append = TRUE)
-    
-    log_message(log_file = out,
-                message = paste0("scheme: ", DB$scheme),
-                append = TRUE)
-    
-    log_message(log_file = out,
-                message = paste0("selected: ", input$db_loci_rows_selected),
-                append = TRUE)                        
-    
-    log_message(log_file = out,
-                message = paste0("loci: ", head(DB$loci, 1)),
-                append = TRUE)
     
     fasta <- readLines(filepath)
     formatted_fasta <- list()
@@ -11311,6 +11292,7 @@ server <- function(input, output, session) {
   })
   
   observeEvent(input$download_cgMLST, {
+    
     log_message(out, message = paste0("Started download of scheme for ", Scheme$folder_name))
     
     show_toast(
@@ -11330,7 +11312,7 @@ server <- function(input, output, session) {
     
     # Check if .downloaded_schemes folder exists and if not create it
     if (!dir.exists(file.path(DB$database, ".downloaded_schemes"))) {
-      dir.create(file.path(DB$database, ".downloaded_schemes"))
+      dir.create(file.path(DB$database, ".downloaded_schemes"), recursive = TRUE)
     }
     
     # Download Loci Fasta Files
@@ -11365,11 +11347,34 @@ server <- function(input, output, session) {
       mode = "wb"
     )
     
+    # Download Loci Info	
+    download(	
+      Scheme$link_targets,	
+      dest = paste0(DB$database, "/", Scheme$folder_name, "/targets.csv"),	
+      mode = "wb"
+    )
+    
     # Send downloaded scheme to database browser overview
     DB$available <- gsub("_", " ", basename(dir_ls(DB$database)))
     
-    DB$exist <-
-      (length(dir_ls(DB$database)) == 0)
+    Scheme$target_table <- read.csv(
+      paste0(DB$database, "/", Scheme$folder_name, "/targets.csv"),	
+      header = TRUE,	
+      sep = "\t",	
+      row.names = NULL,	
+      colClasses = c(	
+        "NULL",	
+        "character",	
+        "character",	
+        "integer",	
+        "integer",	
+        "character",	
+        "integer",	
+        "NULL"	
+      )	
+    )
+    
+    DB$exist <- length(dir_ls(DB$database)) == 0
     
     show_toast(
       title = "Download successful",
diff --git a/execute/automatic_typing.R b/execute/automatic_typing.R
index 9656089..9407258 100644
--- a/execute/automatic_typing.R
+++ b/execute/automatic_typing.R
@@ -323,4 +323,4 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
   log.message(log_file = paste0(meta_info$db_directory, "/logs/output.log"), 
               message = paste0("Assembly typing failed for ", 
                                sub("\\.(fasta|fna|fa)$", "", basename(assembly))))
-}
+}
\ No newline at end of file
diff --git a/execute/single_typing.R b/execute/single_typing.R
index 624229e..8363587 100644
--- a/execute/single_typing.R
+++ b/execute/single_typing.R
@@ -42,7 +42,7 @@ template <- readLines(assembly)
 psl_files <- list.files(paste0(meta_info$db_directory, "/execute/blat_single/results"), pattern = "\\.psl$", full.names = TRUE)
 
 # Initialize an empty vector to store the results
-allele_vector <- integer(length(psl_files))
+allele_vector <- character(length(psl_files))
 
 event_df <- data.frame(Locus = character(0), Event = character(0), Value = character(0))
 
@@ -66,9 +66,6 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
       
       matches <- data.table::fread(psl_files[i], select = c(1, 5, 6, 7, 8, 10, 11, 14, 16, 17), header = FALSE)
       
-      # variant count 
-      n_variants <- max(matches$V10)
-      
       if(any(matches$V1 == matches$V11 & (matches$V5 + matches$V7) == 0)) {
         
         perf_match <- matches[which(matches$V1 == matches$V11)]
@@ -105,16 +102,18 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
         # if valid variant found 
         if(variant_valid != FALSE) {
           
+          hashed_variant <- openssl::sha256(variant_valid)
+          
           # Append new variant number to allele fasta file
-          cat(paste0("\n>", n_variants + 1), file = locus_file, append = TRUE)
+          cat(paste0("\n>", hashed_variant), file = locus_file, append = TRUE)
           
           # Append new variant sequence to allele fasta file
           cat(paste0("\n", variant_valid, "\n"), file = locus_file, append = TRUE)
           
           # Entry in results data frame
-          event_df <- rbind(event_df, data.frame(Locus = allele_index, Event = "New Variant", Value = as.character(n_variants + 1)))
+          event_df <- rbind(event_df, data.frame(Locus = allele_index, Event = "New Variant", Value = hashed_variant))
           
-          allele_vector[[i]] <- n_variants + 1
+          allele_vector[[i]] <- hashed_variant
           
           cat(paste0(allele_index, " has new variant.\n"))
           
@@ -128,15 +127,12 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
           
           cat(paste0(allele_index, " has invalid sequence.\n"))
         }
-        
       }
     }
   }
   
   saveRDS(event_df, "execute/event_df.rds")
   
-  allele_vector <- as.integer(allele_vector)
-  
   # Create Results Data Frame 
   if(!any(grepl("Typing", list.files(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing)))))) {
     
@@ -184,7 +180,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
     
     Database[["Typing"]] <- Typing
     
-    df2 <- dplyr::mutate_all(dplyr::select(Database$Typing, 13:(12+length(list.files(allele_folder)))), function(x) as.integer(x))
+    df2 <- dplyr::mutate_all(dplyr::select(Database$Typing, 13:(12+length(list.files(allele_folder)))), function(x) as.character(x))
     
     df1 <- dplyr::select(Database$Typing, 1:12)
     df1 <- dplyr::mutate(df1, Include = as.logical(Include))

From 9bac2d3f30b75c7feb5787fc335cb719cecd177c Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Thu, 11 Jul 2024 17:52:28 +0200
Subject: [PATCH 03/75] Changed tab name 'Add Scheme' to 'Manage Schemes'

---
 App.R | 44 ++++++++++++++++++++++++++------------------
 1 file changed, 26 insertions(+), 18 deletions(-)

diff --git a/App.R b/App.R
index 43f8b69..3f3658e 100644
--- a/App.R
+++ b/App.R
@@ -651,7 +651,7 @@ ui <- dashboardPage(
         )
       ),
       
-      ## Tab Add Scheme  ----  
+      ## Tab Manage Schemes  ----  
       
       tabItem(
         tabName = "init",
@@ -721,7 +721,7 @@ ui <- dashboardPage(
             br(),
             br(),
             br(),
-            h5(textOutput("scheme_timestamp"), style = "color: white")
+            h5(textOutput("scheme_update_info"), style = "color: white")
           ),
           column(
             width = 2,
@@ -6239,7 +6239,7 @@ server <- function(input, output, session) {
         DB$block_db <- TRUE
         DB$select_new <- FALSE
         
-        # Render menu with Add Scheme as start tab and no Missing values tab
+        # Render menu with Manage Schemes as start tab and no Missing values tab
         output$menu <- renderMenu(
           sidebarMenu(
             menuItem(
@@ -6265,7 +6265,7 @@ server <- function(input, output, session) {
               )
             ),
             menuItem(
-              text = "Add Scheme",
+              text = "Manage Schemes",
               tabName = "init",
               icon = icon("plus"),
               selected = TRUE
@@ -6366,6 +6366,8 @@ server <- function(input, output, session) {
             
             log_message(log_file = out, message = "Missing loci files")
             
+            # TODO Check if changes are needed for robust update changes
+            
             # Show message that loci files are missing
             showModal(
               modalDialog(
@@ -6381,7 +6383,7 @@ server <- function(input, output, session) {
               )
             )
             
-            # Render menu with Add Scheme as start tab
+            # Render menu with Manage Schemes as start tab
             output$menu <- renderMenu(
               sidebarMenu(
                 menuItem(
@@ -6412,7 +6414,7 @@ server <- function(input, output, session) {
                   )
                 ),
                 menuItem(
-                  text = "Add Scheme",
+                  text = "Manage Schemes",
                   tabName = "init",
                   icon = icon("plus"),
                   selected = TRUE
@@ -6435,6 +6437,8 @@ server <- function(input, output, session) {
             
             output$download_scheme_info <- NULL
             
+            # TODO check if changes are needed for robust update changes
+            
             log_message(log_file = out, message = "Scheme info file missing")
             
             # Show message that scheme info is missing
@@ -6452,7 +6456,7 @@ server <- function(input, output, session) {
               )
             )
             
-            # Render menu with Add Scheme as start tab
+            # Render menu with Manage Schemes as start tab
             output$menu <- renderMenu(
               sidebarMenu(
                 menuItem(
@@ -6483,7 +6487,7 @@ server <- function(input, output, session) {
                   )
                 ),
                 menuItem(
-                  text = "Add Scheme",
+                  text = "Manage Schemes",
                   tabName = "init",
                   icon = icon("plus"),
                   selected = TRUE
@@ -6510,6 +6514,8 @@ server <- function(input, output, session) {
             
             log_message(log_file = out, message = "Missing loci info (targets.csv)")
             
+            # TODO check if changes are needed for robust update changes
+            
             # Show message that scheme info is missing
             showModal(
               modalDialog(
@@ -6525,7 +6531,7 @@ server <- function(input, output, session) {
               )
             )
             
-            # Render menu with Add Scheme as start tab
+            # Render menu with Manage Schemes as start tab
             output$menu <- renderMenu(
               sidebarMenu(
                 menuItem(
@@ -6556,7 +6562,7 @@ server <- function(input, output, session) {
                   )
                 ),
                 menuItem(
-                  text = "Add Scheme",
+                  text = "Manage Schemes",
                   tabName = "init",
                   icon = icon("plus"),
                   selected = TRUE
@@ -6645,6 +6651,8 @@ server <- function(input, output, session) {
               )
             )
             
+            # TODO check if changes are needed for robust update
+            
             # Check if number of loci/fastq-files of alleles is coherent with number of targets in scheme
             if(DB$number_loci != length(dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")))) {
               
@@ -6665,7 +6673,7 @@ server <- function(input, output, session) {
                 )
               )
               
-              # Render menu with Add Scheme as start tab
+              # Render menu with Manage Schemes as start tab
               output$menu <- renderMenu(
                 sidebarMenu(
                   menuItem(
@@ -6696,7 +6704,7 @@ server <- function(input, output, session) {
                     )
                   ),
                   menuItem(
-                    text = "Add Scheme",
+                    text = "Manage Schemes",
                     tabName = "init",
                     icon = icon("plus"),
                     selected = TRUE
@@ -6861,7 +6869,7 @@ server <- function(input, output, session) {
                         )
                       ),
                       menuItem(
-                        text = "Add Scheme",
+                        text = "Manage Schemes",
                         tabName = "init",
                         icon = icon("plus")
                       ),
@@ -6909,7 +6917,7 @@ server <- function(input, output, session) {
                         )
                       ),
                       menuItem(
-                        text = "Add Scheme",
+                        text = "Manage Schemes",
                         tabName = "init",
                         icon = icon("plus")
                       ),
@@ -9069,7 +9077,7 @@ server <- function(input, output, session) {
                       )
                     ),
                     menuItem(
-                      text = "Add Scheme",
+                      text = "Manage Schemes",
                       tabName = "init",
                       icon = icon("plus")
                     ),
@@ -9408,7 +9416,7 @@ server <- function(input, output, session) {
                 )
               ),
               menuItem(
-                text = "Add Scheme",
+                text = "Manage Schemes",
                 tabName = "init",
                 icon = icon("plus")
               ),
@@ -9452,7 +9460,7 @@ server <- function(input, output, session) {
               )
             ),
             menuItem(
-              text = "Add Scheme",
+              text = "Manage Schemes",
               tabName = "init",
               icon = icon("plus")
             ),
@@ -11425,7 +11433,7 @@ server <- function(input, output, session) {
                           paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
     
     output$cgmlst_scheme <- renderTable({scheme_overview})
-    output$scheme_timestamp <- renderText({
+    output$scheme_update_info <- renderText({
       req(last_file_change)
       if (last_file_change < last_scheme_change) {
         "(Newer scheme available \u274c)"

From dd0b1b3b50df25cf6c3d52553de6211d2470699f Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Sat, 20 Jul 2024 17:04:49 +0200
Subject: [PATCH 04/75] Database update system and hashing implemented

---
 App.R | 130 +++++++++++++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 116 insertions(+), 14 deletions(-)

diff --git a/App.R b/App.R
index 3f3658e..0f39341 100644
--- a/App.R
+++ b/App.R
@@ -5722,6 +5722,33 @@ server <- function(input, output, session) {
     seq_hash
   }
   
+  # Get locus hashes
+  get_locus_hashes <- function(locus_path) {
+    locus_file <- readLines(locus_path)
+    hash_list <- locus_file[seq(1, length(locus_file), 3)]
+    hash_list <- sapply(strsplit(hash_list, "[>]"), function(x) x[2])
+  }
+  
+  extract_seq <- function(locus_path, hashes) {
+    locus_file <- readLines(locus_path)
+    hash_list <- sapply(strsplit(locus_file[seq(1, length(locus_file), 3)], "[>]"), function(x) x[2])
+    seq_list <- locus_file[seq(2, length(locus_file), 3)]
+    seq_idx <- hash_list %in% hashes
+    
+    list(
+      idx = hash_list[seq_idx],
+      seq = seq_list[seq_idx]
+    )
+  }
+  
+  add_new_sequences <- function(locus_path, sequences) {
+    locus_file <- file(locus_path, open = "a+")
+    for (i in seq_along(sequences$idx)) {
+      writeLines(c("", paste0(">", sequences$idx[i]), sequences$seq[i]), locus_file)
+    }
+    close(locus_file)
+  }
+  
   # Function to check single typing log file
   check_new_entry <- reactive({
     
@@ -6366,8 +6393,6 @@ server <- function(input, output, session) {
             
             log_message(log_file = out, message = "Missing loci files")
             
-            # TODO Check if changes are needed for robust update changes
-            
             # Show message that loci files are missing
             showModal(
               modalDialog(
@@ -6437,8 +6462,6 @@ server <- function(input, output, session) {
             
             output$download_scheme_info <- NULL
             
-            # TODO check if changes are needed for robust update changes
-            
             log_message(log_file = out, message = "Scheme info file missing")
             
             # Show message that scheme info is missing
@@ -6514,8 +6537,6 @@ server <- function(input, output, session) {
             
             log_message(log_file = out, message = "Missing loci info (targets.csv)")
             
-            # TODO check if changes are needed for robust update changes
-            
             # Show message that scheme info is missing
             showModal(
               modalDialog(
@@ -6651,8 +6672,6 @@ server <- function(input, output, session) {
               )
             )
             
-            # TODO check if changes are needed for robust update
-            
             # Check if number of loci/fastq-files of alleles is coherent with number of targets in scheme
             if(DB$number_loci != length(dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")))) {
               
@@ -11320,11 +11339,17 @@ server <- function(input, output, session) {
     
     # Check if .downloaded_schemes folder exists and if not create it
     if (!dir.exists(file.path(DB$database, ".downloaded_schemes"))) {
+      print("Creating download schemes folder")
       dir.create(file.path(DB$database, ".downloaded_schemes"), recursive = TRUE)
     }
     
-    # Download Loci Fasta Files
+    # Check if remains of old temporary folder exists and remove them
+    if (dir.exists(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")))) {
+      print("Deleting old temporary folder")
+      unlink(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")), recursive = TRUE)
+    }
     
+    # Download Loci Fasta Files
     options(timeout = 600)
     
     tryCatch({
@@ -11335,18 +11360,93 @@ server <- function(input, output, session) {
       paste("Error: ", e$message)
     })
     
+    print("Unzipping the scheme")
+    # Unzip the scheme in temporary folder
     unzip(
       zipfile = file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")),
       exdir = file.path(DB$database, 
                         Scheme$folder_name, 
-                        paste0(Scheme$folder_name, "_alleles")
+                        paste0(Scheme$folder_name, ".tmp")
       )
     )
     
-    # Hash database
+    print("Producing hashes for the database")
+    # Hash temporary folder
     hash_database(file.path(DB$database, 
                             Scheme$folder_name, 
-                            paste0(Scheme$folder_name, "_alleles")))
+                            paste0(Scheme$folder_name, ".tmp")))
+    
+    # Get list from local database
+    local_db_filelist <- list.files(file.path(DB$database, 
+                                              Scheme$folder_name, 
+                                              paste0(Scheme$folder_name, "_alleles")))
+    if (!is_empty(local_db_filelist)) {
+      print("Old database is not empty, resolving the files!")
+      # Get list from temporary database
+      tmp_db_filelist <- list.files(file.path(DB$database,
+                                              Scheme$folder_name,
+                                              paste0(Scheme$folder_name, ".tmp")))
+      
+      # Find the difference (extra files in local database)
+      local_db_extra <- setdiff(local_db_filelist, tmp_db_filelist)
+      
+      # Copy extra files to temporary folder
+      file.copy(file.path(DB$database,
+                          Scheme$folder_name, 
+                          paste0(Scheme$folder_name, "_alleles"), local_db_extra),
+                file.path(DB$database,
+                          Scheme$folder_name,
+                          paste0(Scheme$folder_name, ".tmp")))
+      
+      # Check differences in file pairs
+      local_db_hashes <- tools::md5sum(file.path(DB$database,
+                                                 Scheme$folder_name,
+                                                 paste0(Scheme$folder_name, "_alleles"),
+                                                 local_db_filelist))
+      tmp_db_hashes <- tools::md5sum(file.path(DB$database,
+                                               Scheme$folder_name,
+                                               paste0(Scheme$folder_name, ".tmp"),
+                                               local_db_filelist))
+      
+      diff_files <- local_db_hashes %in% tmp_db_hashes
+      diff_loci <- names(local_db_hashes)[diff_files == FALSE]
+      diff_loci <- sapply(strsplit(diff_loci, "/"), function(x) x[length(x)])
+      
+      # Check locus hashes
+      for (locus in diff_loci) {
+        local_db_hashes <- get_locus_hashes(file.path(DB$database,
+                                                      Scheme$folder_name,
+                                                      paste0(Scheme$folder_name, "_alleles"),
+                                                      locus))
+        tmp_db_hashes <- get_locus_hashes(file.path(DB$database,
+                                                    Scheme$folder_name,
+                                                    paste0(Scheme$folder_name, ".tmp"),
+                                                    locus))
+        diff_hashes <- setdiff(local_db_hashes, tmp_db_hashes)
+        
+        sequences <- extract_seq(file.path(DB$database,
+                                     Scheme$folder_name,
+                                     paste0(Scheme$folder_name, "_alleles"),
+                                     locus), diff_hashes)
+        if (!is_empty(sequences$idx) && !is_empty(sequences$seq) &&
+            length(sequences$idx) == length(sequences$seq)) {
+          add_new_sequences(file.path(DB$database,
+                                     Scheme$folder_name,
+                                     paste0(Scheme$folder_name, ".tmp"),
+                                     locus), sequences)
+        }
+      }
+    }
+    
+    print("Delete old alleles folder")
+    unlink(file.path(DB$database, Scheme$folder_name, 
+                         paste0(Scheme$folder_name, "_alleles")), recursive = TRUE)
+
+    print("Overwriting old alleles directory with temporary directory")
+    file.rename(file.path(DB$database, Scheme$folder_name,
+                        paste0(Scheme$folder_name, ".tmp")),
+              file.path(DB$database, Scheme$folder_name,
+                      paste0(Scheme$folder_name, "_alleles")))
     
     # Download Scheme Info
     download(
@@ -11358,7 +11458,7 @@ server <- function(input, output, session) {
     # Download Loci Info	
     download(	
       Scheme$link_targets,	
-      dest = paste0(DB$database, "/", Scheme$folder_name, "/targets.csv"),	
+      dest = file.path(DB$database, Scheme$folder_name, "targets.csv"),
       mode = "wb"
     )
     
@@ -11366,7 +11466,7 @@ server <- function(input, output, session) {
     DB$available <- gsub("_", " ", basename(dir_ls(DB$database)))
     
     Scheme$target_table <- read.csv(
-      paste0(DB$database, "/", Scheme$folder_name, "/targets.csv"),	
+      file.path(DB$database, Scheme$folder_name, "targets.csv"),
       header = TRUE,	
       sep = "\t",	
       row.names = NULL,	
@@ -11392,6 +11492,8 @@ server <- function(input, output, session) {
       width = "400px"
     )
     
+    # TODO Add log message regarding the update of the scheme
+    
     log_message(out, message = "Download successful")
     
     showModal(

From 2b9ee2e706fbf6cdb82cec1e44204712536c263f Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Sat, 20 Jul 2024 17:53:08 +0200
Subject: [PATCH 05/75] Adapted variant detection to hashed sequence indexes

---
 execute/multi_eval.R | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index a164c6f..7cb621b 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -48,7 +48,7 @@ template <- readLines(assembly)
 psl_files <- list.files(results_folder[which(sub("\\.(fasta|fna|fa)$", "", basename(assembly)) == basename(results_folder))], pattern = "\\.psl$", full.names = TRUE)
 
 # Initialize an empty vector to store the results
-allele_vector <- integer(length(psl_files))
+allele_vector <- character(length(psl_files))
 
 # Initiate results list 
 if(length(assembly_folder) == 1) {
@@ -118,16 +118,18 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
         # if valid variant found 
         if(variant_valid != FALSE) {
           
+          hashed_variant <- openssl::sha256(variant_valid)
+
           # Append new variant number to allele fasta file
-          cat(paste0("\n>", n_variants + 1), file = locus_file, append = TRUE)
+          cat(paste0("\n>", hashed_variant), file = locus_file, append = TRUE)
           
           # Append new variant sequence to allele fasta file
           cat(paste0("\n", variant_valid, "\n"), file = locus_file, append = TRUE)
           
           # Entry in results data frame
-          event_list[[basename(assembly)]] <- rbind(event_list[[basename(assembly)]], data.frame(Locus = allele_index, Event = "New Variant", Value = as.character(n_variants + 1)))
+          event_list[[basename(assembly)]] <- rbind(event_list[[basename(assembly)]], data.frame(Locus = allele_index, Event = "New Variant", Value = hashed_variant))
           
-          allele_vector[[i]] <- n_variants + 1
+          allele_vector[[i]] <- hashed_variant
           
           cat(paste0(allele_index, " has new variant.\n"))
           
@@ -207,7 +209,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
     
     Database[["Typing"]] <- Typing
     
-    df2 <- dplyr::mutate_all(dplyr::select(Database$Typing, 13:(12+length(list.files(allele_folder)))), function(x) as.integer(x))
+    df2 <- dplyr::mutate_all(dplyr::select(Database$Typing, 13:(12+length(list.files(allele_folder)))), function(x) as.character(x))
     
     df1 <- dplyr::select(Database$Typing, 1:12)
     df1 <- dplyr::mutate(df1, Include = as.logical(Include))

From d04d43ef30016aae1dd22db80a80711588c05ab1 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Sat, 20 Jul 2024 17:55:29 +0200
Subject: [PATCH 06/75] minor fix

---
 execute/multi_eval.R | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index 7cb621b..7e8e667 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -79,9 +79,6 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
       
       matches <- data.table::fread(psl_files[i], select = c(1, 5, 6, 7, 8, 10, 11, 14, 16, 17), header = FALSE)
       
-      # variant count 
-      n_variants <- max(matches$V10)
-      
       if(any(matches$V1 == matches$V11 & (matches$V5 + matches$V7) == 0)) {
         
         perf_match <- matches[which(matches$V1 == matches$V11)]

From 04a81243d152338cf82de147fd00cf8a8aab755b Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Sun, 21 Jul 2024 19:53:00 +0200
Subject: [PATCH 07/75] Multi Typing bugfix

---
 execute/multi_eval.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index 7e8e667..6e5a560 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -124,7 +124,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
           cat(paste0("\n", variant_valid, "\n"), file = locus_file, append = TRUE)
           
           # Entry in results data frame
-          event_list[[basename(assembly)]] <- rbind(event_list[[basename(assembly)]], data.frame(Locus = allele_index, Event = "New Variant", Value = hashed_variant))
+          event_list[[basename(assembly)]] <- rbind(event_list[[basename(assembly)]], data.frame(Locus = allele_index, Event = "New Variant", Value = as.character(hashed_variant)))
           
           allele_vector[[i]] <- hashed_variant
           

From 6f475b080e362b448c24f2c9a7db6b80ad4b252c Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Wed, 24 Jul 2024 21:27:46 +0200
Subject: [PATCH 08/75] Added show long hash switch

---
 App.R | 96 ++++++++++++++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 79 insertions(+), 17 deletions(-)

diff --git a/App.R b/App.R
index 1de5b50..12a72fb 100644
--- a/App.R
+++ b/App.R
@@ -22046,20 +22046,44 @@ server <- function(input, output, session) {
           output$typing_result_table <- renderRHandsontable({
             typing_result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
             if(nrow(typing_result_table) > 0) {
+              if (input$typing_results_longhash) {
+                renderer <- htmlwidgets::JS(
+                  "function(instance, td, row, col, prop, value, cellProperties) {
+                            if (value.length > 8) {
+                              value = value;
+                            }
+                            td.innerHTML = value;
+                            return td;
+                          }"
+                )
+              } else {
+                renderer <- htmlwidgets::JS(
+                  "function(instance, td, row, col, prop, value, cellProperties) {
+                            if (value.length > 8) {
+                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                            }
+                            td.innerHTML = value;
+                            return td;
+                          }"
+                )
+              }
+              
               if(nrow(typing_result_table) > 15) {
                 rhandsontable(typing_result_table, rowHeaders = NULL, 
                               stretchH = "all", height = 500, readOnly = TRUE,
                               contextMenu = FALSE) %>%
                   hot_cols(columnSorting = TRUE) %>%
                   hot_rows(rowHeights = 25) %>%
-                  hot_col(1:ncol(typing_result_table), valign = "htMiddle", halign = "htCenter")
+                  hot_col(1:ncol(typing_result_table), valign = "htMiddle", halign = "htCenter") %>%
+                  hot_col("Value", renderer = renderer)
               } else {
                 rhandsontable(typing_result_table, rowHeaders = NULL, 
                               stretchH = "all", readOnly = TRUE,
-                              contextMenu = FALSE,) %>%
+                              contextMenu = FALSE) %>%
                   hot_cols(columnSorting = TRUE) %>%
                   hot_rows(rowHeights = 25) %>%
-                  hot_col(1:ncol(typing_result_table), valign = "htMiddle", halign = "htCenter")
+                  hot_col(1:ncol(typing_result_table), valign = "htMiddle", halign = "htCenter") %>%
+                  hot_col("Value", renderer = renderer)
               }
             }
           })
@@ -22089,7 +22113,14 @@ server <- function(input, output, session) {
                     HTML(paste("<span style='color: white;'>", 
                                n_new,
                                if(n_new == 1) " locus with new variant."  else " loci with new variants.")),
-                    br(), br(),
+                    br(),
+                    materialSwitch(
+                      "typing_results_longhash",
+                      h5(p("Show Long Hash"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                      value = FALSE,
+                      right = TRUE
+                    ),
+                    br(),
                     rHandsontableOutput("typing_result_table")
                   )
                 } else {
@@ -23467,23 +23498,45 @@ server <- function(input, output, session) {
                           rowHeaders = NULL, stretchH = "all",
                           readOnly = TRUE, contextMenu = FALSE) %>%
               hot_rows(rowHeights = 25) %>%
-              hot_col(1:3, valign = "htMiddle", halign = "htCenter")})
-          
+              hot_col(1:3, valign = "htMiddle", halign = "htCenter")
+            })
         } else {
+          if (input$multi_results_longhash) {
+            renderer <- NULL
+          } else {
+            renderer <- htmlwidgets::JS(
+              "function(instance, td, row, col, prop, value, cellProperties) {
+                            if (value.length > 8) {
+                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                            }
+                            td.innerHTML = value;
+                            td.style.verticalAlign = 'middle';
+                            td.style.textAlign = 'center';
+                            return td;
+                          }"
+            )
+          }
+          
           if(Typing$multi_table_length > 15) {
             output$multi_typing_result_table <- renderRHandsontable({
               rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
                             stretchH = "all", height = 500,
                             readOnly = TRUE, contextMenu = FALSE) %>%
                 hot_rows(rowHeights = 25) %>%
-                hot_col(1:3, valign = "htMiddle", halign = "htCenter")})
+                hot_col(1:3, valign = "htMiddle", halign = "htCenter") %>%
+                hot_col("Value",
+                        renderer = renderer)
+              })
           } else {
             output$multi_typing_result_table <- renderRHandsontable({
               rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
                             stretchH = "all", readOnly = TRUE,
                             contextMenu = FALSE) %>%
                 hot_rows(rowHeights = 25) %>%
-                hot_col(1:3, valign = "htMiddle", halign = "htCenter")})
+                hot_col(1:3, valign = "htMiddle", halign = "htCenter") %>%
+                hot_col("Value",
+                        renderer = renderer)
+              })
             
           }
         }
@@ -23522,17 +23575,26 @@ server <- function(input, output, session) {
                 width = 9,
                 br(), br(),
                 br(), br(),
-                br(), 
-                div(
-                  class = "mult_res_sel",
-                  selectInput(
-                    "multi_results_picker",
-                    label = h5("Select Typing Results", style = "color:white"),
-                    choices = names(Typing$result_list),
-                    selected = names(Typing$result_list)[length(names(Typing$result_list))],
+                br(),
+                fluidRow(
+                  div(
+                    class = "mult_res_sel",
+                    selectInput(
+                      "multi_results_picker",
+                      label = h5("Select Typing Results", style = "color:white"),
+                      choices = names(Typing$result_list),
+                      selected = names(Typing$result_list)[length(names(Typing$result_list))],
+                    )
                   )
                 ),
-                br(), br(), 
+                br(), 
+                materialSwitch(
+                  "multi_results_longhash",
+                  h5(p("Show Long Hash"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                  value = FALSE,
+                  right = TRUE
+                ),
+                br(), 
                 rHandsontableOutput("multi_typing_result_table")
               )
             )

From 9e1a6dd2780afab71193188b3e2d297d04dd79af Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Thu, 25 Jul 2024 15:42:33 +0200
Subject: [PATCH 09/75] Changes typing evaluation logic to consider ambiguous
 nucleotides, additions to status bar

---
 App.R                        |  465 ++++++-----
 execute/multi_eval.R         |   14 +-
 execute/single_eval.R        |   14 +-
 execute/variant_validation.R |   18 +-
 www/body.css                 | 1474 +++++++++++++++++-----------------
 www/head.css                 |   25 +
 6 files changed, 1050 insertions(+), 960 deletions(-)

diff --git a/App.R b/App.R
index 12a72fb..0649108 100644
--- a/App.R
+++ b/App.R
@@ -280,6 +280,8 @@ ui <- dashboardPage(
         )
       )
     ),
+    uiOutput("databasetext"),
+    uiOutput("statustext"),
     tags$li(class = "dropdown", 
             tags$span(id = "currentTime", style = "color:white; font-weight:bold;")),
     disable = FALSE
@@ -5801,7 +5803,8 @@ server <- function(input, output, session) {
                            progress = 0, 
                            progress_format_start = 0, 
                            progress_format_end = 0,
-                           result_list = NULL) # reactive variables related to typing process
+                           result_list = NULL,
+                           status = "") # reactive variables related to typing process
   
   Vis <- reactiveValues(cluster = NULL, 
                         metadata = list(),
@@ -5953,7 +5956,7 @@ server <- function(input, output, session) {
   })
   
   observeEvent(input$db_location, {
-     log_print("Input db_location")
+    log_print("Input db_location")
     DB$select_new <- FALSE
   })
   
@@ -6110,7 +6113,79 @@ server <- function(input, output, session) {
   
   observeEvent(input$load, {
     
-     log_print("Input load")
+    log_print("Input load")
+    
+    observe({
+      if(!is.null(DB$database)){
+        output$databasetext <- renderUI({
+          fluidRow(
+            tags$li(
+              class = "dropdown", 
+              tags$span(HTML(
+                paste('<i class="fa-solid fa-folder-open"></i>', 
+                      "Database:&nbsp;&nbsp;&nbsp;<i>",
+                      DB$database,
+                      "</i>")), 
+                style = "color:white;")
+            )
+          )
+        })
+      }
+    })
+    
+    observe({
+      if(!is.null(DB$database)) {
+        if(Typing$status == "Finalized"){
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp; <i>typing finalized</i>")),
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(Typing$status == "Attaching"){
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp; <i>evaluating typing results</i>")),
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(Typing$status == "Processing") {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> running typing</i>")), 
+                  style = "color:white;")
+              )
+            )
+          )
+        } else {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
+                  style = "color:white;")
+              )
+            )
+          )
+        }    
+      }
+    })
     
     # Null single typing status
     if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
@@ -6152,13 +6227,13 @@ server <- function(input, output, session) {
           title = "Directory already contains a database",
           type = "error",
           width = "500px",
-          position = "top-end",
+          position = "bottom-end",
           timer = 6000
         )
         DB$load_selected <- FALSE
         
       } else if(DB$select_new | (DB$select_new == FALSE & is.null(input$scheme_db))) {
-         
+        
         log_print(paste0("New database created in ", DB$new_database))
         
         DB$check_new_entries <- TRUE
@@ -6410,7 +6485,7 @@ server <- function(input, output, session) {
             
             output$download_scheme_info <- NULL
             
-             log_print("Scheme info file missing")
+            log_print("Scheme info file missing")
             
             # Show message that scheme info is missing
             showModal(
@@ -6483,7 +6558,7 @@ server <- function(input, output, session) {
             # Dont render target download button
             output$download_loci <- NULL
             
-             log_print("Missing loci info (targets.csv)")
+            log_print("Missing loci info (targets.csv)")
             
             # Show message that scheme info is missing
             showModal(
@@ -6623,7 +6698,7 @@ server <- function(input, output, session) {
             # Check if number of loci/fastq-files of alleles is coherent with number of targets in scheme
             if(DB$number_loci != length(dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")))) {
               
-               log_print(paste0("Loci files are missing in the local ", DB$scheme, " folder"))
+              log_print(paste0("Loci files are missing in the local ", DB$scheme, " folder"))
               
               # Show message that loci files are missing
               showModal(
@@ -8999,11 +9074,11 @@ server <- function(input, output, session) {
         }
       } else {
         
-         log_print("Invalid scheme folder")
+        log_print("Invalid scheme folder")
         show_toast(
           title = "Invalid scheme folder",
           type = "warning",
-          position = "top-end",
+          position = "bottom-end",
           width = "500px",
           timer = 4000
         )
@@ -9012,6 +9087,12 @@ server <- function(input, output, session) {
     
   })
   
+  # _______________________ ####
+  
+  ## Status ----
+  
+  
+  
   # _______________________ ####
   
   ## Database ----
@@ -9353,7 +9434,7 @@ server <- function(input, output, session) {
       show_toast(
         title = "Invalid date",
         type = "warning",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "300px"
       )
@@ -9362,7 +9443,7 @@ server <- function(input, output, session) {
       show_toast(
         title = "Empty name",
         type = "warning",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "300px"
       )
@@ -9371,7 +9452,7 @@ server <- function(input, output, session) {
       show_toast(
         title = "Empty ID",
         type = "warning",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "300px"
       )
@@ -9384,16 +9465,13 @@ server <- function(input, output, session) {
   # Change scheme
   observeEvent(input$reload_db, {
     
-    fill1 <<- brewer.pal(3, input$upgma_clade_scale)
-    trest <<- input$upgma_clade_scale
-    
     log_print("Input reload_db")
     
     if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
       show_toast(
         title = "Pending Multi Typing",
         type = "warning",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "500px"
       )
@@ -9401,7 +9479,7 @@ server <- function(input, output, session) {
       show_toast(
         title = "Pending Single Typing",
         type = "warning",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "500px"
       )
@@ -9444,7 +9522,7 @@ server <- function(input, output, session) {
   
   # Undo db changes
   observeEvent(input$undo_changes, {
-     log_print("Input undo_changes")
+    log_print("Input undo_changes")
     
     DB$inhibit_change <- FALSE
     
@@ -10186,34 +10264,34 @@ server <- function(input, output, session) {
   DB$count <- 0
   
   observeEvent(input$add_new_variable, {
-     log_print("Input add_new_variable")
+    log_print("Input add_new_variable")
     
     if(nchar(input$new_var_name) > 12) {
-       log_print("Add variable; max. 10 character")
+      log_print("Add variable; max. 10 character")
       show_toast(
         title = "Max. 10 characters",
         type = "warning",
-        position = "top-end",
+        position = "bottom-end",
         width = "500px",
         timer = 6000
       )
     } else {
       if (input$new_var_name == "") {
-         log_print("Add variable; min. 1 character")
+        log_print("Add variable; min. 1 character")
         show_toast(
           title = "Min. 1 character",
           type = "error",
-          position = "top-end",
+          position = "bottom-end",
           width = "500px",
           timer = 6000
         )
       } else {
         if(trimws(input$new_var_name) %in% names(DB$meta)) {
-           log_print("Add variable; name already existing")
+          log_print("Add variable; name already existing")
           show_toast(
             title = "Variable name already existing",
             type = "warning",
-            position = "top-end",
+            position = "bottom-end",
             width = "500px",
             timer = 6000
           )
@@ -10239,7 +10317,7 @@ server <- function(input, output, session) {
   })
   
   observeEvent(input$conf_new_var, {
-     log_print("Input conf_new_var")
+    log_print("Input conf_new_var")
     
     removeModal()
     
@@ -10274,7 +10352,7 @@ server <- function(input, output, session) {
     show_toast(
       title = paste0("Variable ", trimws(input$new_var_name), " added"),
       type = "success",
-      position = "top-end",
+      position = "bottom-end",
       width = "500px",
       timer = 6000
     )
@@ -10282,14 +10360,14 @@ server <- function(input, output, session) {
   })
   
   observeEvent(input$delete_new_variable, {
-     log_print("Input delete_new_variable")
+    log_print("Input delete_new_variable")
     
     if (input$del_which_var == "") {
-       log_print("Delete custom variables; no custom variable")
+      log_print("Delete custom variables; no custom variable")
       show_toast(
         title = "No custom variables",
         type = "error",
-        position = "top-end",
+        position = "bottom-end",
         width = "500px",
         timer = 6000
       )
@@ -10314,7 +10392,7 @@ server <- function(input, output, session) {
   })
   
   observeEvent(input$conf_var_del, {
-     log_print("Input conf_var_del")
+    log_print("Input conf_var_del")
     
     DB$change <- TRUE
     
@@ -10327,12 +10405,12 @@ server <- function(input, output, session) {
     show_toast(
       title = paste0("Variable ", input$del_which_var, " removed"),
       type = "warning",
-      position = "top-end",
+      position = "bottom-end",
       width = "500px",
       timer = 6000
     )
     
-     log_print(paste0("Variable ", input$del_which_var, " removed"))
+    log_print(paste0("Variable ", input$del_which_var, " removed"))
     
     DB$cust_var <- DB$cust_var[-which(DB$cust_var$Variable == input$del_which_var),]
     DB$data <- select(DB$data, -(input$del_which_var))
@@ -10347,13 +10425,13 @@ server <- function(input, output, session) {
   # Select all button
   
   observeEvent(input$sel_all_entries, {
-     log_print("Input sel_all_entries")
+    log_print("Input sel_all_entries")
     
     DB$data$Include <- TRUE
   })
   
   observeEvent(input$desel_all_entries, {
-     log_print("Input desel_all_entries")
+    log_print("Input desel_all_entries")
     
     DB$data$Include <- FALSE
   })
@@ -10361,7 +10439,7 @@ server <- function(input, output, session) {
   # Switch to entry table
   
   observeEvent(input$change_entries, {
-     log_print("Input change_entries")
+    log_print("Input change_entries")
     
     removeModal()
     updateTabItems(session, "tabs", selected = "db_browse_entries")
@@ -10371,7 +10449,7 @@ server <- function(input, output, session) {
   
   output$download_na_matrix <- downloadHandler(
     filename = function() {
-       log_print(paste0("Save missing values table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")))
+      log_print(paste0("Save missing values table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")))
       paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")
     },
     content = function(file) {
@@ -10384,7 +10462,7 @@ server <- function(input, output, session) {
   
   output$download_schemeinfo <- downloadHandler(
     filename = function() {
-       log_print(paste0("Save scheme info table ", paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")))
+      log_print(paste0("Save scheme info table ", paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")))
       
       paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")
     },
@@ -10404,7 +10482,7 @@ server <- function(input, output, session) {
   
   output$download_loci_info <- downloadHandler(
     filename = function() {
-       log_print(paste0("Save loci info table ", paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")))
+      log_print(paste0("Save loci info table ", paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")))
       
       paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")
     },
@@ -10423,7 +10501,7 @@ server <- function(input, output, session) {
   
   output$download_entry_table <- downloadHandler(
     filename = function() {
-       log_print(paste0("Save entry table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")))
+      log_print(paste0("Save entry table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")))
       
       paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")
     },
@@ -10449,13 +10527,13 @@ server <- function(input, output, session) {
       show_toast(
         title = "Invalid rows entered. Saving not possible.",
         type = "error",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "600px"
       )
     } else {
       if(!isTRUE(DB$inhibit_change)) {
-         log_print("Input edit_button")
+        log_print("Input edit_button")
         
         showModal(
           modalDialog(
@@ -10482,11 +10560,11 @@ server <- function(input, output, session) {
           )
         )
       } else {
-         log_print("Input edit_button, invalid values.")
+        log_print("Input edit_button, invalid values.")
         show_toast(
           title = "Invalid values entered. Saving not possible.",
           type = "error",
-          position = "top-end",
+          position = "bottom-end",
           timer = 6000,
           width = "600px"
         )
@@ -10495,12 +10573,12 @@ server <- function(input, output, session) {
   })
   
   observeEvent(input$Cancel, {
-     log_print("Input Cancel")
+    log_print("Input Cancel")
     removeModal()
   })
   
   observeEvent(input$conf_db_save, {
-     log_print("Input conf_db_save")
+    log_print("Input conf_db_save")
     
     Data <- readRDS(paste0(
       DB$database, "/",
@@ -10579,32 +10657,32 @@ server <- function(input, output, session) {
     show_toast(
       title = "Database successfully saved",
       type = "success",
-      position = "top-end",
+      position = "bottom-end",
       timer = 4000,
       width = "500px"
     )
   })
   
   observeEvent(input$del_button, {
-     log_print("Input del_button")
+    log_print("Input del_button")
     
     if (length(input$select_delete) < 1) {
-       log_print("Delete entries; no entry selected")
+      log_print("Delete entries; no entry selected")
       show_toast(
         title = "No entry selected",
         type = "warning",
-        position = "top-end",
+        position = "bottom-end",
         timer = 4000,
         width = "500px"
       )
     } else if((readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") |
               (tail(readLogFile(), 1) != "0")) {
-       log_print("Delete entries; pending typing")
+      log_print("Delete entries; pending typing")
       
       show_toast(
         title = "Pending Typing",
         type = "warning",
-        position = "top-end",
+        position = "bottom-end",
         timer = 4000,
         width = "500px"
       )
@@ -10644,7 +10722,7 @@ server <- function(input, output, session) {
   })
   
   observeEvent(input$conf_delete_all, {
-     log_print("Input conf_delete_all")
+    log_print("Input conf_delete_all")
     
     # remove file with typing data
     file.remove(paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/Typing.rds"))
@@ -10673,7 +10751,7 @@ server <- function(input, output, session) {
   
   observeEvent(input$conf_delete, {
     
-     log_print("Input conf_delete")
+    log_print("Input conf_delete")
     
     DB$deleted_entries <- append(DB$deleted_entries, DB$data$Index[as.numeric(input$select_delete)])
     
@@ -10698,7 +10776,7 @@ server <- function(input, output, session) {
       show_toast(
         title = "Entries deleted",
         type = "success",
-        position = "top-end",
+        position = "bottom-end",
         timer = 4000,
         width = "500px"
       )
@@ -10706,7 +10784,7 @@ server <- function(input, output, session) {
       show_toast(
         title = "Entry deleted",
         type = "success",
-        position = "top-end",
+        position = "bottom-end",
         timer = 4000,
         width = "500px"
       )
@@ -10914,7 +10992,7 @@ server <- function(input, output, session) {
     show_toast(
       title = "Copied sequence",
       type = "success",
-      position = "top-end",
+      position = "bottom-end",
       timer = 3000,
       width = "400px"
     )
@@ -10923,7 +11001,7 @@ server <- function(input, output, session) {
   output$get_locus <- downloadHandler(
     filename = function() {
       fname <- basename(DB$loci[input$db_loci_rows_selected])
-       log_print(paste0("Get locus fasta ", fname))
+      log_print(paste0("Get locus fasta ", fname))
       fname
     },
     content = function(file) {
@@ -11127,12 +11205,12 @@ server <- function(input, output, session) {
   })
   
   observeEvent(input$download_cgMLST, {
-     log_print(paste0("Started download of scheme for ", Scheme$folder_name))
+    log_print(paste0("Started download of scheme for ", Scheme$folder_name))
     
     show_toast(
       title = "Download started",
       type = "success",
-      position = "top-end",
+      position = "bottom-end",
       timer = 5000,
       width = "400px"
     )
@@ -11232,28 +11310,28 @@ server <- function(input, output, session) {
         diff_hashes <- setdiff(local_db_hashes, tmp_db_hashes)
         
         sequences <- extract_seq(file.path(DB$database,
-                                     Scheme$folder_name,
-                                     paste0(Scheme$folder_name, "_alleles"),
-                                     locus), diff_hashes)
+                                           Scheme$folder_name,
+                                           paste0(Scheme$folder_name, "_alleles"),
+                                           locus), diff_hashes)
         if (!is_empty(sequences$idx) && !is_empty(sequences$seq) &&
             length(sequences$idx) == length(sequences$seq)) {
           add_new_sequences(file.path(DB$database,
-                                     Scheme$folder_name,
-                                     paste0(Scheme$folder_name, ".tmp"),
-                                     locus), sequences)
+                                      Scheme$folder_name,
+                                      paste0(Scheme$folder_name, ".tmp"),
+                                      locus), sequences)
         }
       }
     }
     
     print("Delete old alleles folder")
     unlink(file.path(DB$database, Scheme$folder_name, 
-                         paste0(Scheme$folder_name, "_alleles")), recursive = TRUE)
-
+                     paste0(Scheme$folder_name, "_alleles")), recursive = TRUE)
+    
     print("Overwriting old alleles directory with temporary directory")
     file.rename(file.path(DB$database, Scheme$folder_name,
-                        paste0(Scheme$folder_name, ".tmp")),
-              file.path(DB$database, Scheme$folder_name,
-                      paste0(Scheme$folder_name, "_alleles")))
+                          paste0(Scheme$folder_name, ".tmp")),
+                file.path(DB$database, Scheme$folder_name,
+                          paste0(Scheme$folder_name, "_alleles")))
     
     # Download Scheme Info
     download(
@@ -11294,13 +11372,13 @@ server <- function(input, output, session) {
     show_toast(
       title = "Download successful",
       type = "success",
-      position = "top-end",
+      position = "bottom-end",
       timer = 5000,
       width = "400px"
     )
     
     # TODO Add log message regarding the update of the scheme
-     log_print("Download successful")
+    log_print("Download successful")
     
     showModal(
       modalDialog(
@@ -11324,13 +11402,13 @@ server <- function(input, output, session) {
   # Download Target Info (CSV Table)
   observe({
     input$download_cgMLST
-
+    
     scheme_overview <- read_html(Scheme$link_scheme) %>%
       html_table(header = FALSE) %>%
       as.data.frame(stringsAsFactors = FALSE)
     
     last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"], 
-                            format = "%B %d, %Y, %H:%M %p")
+                                   format = "%B %d, %Y, %H:%M %p")
     names(scheme_overview) <- NULL
     
     last_file_change <- format(
@@ -11499,7 +11577,7 @@ server <- function(input, output, session) {
         show_toast(
           title = "Label already exists",
           type = "error",
-          position = "top-end",
+          position = "bottom-end",
           timer = 6000,
           width = "500px"
         )
@@ -11508,7 +11586,7 @@ server <- function(input, output, session) {
       show_toast(
         title = "Min. 1 character",
         type = "error",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "500px"
       )
@@ -11527,7 +11605,7 @@ server <- function(input, output, session) {
         show_toast(
           title = "Label already exists",
           type = "error",
-          position = "top-end",
+          position = "bottom-end",
           timer = 6000,
           width = "500px"
         )
@@ -11536,7 +11614,7 @@ server <- function(input, output, session) {
       show_toast(
         title = "Min. 1 character",
         type = "error",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "500px"
       )
@@ -15170,7 +15248,6 @@ server <- function(input, output, session) {
         multiple = TRUE,
         options = list(
           `live-search` = TRUE,
-          `noneSelectedText` = "Test",
           size = 10,
           style = "background-color: white; border-radius: 5px;"
         ),
@@ -15184,7 +15261,6 @@ server <- function(input, output, session) {
         multiple = TRUE,
         options = list(
           `live-search` = TRUE,
-          noneSelectedText = "Test",
           size = 10,
           style = "background-color: white; border-radius: 5px;"
         ),
@@ -15202,7 +15278,6 @@ server <- function(input, output, session) {
         multiple = TRUE,
         options = list(
           `live-search` = TRUE,
-          `noneSelectedText` = "Test",
           size = 10,
           style = "background-color: white; border-radius: 5px;"
         ),
@@ -15216,7 +15291,6 @@ server <- function(input, output, session) {
         multiple = TRUE,
         options = list(
           `live-search` = TRUE,
-          noneSelectedText = "Test",
           size = 10,
           style = "background-color: white; border-radius: 5px;"
         ),
@@ -18035,7 +18109,7 @@ server <- function(input, output, session) {
                      fill = fill,
                      type = input$nj_clade_type,
                      to.bottom = TRUE
-                     )
+        )
       } else {NULL}
     }
   })
@@ -20384,7 +20458,7 @@ server <- function(input, output, session) {
   ### Save MST Plot ----
   output$save_plot_html <- downloadHandler(
     filename = function() {
-       log_print(paste0("Save MST;", paste0("MST_", Sys.Date(), ".html")))
+      log_print(paste0("Save MST;", paste0("MST_", Sys.Date(), ".html")))
       paste0("MST_", Sys.Date(), ".html")
     },
     content = function(file) {
@@ -20398,7 +20472,7 @@ server <- function(input, output, session) {
   
   output$download_nj <- downloadHandler(
     filename = function() {
-       log_print(paste0("Save NJ;", paste0("NJ_", Sys.Date(), ".", input$filetype_nj)))
+      log_print(paste0("Save NJ;", paste0("NJ_", Sys.Date(), ".", input$filetype_nj)))
       paste0("NJ_", Sys.Date(), ".", input$filetype_nj)
     },
     content = function(file) {
@@ -20428,7 +20502,7 @@ server <- function(input, output, session) {
   
   output$download_upgma <- downloadHandler(
     filename = function() {
-       log_print(paste0("Save UPGMA;", paste0("UPGMA_", Sys.Date(), ".", input$filetype_upgma)))
+      log_print(paste0("Save UPGMA;", paste0("UPGMA_", Sys.Date(), ".", input$filetype_upgma)))
       paste0("UPGMA_", Sys.Date(), ".", input$filetype_upgma)
     },
     content = function(file) {
@@ -20908,32 +20982,32 @@ server <- function(input, output, session) {
   })
   
   observeEvent(input$create_tree, {
-     log_print("Input create_tree")
+    log_print("Input create_tree")
     
     if(is.null(DB$data)) {
-       log_print("Missing data")
+      log_print("Missing data")
       
       show_toast(
         title = "Missing data",
         type = "error",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "500px"
       )
     } else if(nrow(DB$allelic_profile_true) < 3) {
-       log_print("Min. of 3 entries required for visualization")
+      log_print("Min. of 3 entries required for visualization")
       
       show_toast(
         title = "Min. of 3 entries required for visualization",
         type = "error",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "500px"
       )
     } else {
       
       if(any(duplicated(DB$meta$`Assembly Name`)) | any(duplicated(DB$meta$`Assembly ID`))) {
-         log_print("Duplicated assemblies")
+        log_print("Duplicated assemblies")
         
         dup_name <- which(duplicated(DB$meta_true$`Assembly Name`))
         dup_id <- which(duplicated(DB$meta_true$`Assembly ID`))
@@ -20953,10 +21027,10 @@ server <- function(input, output, session) {
             } else {
               if(length(dup_name) == 0) {
                 HTML(c("Entries contain duplicated IDs <br><br>",
-                            paste0(unique(DB$meta_true$`Assembly ID`[dup_id]), "<br>")))
+                       paste0(unique(DB$meta_true$`Assembly ID`[dup_id]), "<br>")))
               } else if(length(dup_id) == 0) {
                 HTML(c("Entries contain duplicated names<br><br>",
-                            paste0(unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>")))
+                       paste0(unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>")))
               } else {
                 HTML(c("Entries contain duplicated names and IDs <br><br>",
                        paste0("Name: ", unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>"),
@@ -20994,7 +21068,7 @@ server <- function(input, output, session) {
             show_toast(
               title = "Conflicting Custom Variable Names",
               type = "warning",
-              position = "top-end",
+              position = "bottom-end",
               width = "500px",
               timer = 6000
             )
@@ -21150,7 +21224,7 @@ server <- function(input, output, session) {
             show_toast(
               title = "Conflicting Custom Variable Names",
               type = "warning",
-              position = "top-end",
+              position = "bottom-end",
               width = "500px",
               timer = 6000
             )
@@ -21311,7 +21385,7 @@ server <- function(input, output, session) {
             show_toast(
               title = "Computation might take a while",
               type = "warning",
-              position = "top-end",
+              position = "bottom-end",
               width = "500px",
               timer = 10000
             )
@@ -21746,7 +21820,7 @@ server <- function(input, output, session) {
       show_toast(
         title = "No tree created",
         type = "error",
-        position = "top-end",
+        position = "bottom-end",
         width = "500px",
         timer = 6000
       )
@@ -21902,7 +21976,7 @@ server <- function(input, output, session) {
         # Save data to an RDS file if any elements were selected
         if (!is.null(report)) {
           
-           log_print("Creating MST report")
+          log_print("Creating MST report")
           
           saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
           
@@ -21925,7 +21999,7 @@ server <- function(input, output, session) {
         
         # Save data to an RDS file if any elements were selected
         if (!is.null(report)) {
-           log_print("Creating NJ report")
+          log_print("Creating NJ report")
           
           saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
           
@@ -21933,7 +22007,7 @@ server <- function(input, output, session) {
           
           file.copy(paste0(getwd(), "/Report/Report.html"), file)
         } else {
-           log_print("Creating NJ report failed (report is null)")
+          log_print("Creating NJ report failed (report is null)")
         }
         
       } else {
@@ -21949,7 +22023,7 @@ server <- function(input, output, session) {
         
         # Save data to an RDS file if any elements were selected
         if (!is.null(report)) {
-           log_print("Creating UPGMA report")
+          log_print("Creating UPGMA report")
           
           saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
           
@@ -21957,7 +22031,7 @@ server <- function(input, output, session) {
           
           file.copy(paste0(getwd(), "/Report/Report.html"), file)
         } else {
-           log_print("Creating UPGMA report failed (report is null)")
+          log_print("Creating UPGMA report failed (report is null)")
         }
         
       }
@@ -22044,46 +22118,22 @@ server <- function(input, output, session) {
       if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
         if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
           output$typing_result_table <- renderRHandsontable({
-            typing_result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
-            if(nrow(typing_result_table) > 0) {
-              if (input$typing_results_longhash) {
-                renderer <- htmlwidgets::JS(
-                  "function(instance, td, row, col, prop, value, cellProperties) {
-                            if (value.length > 8) {
-                              value = value;
-                            }
-                            td.innerHTML = value;
-                            return td;
-                          }"
-                )
-              } else {
-                renderer <- htmlwidgets::JS(
-                  "function(instance, td, row, col, prop, value, cellProperties) {
-                            if (value.length > 8) {
-                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                            }
-                            td.innerHTML = value;
-                            return td;
-                          }"
-                )
-              }
-              
-              if(nrow(typing_result_table) > 15) {
-                rhandsontable(typing_result_table, rowHeaders = NULL, 
+            Typing$typing_result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
+            if(nrow(Typing$typing_result_table) > 0) {
+              if(nrow(Typing$typing_result_table) > 15) {
+                rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
                               stretchH = "all", height = 500, readOnly = TRUE,
                               contextMenu = FALSE) %>%
                   hot_cols(columnSorting = TRUE) %>%
                   hot_rows(rowHeights = 25) %>%
-                  hot_col(1:ncol(typing_result_table), valign = "htMiddle", halign = "htCenter") %>%
-                  hot_col("Value", renderer = renderer)
+                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter")
               } else {
-                rhandsontable(typing_result_table, rowHeaders = NULL, 
+                rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
                               stretchH = "all", readOnly = TRUE,
-                              contextMenu = FALSE) %>%
+                              contextMenu = FALSE,) %>%
                   hot_cols(columnSorting = TRUE) %>%
                   hot_rows(rowHeights = 25) %>%
-                  hot_col(1:ncol(typing_result_table), valign = "htMiddle", halign = "htCenter") %>%
-                  hot_col("Value", renderer = renderer)
+                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter")
               }
             }
           })
@@ -22113,14 +22163,7 @@ server <- function(input, output, session) {
                     HTML(paste("<span style='color: white;'>", 
                                n_new,
                                if(n_new == 1) " locus with new variant."  else " loci with new variants.")),
-                    br(),
-                    materialSwitch(
-                      "typing_results_longhash",
-                      h5(p("Show Long Hash"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                      value = FALSE,
-                      right = TRUE
-                    ),
-                    br(),
+                    br(), br(),
                     rHandsontableOutput("typing_result_table")
                   )
                 } else {
@@ -22375,7 +22418,7 @@ server <- function(input, output, session) {
         show_toast(
           title = "Wrong file type (only fasta/fna/fa)",
           type = "error",
-          position = "top-end",
+          position = "bottom-end",
           width = "500px",
           timer = 6000
         )
@@ -22404,15 +22447,15 @@ server <- function(input, output, session) {
   
   observeEvent(input$typing_start, {
     
-     log_print("Input typing_start")
+    log_print("Input typing_start")
     
     if(tail(readLogFile(), 1) != "0") {
-       log_print("Pending multi typing")
+      log_print("Pending multi typing")
       
       show_toast(
         title = "Pending Multi Typing",
         type = "warning",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "500px"
       )
@@ -22439,6 +22482,9 @@ server <- function(input, output, session) {
       output$metadata_single_box <- NULL
       output$start_typing_ui <- NULL
       
+      # status feedback
+      Typing$status <- "Processing"
+      
       # Locate folder containing cgMLST scheme
       search_string <- paste0(gsub(" ", "_", DB$scheme), "_alleles")
       
@@ -22457,12 +22503,12 @@ server <- function(input, output, session) {
         show_toast(
           title = "Typing Initiated",
           type = "success",
-          position = "top-end",
-          timer = 12000,
-          width = "500px"
+          position = "bottom-end",
+          timer = 6000,
+          width = "400px"
         )
         
-         log_print("Initiated single typing")
+        log_print("Initiated single typing")
         
         ### Run blat Typing
         
@@ -22537,7 +22583,7 @@ server <- function(input, output, session) {
           )
         })
       } else {
-         log_print("Folder containing cgMLST alleles not in working directory")
+        log_print("Folder containing cgMLST alleles not in working directory")
         
         show_alert(
           title = "Error",
@@ -22640,9 +22686,19 @@ server <- function(input, output, session) {
             br(), br(),
             if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
               if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
-                HTML(paste("<span style='color: white;'>", 
-                           sub(".*Successful", "Successful", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
-                           "Reset to start another typing process.", sep = '<br/>'))
+                req(Typing$scheme_loci_f, Typing$typing_result_table)
+                if(sum(Typing$typing_result_table$Event != "New Variant") >  (0.5 * length(Typing$scheme_loci_f))){
+                  HTML(
+                    paste("<span style='color: white;'>", 
+                          sub(".*Successful", "Finished", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
+                          paste("<span style='color: orange;'>", "Warning: Isolate contains large number of failed allele assignments."),
+                          paste("<span style='color: white;'>", "Reset to start another typing process."),
+                          sep = '<br/>\n'))                    
+                } else {
+                  HTML(paste("<span style='color: white;'>", 
+                             sub(".*Successful", "Successful", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
+                             "Reset to start another typing process.", sep = '<br/>'))
+                }
               } else {
                 HTML(paste("<span style='color: white;'>", 
                            sub(".*typing", "Typing", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
@@ -22668,7 +22724,7 @@ server <- function(input, output, session) {
   #### Declare Metadata  ----
   
   observeEvent(input$conf_meta_single, {
-     log_print("Single typing metadata confirmed")
+    log_print("Single typing metadata confirmed")
     
     if(nchar(trimws(input$assembly_id)) < 1) {
       ass_id <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
@@ -22700,7 +22756,7 @@ server <- function(input, output, session) {
     show_toast(
       title = "Metadata declared",
       type = "success",
-      position = "top-end",
+      position = "bottom-end",
       timer = 3000,
       width = "500px"
     )
@@ -22738,7 +22794,7 @@ server <- function(input, output, session) {
   ####  Events Single Typing ----
   
   observeEvent(input$reset_single_typing, {
-     log_print("Reset single typing")
+    log_print("Reset single typing")
     
     Typing$progress <- 0
     
@@ -22808,7 +22864,7 @@ server <- function(input, output, session) {
         show_toast(
           title = "Single Typing finalized",
           type = "success",
-          position = "top-end",
+          position = "bottom-end",
           timer = 8000,
           width = "500px"
         )
@@ -23090,7 +23146,7 @@ server <- function(input, output, session) {
   })
   
   observeEvent(input$conf_meta_multi, {
-     log_print("Multi typing metadata confirmed")
+    log_print("Multi typing metadata confirmed")
     
     meta_info <- data.frame(cgmlst_typing = DB$scheme,
                             append_isodate = trimws(input$append_isodate_multi),
@@ -23105,7 +23161,7 @@ server <- function(input, output, session) {
     show_toast(
       title = "Metadata declared",
       type = "success",
-      position = "top-end",
+      position = "bottom-end",
       timer = 3000,
       width = "500px"
     )
@@ -23143,7 +23199,7 @@ server <- function(input, output, session) {
   # Print Log
   output$print_log <- downloadHandler(
     filename = function() {
-       log_print(paste0("Save multi typing log ", paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")))
+      log_print(paste0("Save multi typing log ", paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")))
       paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")
     },
     content = function(file) {
@@ -23170,7 +23226,7 @@ server <- function(input, output, session) {
       )
     } else {
       
-       log_print("Reset multi typing")
+      log_print("Reset multi typing")
       
       # Reset multi typing result list
       saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
@@ -23245,7 +23301,7 @@ server <- function(input, output, session) {
     show_toast(
       title = "Execution cancelled",
       type = "warning",
-      position = "top-end",
+      position = "bottom-end",
       timer = 6000,
       width = "500px"
     )
@@ -23316,19 +23372,19 @@ server <- function(input, output, session) {
       show_toast(
         title = "Pending Single Typing",
         type = "warning",
-        position = "top-end",
+        position = "bottom-end",
         timer = 6000,
         width = "500px"
       )
     } else {
       if (any(!grepl("\\.fasta|\\.fna|\\.fa", str_sub(Typing$genome_selected$Files[which(Typing$genome_selected$Include == TRUE)], start = -6)))) {
         
-         log_print("Wrong file type (include only fasta/fna/fa)")
+        log_print("Wrong file type (include only fasta/fna/fa)")
         
         show_toast(
           title = "Wrong file type (include only fasta/fna/fa)",
           type = "error",
-          position = "top-end",
+          position = "bottom-end",
           timer = 6000,
           width = "500px"
         )
@@ -23339,7 +23395,7 @@ server <- function(input, output, session) {
         show_toast(
           title = "Multi Typing started",
           type = "success",
-          position = "top-end",
+          position = "bottom-end",
           timer = 10000,
           width = "500px"
         )
@@ -23418,7 +23474,7 @@ server <- function(input, output, session) {
         title = paste0("Successful", sub(".*Successful", "", tail(log, 1))),
         type = "success",
         width = "500px",
-        position = "top-end",
+        position = "bottom-end",
         timer = 8000
       )
     } else if(str_detect(tail(log, 1), "failed")) {
@@ -23427,7 +23483,7 @@ server <- function(input, output, session) {
         title = paste0("Failed typing of ", sub(".*failed for ", "", tail(log, 1))),
         type = "error",
         width = "500px",
-        position = "top-end",
+        position = "bottom-end",
         timer = 8000
       )
     } else if(str_detect(tail(log, 1), "Processing")) {
@@ -23441,7 +23497,7 @@ server <- function(input, output, session) {
             title = paste0("Successful", sub(".*Successful", "", tail(log, 2)[1])),
             type = "success",
             width = "500px",
-            position = "top-end",
+            position = "bottom-end",
             timer = 8000
           )
           
@@ -23454,7 +23510,7 @@ server <- function(input, output, session) {
             title = paste0("Failed typing of ", sub(".*failed for ", "", tail(log, 2)[1])),
             type = "error",
             width = "500px",
-            position = "top-end",
+            position = "bottom-end",
             timer = 8000
           )
           
@@ -23470,7 +23526,7 @@ server <- function(input, output, session) {
           title = "Typing finalized",
           type = "success",
           width = "500px",
-          position = "top-end",
+          position = "bottom-end",
           timer = 8000
         )
         
@@ -23498,45 +23554,23 @@ server <- function(input, output, session) {
                           rowHeaders = NULL, stretchH = "all",
                           readOnly = TRUE, contextMenu = FALSE) %>%
               hot_rows(rowHeights = 25) %>%
-              hot_col(1:3, valign = "htMiddle", halign = "htCenter")
-            })
-        } else {
-          if (input$multi_results_longhash) {
-            renderer <- NULL
-          } else {
-            renderer <- htmlwidgets::JS(
-              "function(instance, td, row, col, prop, value, cellProperties) {
-                            if (value.length > 8) {
-                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                            }
-                            td.innerHTML = value;
-                            td.style.verticalAlign = 'middle';
-                            td.style.textAlign = 'center';
-                            return td;
-                          }"
-            )
-          }
+              hot_col(1:3, valign = "htMiddle", halign = "htCenter")})
           
+        } else {
           if(Typing$multi_table_length > 15) {
             output$multi_typing_result_table <- renderRHandsontable({
               rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
                             stretchH = "all", height = 500,
                             readOnly = TRUE, contextMenu = FALSE) %>%
                 hot_rows(rowHeights = 25) %>%
-                hot_col(1:3, valign = "htMiddle", halign = "htCenter") %>%
-                hot_col("Value",
-                        renderer = renderer)
-              })
+                hot_col(1:3, valign = "htMiddle", halign = "htCenter")})
           } else {
             output$multi_typing_result_table <- renderRHandsontable({
               rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
                             stretchH = "all", readOnly = TRUE,
                             contextMenu = FALSE) %>%
                 hot_rows(rowHeights = 25) %>%
-                hot_col(1:3, valign = "htMiddle", halign = "htCenter") %>%
-                hot_col("Value",
-                        renderer = renderer)
-              })
+                hot_col(1:3, valign = "htMiddle", halign = "htCenter")})
             
           }
         }
@@ -23575,26 +23609,17 @@ server <- function(input, output, session) {
                 width = 9,
                 br(), br(),
                 br(), br(),
-                br(),
-                fluidRow(
-                  div(
-                    class = "mult_res_sel",
-                    selectInput(
-                      "multi_results_picker",
-                      label = h5("Select Typing Results", style = "color:white"),
-                      choices = names(Typing$result_list),
-                      selected = names(Typing$result_list)[length(names(Typing$result_list))],
-                    )
-                  )
-                ),
                 br(), 
-                materialSwitch(
-                  "multi_results_longhash",
-                  h5(p("Show Long Hash"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                  value = FALSE,
-                  right = TRUE
+                div(
+                  class = "mult_res_sel",
+                  selectInput(
+                    "multi_results_picker",
+                    label = h5("Select Typing Results", style = "color:white"),
+                    choices = names(Typing$result_list),
+                    selected = names(Typing$result_list)[length(names(Typing$result_list))],
+                  )
                 ),
-                br(), 
+                br(), br(), 
                 rHandsontableOutput("multi_typing_result_table")
               )
             )
@@ -23719,6 +23744,8 @@ server <- function(input, output, session) {
     }
   })
   
+  
+  
 } # end server
 
 # _______________________ ####
diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index 6e5a560..3dc5277 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -113,10 +113,18 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
                                             start_codons = start_codons, stop_codons = stop_codons)
         
         # if valid variant found 
-        if(variant_valid != FALSE) {
+        if(variant_valid == "Ambigous Nucleotides") {
+          allele_vector[[i]] <- NA
+          event_list[[basename(assembly)]] <- rbind(event_list[[basename(assembly)]], 
+                                                    data.frame(Locus = allele_index, 
+                                                               Event = "Ambigous Nucleotides Sequence", 
+                                                               Value = "NA"))
+          cat(paste0(allele_index, " Invalid - Ambigous Nucleotides.\n"))
+          
+        } else if(variant_valid != FALSE) {
           
           hashed_variant <- openssl::sha256(variant_valid)
-
+          
           # Append new variant number to allele fasta file
           cat(paste0("\n>", hashed_variant), file = locus_file, append = TRUE)
           
@@ -324,7 +332,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
               message = paste0("Assembly typing failed for ", 
                                sub("\\.(fasta|fna|fa)$", "", basename(assembly))))
   log_print(paste0("Assembly typing failed for ", 
-                         sub("\\.(fasta|fna|fa)$", "", basename(assembly))))
+                   sub("\\.(fasta|fna|fa)$", "", basename(assembly))))
 }
 
 log_close()
diff --git a/execute/single_eval.R b/execute/single_eval.R
index dfb9f52..9b65f81 100644
--- a/execute/single_eval.R
+++ b/execute/single_eval.R
@@ -91,10 +91,9 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
         
         variants <- readLines(locus_file)
         
-        # new variant validation 
-        # decision what is reference sequence
+        ### new variant validation ### 
         
-        # sort by score, then number of gaps then number of bases in the gaps
+        # sort by i) score, ii) number of gaps, iii) number of nt in the gaps
         matches <- dplyr::arrange(matches, desc(V1), desc(V5 + V7), desc(V6 + V7))
         
         # check which reference sequences have different alignment positions with the template
@@ -102,10 +101,15 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
         
         # loop over all unique template alignments (regarding position)
         variant_valid <- variant_validation(references = unique_template_seq, 
-                           start_codons = start_codons, stop_codons = stop_codons)
+                                            start_codons = start_codons, stop_codons = stop_codons)
         
         # if valid variant found 
-        if(variant_valid != FALSE) {
+        if(variant_valid == "Ambigous Nucleotides") {
+          allele_vector[[i]] <- NA
+          event_df <- rbind(event_df, data.frame(Locus = allele_index, Event = "Ambigous Nucleotides", Value = "NA"))
+          cat(paste0(allele_index, " Invalid - Ambigous Nucleotides.\n"))
+          
+        } else if(variant_valid != FALSE) {
           
           hashed_variant <- openssl::sha256(variant_valid)
           
diff --git a/execute/variant_validation.R b/execute/variant_validation.R
index c9dd4fe..9c9524e 100644
--- a/execute/variant_validation.R
+++ b/execute/variant_validation.R
@@ -1,4 +1,13 @@
 require(Biostrings, quietly = TRUE)
+
+check_gene_sequence <- function(sequence) {
+  if (grepl("[^atgc]", sequence, ignore.case = TRUE)) {
+    return(TRUE)
+  } else {
+    return(FALSE)
+  }     
+}
+
 # Function to check for length and frameshift of new variant sequence
 check_length_frameshift <- function(seq, ref_seq) {
   
@@ -65,8 +74,8 @@ validate_start_stop <- function(seq, start_codons, stop_codons) {
           }
         }
       }
-    
-    # Check if reverse sequence has start codon    
+      
+      # Check if reverse sequence has start codon    
     } else if (length(reverse_match@ranges) != 0) {
       
       # Verify if stop codon is at other end
@@ -99,6 +108,11 @@ variant_validation <- function(references, start_codons, stop_codons) {
     
     seq <- substring(contig, references$V16[i] + 1, references$V17[i])
     
+    # invalid if nucleic acid code other than ATGC
+    if(check_gene_sequence(seq)) {
+      return("Ambigous Nucleotides")
+    }
+    
     ref_seq_index <- grep(paste0("^>", references$V10[i], "$"), readLines(locus_file)) + 1
     
     ref_seq <- variants[ref_seq_index]
diff --git a/www/body.css b/www/body.css
index 58bff78..50e3583 100644
--- a/www/body.css
+++ b/www/body.css
@@ -1,10 +1,10 @@
 /* CSS Styling for PhyloTrace */
-
-/* General */
-
-h1, h2, h3, h4, h5, p, body {
-  font-family: 'Liberation Sans', sans-serif;
-}
+  
+  /* General */
+  
+  h1, h2, h3, h4, h5, p, body {
+    font-family: 'Liberation Sans', sans-serif;
+  }
 
 label {
   color: white;
@@ -17,31 +17,31 @@ label {
 }
 
 .btn-primary.focus, .btn-primary:focus {
-    color: #000000;
+  color: #000000;
     background-color: #20E6E5;  
     border-color: #20E6E5;  
 }
 
 .btn-primary.focus, .btn-primary:active:focus {
   color: #ffffff;
-  background-color: #282F38;  
-  border-color: white;  
+    background-color: #282F38;  
+    border-color: white;  
 }
 
 .datepicker table tr td.active:active, .datepicker table tr td.active.active, .datepicker table tr td.active.highlighted:active, .datepicker table tr td.active.highlighted.active {
   color: #000000;
-  background-color: #20E6E5;  
-  border-color: #20E6E5;  
+    background-color: #20E6E5;  
+    border-color: #20E6E5;  
 }
 
 .table>caption+thead>tr:first-child>td, .table>caption+thead>tr:first-child>th, .table>colgroup+thead>tr:first-child>td, .table>colgroup+thead>tr:first-child>th, .table>thead:first-child>tr:first-child>td, .table>thead:first-child>tr:first-child>th,
 .table>caption+thead>tr:last-child>td, .table>caption+thead>tr:last-child>th, .table>colgroup+thead>tr:last-child>td, .table>colgroup+thead>tr:last-child>th, .table>thead:last-child>tr:last-child>td, .table>thead:last-child>tr:last-child>th {
-    border-top: 1px !important;
-    border-radius: 5px;
+  border-top: 1px !important;
+  border-radius: 5px;
 }
 
 .dropdown-menu>li.selected {
-    color: #ffffff;
+  color: #ffffff;
     background-color: #282F38;  
 }
 
@@ -54,13 +54,13 @@ label {
 }
 
 .dropdown-menu>li>a:hover {
-    color: #000000;
+  color: #000000;
     background-color: #20E6E5;  
 }
 
 .selectize-dropdown .selected {
   background-color: #20E6E5;
-  color: black;
+    color: black;
 }
 
 .bs-searchbox .form-control {
@@ -82,7 +82,7 @@ label {
 
 .main-sidebar .sidebar .sidebar-menu .treeview-menu a {
   color: #ffffff !important; 
-  margin-left: 25px; 
+    margin-left: 25px; 
   border-radius: 20px; 
   margin-top: 7px; 
   margin-bottom: 7px;
@@ -106,7 +106,7 @@ label {
   border: 1px solid #00000000;
   border-width: 1px;
   display: inline-block; /* Make the element inline-block */
-  transition: border-color 0.3s ease; /* Smooth transition for border color */
+    transition: border-color 0.3s ease; /* Smooth transition for border color */
 }
 
 .bttn-material-flat:hover{
@@ -115,20 +115,20 @@ label {
 
 .action-button.bttn.bttn-material-flat.bttn-sm.bttn-default.bttn-no-outline.shiny-bound-input {
   background: #282F38 !important;
-  border: 1px solid transparent; /* Default border color */
-  display: inline-block; /* Make the element inline-block */
-  transition: border-color 0.3s ease; /* Smooth transition for border color */
-  border-width: 1px !important;
+    border: 1px solid transparent; /* Default border color */
+    display: inline-block; /* Make the element inline-block */
+    transition: border-color 0.3s ease; /* Smooth transition for border color */
+    border-width: 1px !important;
   border-color: white !important;
   color: white !important;
   transition: background 0.3s ease; /* Smooth transition for border color */
-  transition: color 0.3s ease; /* Smooth transition for border color */
+    transition: color 0.3s ease; /* Smooth transition for border color */
 }
 
 .action-button.bttn.bttn-material-flat.bttn-sm.bttn-default.bttn-no-outline.shiny-bound-input:hover {
   border-color: transparent !important; /* Change border color to white on hover */
-  background: #20E6E5 !important;
-  color: black !important;
+    background: #20E6E5 !important;
+    color: black !important;
 }
 
 .shiny-input-container input[type = "text"]:hover {
@@ -141,14 +141,14 @@ label {
 
 .main-sidebar .sidebar .sidebar-menu .treeview-menu li.active a {
   color: #000000 !important; 
-  border-radius: 20px; 
+    border-radius: 20px; 
   margin-top: 7px; 
   margin-bottom: 7px;
 }
 
 .main-sidebar .sidebar .sidebar-menu .treeview-menu li:hover a {
   color: #000000; 
-  border-radius: 20px; 
+    border-radius: 20px; 
   margin-top: 7px; 
   margin-bottom: 7px;
 }
@@ -159,7 +159,7 @@ label {
 
 .main-sidebar .sidebar .sidebar-menu li:hover a {
   color: #000000; 
-  border: none;
+    border: none;
 }
 
 file.select {
@@ -167,14 +167,14 @@ file.select {
 }
 
 .box.box-solid.box-info{
-    background: #282F38;
+  background: #282F38;
     margin-top: 20px;
-    position: relative;
-    left: 30px;
+  position: relative;
+  left: 30px;
 }
 
 .box.box-solid.box-info, .box.box-info {
-    border-color: #ffffff;
+  border-color: #ffffff;
     border-left-color: #ffffff;
     border-right-color: #ffffff;
     border-top-color: #ffffff;
@@ -186,7 +186,7 @@ file.select {
 }
 
 #scheme_db .selectize-control {
-  font-size: 12px;
+font-size: 12px;
 }
 
 .scheme_start {
@@ -206,17 +206,17 @@ file.select {
 }
 
 #reload_db i.fas.fa-rotate {
-  position: relative; 
-  left: -5px;
-  top: -2px;
+position: relative; 
+left: -5px;
+top: -2px;
 }
 
 button#reload_db.btn.btn-default.action-button.shiny-bound-input {
-  height: 30px; 
-  width: 30px; 
-  position: relative; 
-  left: -20px;
-  border: 1px solid white;
+height: 30px; 
+width: 30px; 
+position: relative; 
+left: -20px;
+border: 1px solid white;
 }
 
 .irs.irs--shiny.js-irs-0 {
@@ -232,19 +232,19 @@ button#reload_db.btn.btn-default.action-button.shiny-bound-input {
 }
 
 div#scheme_db .form-control, .selectize-input, .selectize-control.single .selectize-input {
-  border-color: #000000 !important;
-}
+border-color: #000000 !important;
+  }
 
 #distmatrix_triangle {
-  margin-top: -35px;
+margin-top: -35px;
 }
 
 #distmatrix_diag {
-  margin-top: -55px;
+margin-top: -55px;
 }
 
 #distmatrix_true {
-  margin-top: -15px;
+margin-top: -15px;
 }
 
 .format {
@@ -271,7 +271,7 @@ div#scheme_db .form-control, .selectize-input, .selectize-control.single .select
 }
 
 button#load.pulsating-button.btn.btn-default.action-button.shiny-bound-input {
-  background: #20E6E5; 
+background: #20E6E5; 
   color: #000000; 
   width: 40px;
 }
@@ -281,8 +281,8 @@ button#load.pulsating-button.btn.btn-default.action-button.shiny-bound-input {
 }
 
 #load .fas.fa-rotate {
-  position: relative; 
-  left: 0px !important;
+position: relative; 
+left: 0px !important;
 }
 
 .shiny-input-container input[type="text"] {
@@ -303,7 +303,7 @@ button#load.pulsating-button.btn.btn-default.action-button.shiny-bound-input {
 }
 
 .loci_table .dataTables_wrapper .dataTables_length, .dataTables_wrapper .dataTables_filter, .dataTables_wrapper .dataTables_info, .dataTables_wrapper .dataTables_processing, .dataTables_wrapper .dataTables_paginate {
-    color: #ffffff !important;
+  color: #ffffff !important;
 }
 
 thead {
@@ -311,20 +311,20 @@ thead {
 }
 
 .dataTables_wrapper .dataTables_filter input {
-    border-radius: 5px;
-    padding: 5px;
-    background-color: white;
-    color: black;
-    font-weight: 100;
-    margin-left: 3px;
+  border-radius: 5px;
+  padding: 5px;
+  background-color: white;
+  color: black;
+  font-weight: 100;
+  margin-left: 3px;
 }
 
 .dataTables_wrapper .dataTables_length select {
-    border-radius: 5px;
-    padding: 5px;
-    background-color: white;
-    color: black;
-    font-weight: 100;
+  border-radius: 5px;
+  padding: 5px;
+  background-color: white;
+  color: black;
+  font-weight: 100;
 }
 
 .dataTables_wrapper .dataTables_paginate .paginate_button {
@@ -332,75 +332,75 @@ thead {
 }
 
 table.dataTable tbody tr {
-    background-color: transparent;
-    border-radius: 5px !important;
+  background-color: transparent;
+  border-radius: 5px !important;
 }
 
 table.dataTable.stripe>tbody>tr.odd.selected>*, table.dataTable.display>tbody>tr.odd.selected>* {
-    box-shadow: inset 0 0 0 9999px #282F38;
-    box-shadow: inset 0 0 0 9999px #282F38;
-    color: white !important;
+  box-shadow: inset 0 0 0 9999px #282F38;
+  box-shadow: inset 0 0 0 9999px #282F38;
+  color: white !important;
 }
 
 table.dataTable.stripe>tbody>tr.even.selected>*, table.dataTable.display>tbody>tr.even.selected>* {
-    box-shadow: inset 0 0 0 9999px #282F38;
-    box-shadow: inset 0 0 0 9999px #282F38;
-    color: white !important;
+  box-shadow: inset 0 0 0 9999px #282F38;
+  box-shadow: inset 0 0 0 9999px #282F38;
+  color: white !important;
 }
 
 table.dataTable.display>tbody>tr.selected:hover>* {
-    box-shadow: inset 0 0 0 9999px #20E6E5 !important;
-    color: black !important;
+  box-shadow: inset 0 0 0 9999px #20E6E5 !important;
+  color: black !important;
 }
 
 table.dataTable.display>tbody>tr:hover>* {
-    box-shadow: inset 0 0 0 9999px #20E6E5 !important;
-    color: black !important;
+  box-shadow: inset 0 0 0 9999px #20E6E5 !important;
+  color: black !important;
 }
 
 .dataTables_wrapper .dataTables_paginate .paginate_button:hover {
-    color: white !important;
-    border: 1px solid #111;
-    background-color: #20E6E5;
+  color: white !important;
+  border: 1px solid #111;
+  background-color: #20E6E5;
     background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, #585858), color-stop(100%, #111));
-    background: -webkit-linear-gradient(top, #585858 0%, #111 100%);
-    background: -moz-linear-gradient(top, #585858 0%, #111 100%);
-    background: -ms-linear-gradient(top, #585858 0%, #111 100%);
-    background: -o-linear-gradient(top, #585858 0%, #111 100%);
-    background: linear-gradient(to bottom, #585858 0%, #111 100%);
+                                                                           background: -webkit-linear-gradient(top, #585858 0%, #111 100%);
+                                                                                                               background: -moz-linear-gradient(top, #585858 0%, #111 100%);
+                                                                                                                                                background: -ms-linear-gradient(top, #585858 0%, #111 100%);
+                                                                                                                                                                                background: -o-linear-gradient(top, #585858 0%, #111 100%);
+                                                                                                                                                                                                               background: linear-gradient(to bottom, #585858 0%, #111 100%);
 }
 
 .dataTables_wrapper .dataTables_paginate .paginate_button.disabled, .dataTables_wrapper .dataTables_paginate .paginate_button.disabled:hover, .dataTables_wrapper .dataTables_paginate .paginate_button.disabled:active {
-    cursor: default;
-    color: #fff !important;
+  cursor: default;
+  color: #fff !important;
     border: 1px solid transparent;
-    background: transparent;
-    box-shadow: none;
+  background: transparent;
+  box-shadow: none;
 }
 
 .dataTables_wrapper .dataTables_paginate .paginate_button.current, .dataTables_wrapper .dataTables_paginate .paginate_button.current:hover {
-    color: black !important;
-    border: 1px solid rgb(255 255 255 / 0%);
-    background-color: #20E6E5 !important;
+  color: black !important;
+  border: 1px solid rgb(255 255 255 / 0%);
+  background-color: #20E6E5 !important;
     border-radius: 5px;
-    background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, rgba(230, 230, 230, 0.05)), color-stop(100%, rgba(0, 0, 0, 0.05)));
-    background: -webkit-linear-gradient(top, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
-    background: -moz-linear-gradient(top, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
-    background: -ms-linear-gradient(top, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
-    background: -o-linear-gradient(top, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
-    background: linear-gradient(to bottom, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
+  background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, rgba(230, 230, 230, 0.05)), color-stop(100%, rgba(0, 0, 0, 0.05)));
+  background: -webkit-linear-gradient(top, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
+  background: -moz-linear-gradient(top, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
+  background: -ms-linear-gradient(top, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
+  background: -o-linear-gradient(top, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
+  background: linear-gradient(to bottom, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
 }
 
 .dataTables_wrapper .dataTables_paginate .paginate_button:hover {
-    color: white !important;
-    border: 1px solid #00f3ff;
-    background-color: #111;
+  color: white !important;
+  border: 1px solid #00f3ff;
+  background-color: #111;
     background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, #585858), color-stop(100%, #111));
-    background: -webkit-linear-gradient(top, #585858 0%, #111 100%);
-    background: -moz-linear-gradient(top, #585858 0%, #111 100%);
-    background: -ms-linear-gradient(top, #585858 0%, #111 100%);
-    background: -o-linear-gradient(top, #585858 0%, #111 100%);
-    background: transparent;
+                                                                           background: -webkit-linear-gradient(top, #585858 0%, #111 100%);
+                                                                                                               background: -moz-linear-gradient(top, #585858 0%, #111 100%);
+                                                                                                                                                background: -ms-linear-gradient(top, #585858 0%, #111 100%);
+                                                                                                                                                                                background: -o-linear-gradient(top, #585858 0%, #111 100%);
+                                                                                                                                                                                                               background: transparent;
 }
 
 input.form-control.pickr-color {
@@ -431,32 +431,44 @@ input.form-control.pickr-color {
 }
 
 button#copy_seq {
-    background: #282F38;
-    color: #ffffff;
-    border: 1px solid white;
-    transition: border-color 0.3s ease;
+background: #282F38;
+  color: #ffffff;
+  border: 1px solid white;
+transition: border-color 0.3s ease;
 }
 
 button#get_locus_bttn {
-    background: #282F38;
-    color: #ffffff;
-    border: 1px solid white;
-    transition: border-color 0.3s ease;
-    opacity: 1;
-    font-size: 15px;
-    width: 147px;
+background: #282F38;
+  color: #ffffff;
+  border: 1px solid white;
+transition: border-color 0.3s ease;
+opacity: 1;
+font-size: 15px;
+width: 147px;
 }
 
 button#get_locus_bttn i.fas.fa-download {
-    position: relative;
-    top: -1px;
-    left: -6px;
+position: relative;
+top: -1px;
+left: -6px;
 }
 
 /* Icons */
+  
+  i.fas {
+    margin-right: 5px;
+  }
 
-i.fas {
-  margin-right: 5px;
+i.greenstatus.fa-solid.fa-circle-dot. {
+  lightgreen
+}
+
+i.orangestatus.fa-solid.fa-circle-dot {
+  orange
+}
+
+i.fa-solid.fa-folder-open {
+  color: #FFDA73 !important;
 }
 
 i.fas.fa-rotate {
@@ -472,7 +484,7 @@ i.fas.fa-sliders {
   margin-right: 0px; 
   margin-top: 5px;
 }
- 
+
 i.fas.fa-xmark, i.fas.fa-download, i.far.fa-bookmark {
   margin-right: 0px;
 }
@@ -498,28 +510,28 @@ i.far.fa-pen-to-square {
 }
 
 /* Database */
-
-#db_entries > div > div > div > div > table > tbody > tr > td,
-#db_distancematrix > div > div > div > div > table > tbody > tr > td,
-#table_missing_values > div > div > div > div > table > tbody > tr > td,
-#multi_select_table > div > div > div > div > table > tbody > tr > td,
-#multi_typing_result_table > div > div > div > div > table > tbody > tr > td,
-#typing_result_table > div > div > div > div > table > tbody > tr > td{
+  
+  #db_entries > div > div > div > div > table > tbody > tr > td,
+  #db_distancematrix > div > div > div > div > table > tbody > tr > td,
+  #table_missing_values > div > div > div > div > table > tbody > tr > td,
+  #multi_select_table > div > div > div > div > table > tbody > tr > td,
+  #multi_typing_result_table > div > div > div > div > table > tbody > tr > td,
+  #typing_result_table > div > div > div > div > table > tbody > tr > td{
   color: black !important;
 }
 
 .miss_val_box,
 #table_missing_values{
-  margin-left: 50px;
+margin-left: 50px;
 }
 
 #download_na_matrix_bttn > i {
-  top: 1px !important;
+top: 1px !important;
 }
 
 #sel_all_entries, #desel_all_entries, #typing_start, #start_typ_multi, 
 #undo_changes, #genome_file, #genome_file_multi, #reset_multi, #save_cust {
-  border-color: white;
+border-color: white;
 }
 
 .btn-default:hover {
@@ -527,24 +539,24 @@ i.far.fa-pen-to-square {
 }
 
 #cgmlst_scheme {
-  margin-top: 41px;
+margin-top: 41px;
 }
 
 .dropdown-menu>.active>a, .dropdown-menu>.active>a:focus, .dropdown-menu>.active>a:hover {
-    color: #ffffff !important;
+  color: #ffffff !important;
     background-color: #282F38 !important;
 }
 
 #shiny-tab-db_browse_entries > div:nth-child(11) > div.col-sm-1,
 #shiny-tab-init > div:nth-child(4) > div.col-sm-1,
 #shiny-tab-init > div:nth-child(3) > div.col-sm-1 {
-  width: 4.333333%;
+width: 4.333333%;
 }
 
 .bttn-simple:hover {
   border-color: #20E6E5 !important;
-  background: #20E6E5 !important;
-  color: black !important;
+    background: #20E6E5 !important;
+    color: black !important;
   opacity: 1;
 }
 
@@ -567,154 +579,154 @@ i.far.fa-pen-to-square {
 
 #db_entries, #db_distancematrix, #table_missing_values, 
 #multi_select_table, #typing_result_table, #multi_typing_result_table {
-  border-radius: 8px;
-  color: black;
+border-radius: 8px;
+color: black;
 }
 
 #multi_typing_result_table {
-  margin-top: -15px;
+margin-top: -15px;
 }
 
 #add_new_variable {
-  background: green; 
-  height: 35px; 
-  width: 38px;
-  margin-left: -5px;
-  margin-top: 19px;
+background: green; 
+height: 35px; 
+width: 38px;
+margin-left: -5px;
+margin-top: 19px;
 }
 
 #delete_new_variable {
-  background: #FF5964; 
+background: #FF5964; 
   height: 35px; 
-  width: 38px;
-  margin-left: -5px;
-  margin-top: 20px;
+width: 38px;
+margin-left: -5px;
+margin-top: 20px;
 }
 
 #new_var_name {
-  height: 33px;
-  margin-left: -6px;
-  width: 123px;
-  margin-top: -12px;
+height: 33px;
+margin-left: -6px;
+width: 123px;
+margin-top: -12px;
 }
 
 #cust_var_select {
-  margin-top: -40px;
+margin-top: -40px;
 }
 
 #cust_var_select .selectize-dropdown-content {
-  max-height: 80px;
+max-height: 80px;
 }
 
 div#db_distancematrix.rhandsontable {
-  font-size: 11px;
+font-size: 11px;
 }
 
 button#download_cgMLST {
-  font-size: 14px; 
-  height: 34px; 
-  background: #282F38;
+font-size: 14px; 
+height: 34px; 
+background: #282F38;
   color: #ffffff;
   border: 1px solid white;
 }
 
 .btn-primary:hover {
   background-color: #20e6e5;
-  border-color: #20e6e5;
-  color: black;
+    border-color: #20e6e5;
+    color: black;
   border-radius: 5px;
   height: 35px;
 }
 
 .btn-primary {
   background: #282F38;
-  color: #ffffff;
-  border-color: #282F38;
-  border-radius: 5px;
+    color: #ffffff;
+    border-color: #282F38;
+    border-radius: 5px;
   height: 35px;
   padding: 6px 12px;
 }
 
 .btn-default:hover {
   border-color: #20e6e5 !important;
-  background: #20e6e5 !important;
-  color: black !important;
+    background: #20e6e5 !important;
+    color: black !important;
 }
 
 button#download_cgMLST i.fas.fa-download {
-  margin-right: 5px !important
+margin-right: 5px !important
 }
 
 #show_cust_var {
-  color:black; 
-  font-size: 14px;
-  margin-left: 15px;
+color:black; 
+font-size: 14px;
+margin-left: 15px;
 }
 
 button#download_distmatrix_bttn {
-  font-size: 14px;
-  height: 34px;
-  background: #282F38;
+font-size: 14px;
+height: 34px;
+background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-  position: absolute;
-  top: -50px;
-  transition: border-color 0.3s ease; /* Smooth transition for border color */
-}
+position: absolute;
+top: -50px;
+transition: border-color 0.3s ease; /* Smooth transition for border color */
+  }
 
 button#download_entry_table_bttn {
-  height: 34px; 
-  background: #282F38;
+height: 34px; 
+background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-  transition: border-color 0.3s ease; /* Smooth transition for border color */
-}
+transition: border-color 0.3s ease; /* Smooth transition for border color */
+  }
 
 button#download_schemeinfo_bttn {
-  height: 28px;
-  background: #282F38;
+height: 28px;
+background: #282F38;
   color: #ffffff;
   margin-top: 19px;
-  border: 1px solid white;
-  margin-left: 10px;
-  transition: border-color 0.3s ease; /* Smooth transition for border color */
-}
+border: 1px solid white;
+margin-left: 10px;
+transition: border-color 0.3s ease; /* Smooth transition for border color */
+  }
 
 button#download_loci_info_bttn {
-    height: 28px;
-    background: #282F38;
-    color: #ffffff;
-    margin-top: 19px;
-    border: 1px solid white;
-    margin-left: 10px;
-    transition: border-color 0.3s ease;
+height: 28px;
+background: #282F38;
+  color: #ffffff;
+  margin-top: 19px;
+border: 1px solid white;
+margin-left: 10px;
+transition: border-color 0.3s ease;
 }
 
 button#download_na_matrix_bttn {
-  height: 34px; 
-  background: #282F38;
+height: 34px; 
+background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-  margin-top: 14px; 
-  margin-left: 10px;
-  transition: border-color 0.3s ease;
+margin-top: 14px; 
+margin-left: 10px;
+transition: border-color 0.3s ease;
 }
 
 button#edit_button.btn.btn-default.action-button.shiny-bound-input {
-  background: #20E6E5; 
+background: #20E6E5; 
   color: #000000;
-}
+  }
 
 /* Typing */
-
-.mult_res_sel {
-  margin-bottom: 15px;
-}
+  
+  .mult_res_sel {
+    margin-bottom: 15px;
+  }
 
 body > div.htDatepickerHolder > div > div > table > tbody > tr > td.is-today.is-selected > button{
   color: white;
   background: #282F38;
-  border-radius: 5px;
+    border-radius: 5px;
   box-shadow: inset 0 1px 3px rgb(0 0 0)
 }
 
@@ -723,13 +735,13 @@ body > div.htDatepickerHolder > div > div > table > tbody > tr > td.is-selected,
 .is-selected .pika-button {
   color: white;
   background: #282F38;
-  border-radius: 5px;
+    border-radius: 5px;
   box-shadow: inset 0 1px 3px rgb(0 0 0)
 }
 
 .pika-button:hover {
   background: #20E6E5; 
-  color: #000000;
+    color: #000000;
 }
 
 .pika-button {
@@ -746,23 +758,23 @@ body > div.htDatepickerHolder > div > div > table > tbody > tr > td.is-today > b
 
 body > div.datepicker.datepicker-dropdown.dropdown-menu.datepicker-orient-left.datepicker-orient-top > div.datepicker-days > table > tbody > tr > td.active.day {
   background: #282F38;
-  color: white;
-    
+    color: white;
+  
 }
 
 .datepicker table tr td.day:hover, 
 .datepicker table tr td.focused {
   color: #000;
-  background: rgba(0,255,213,1);
+    background: rgba(0,255,213,1);
   cursor: pointer;
 }
 
 #print_log {
-  border-color: white;
+border-color: white;
 }
 
 #logText, #logTextFull {
-  margin-top: 5px;
+margin-top: 5px;
 }
 
 .append_table {
@@ -779,16 +791,16 @@ body > div.datepicker.datepicker-dropdown.dropdown-menu.datepicker-orient-left.d
   border-color: black;
 }
 
-    
+
 span#progress_bar-title.progress-text {
-  color: white; 
-  font-size: 13px; 
-  font-weight: normal;
+color: white; 
+font-size: 13px; 
+font-weight: normal;
 }
 
 div#progress_bar.progress-bar {
-  font-size:13px; 
-  line-height: 30px;
+font-size:13px; 
+line-height: 30px;
 }
 
 .progress {
@@ -802,8 +814,8 @@ border-color: white;
 }
 
 /* Visualization MST */
-
-#mst_title_color {
+  
+  #mst_title_color {
   margin-bottom: 21px;
 }
 
@@ -823,7 +835,7 @@ border-color: white;
 }
 
 #maindivtree_mst, #graphtree_mst {
-  border-radius: 10px;
+border-radius: 10px;
 }
 
 button#create_tree {
@@ -868,110 +880,110 @@ left: -7px;
 }
 
 #mst_ratio {
-  position: absolute; 
-  right: 36px; 
-  top: 23px;
+position: absolute; 
+right: 36px; 
+top: 23px;
 }
 
 button#mst_general_menu {
-  height: 27px; 
-  width: 27px; 
-  background: #20E6E5; 
+height: 27px; 
+width: 27px; 
+background: #20E6E5; 
   color: #000000; 
   border-radius: 5px; 
-  margin-top: 2px;
+margin-top: 2px;
 }
 
 button#mst_analysis_menu {
-  height: 27px; 
-  width: 27px; 
-  background: #20E6E5; 
+height: 27px; 
+width: 27px; 
+background: #20E6E5; 
   color: #000000; 
   border-radius: 5px; 
-  margin-top: -17px;
-  position: relative;
-  top: -10px;
+margin-top: -17px;
+position: relative;
+top: -10px;
 }
 
 button#mst_node_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   border-radius: 5px; 
-  margin-top: 10px;
-  margin-bottom: -1px;
+margin-top: 10px;
+margin-bottom: -1px;
 }
 
 button#mst_edge_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   border-radius: 5px;
 }
 
 button#mst_title_menu {
-  height: 34px; 
-  margin-top: 20px; 
-  border-radius: 5px
+height: 34px; 
+margin-top: 20px; 
+border-radius: 5px
 }
 
 button#mst_edgelabel_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 37px; 
-  border-radius: 5px
+border-radius: 5px
 }
 
 button#mst_edgecolor_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 20px; 
-  border-radius: 5px
+border-radius: 5px
 }
 
 button#mst_subtitle_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 20px; 
-  border-radius: 5px
+border-radius: 5px
 }
 
 button#mst_legend_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 20px; 
-  border-radius: 5px
+border-radius: 5px
 }
 
 button#mst_label_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 37px; 
-  border-radius: 5px
+border-radius: 5px
 }
 
 button#mst_col_menu {
-  height: 34px;
-  background: #20E6E5;
+height: 34px;
+background: #20E6E5;
   color: #000000;
   margin-top: 11px;
-  margin-bottom: -2px;
-  border-radius: 5px;
+margin-bottom: -2px;
+border-radius: 5px;
 }
 
 button#mst_col_map_menu {
-  height: 34px;
-  background: #20E6E5;
+height: 34px;
+background: #20E6E5;
   color: #000000;
   margin-top: 10px;
-  margin-left: -10px;
-  border-radius: 5px;
-  margin-bottom: -1px;
+margin-left: -10px;
+border-radius: 5px;
+margin-bottom: -1px;
 }
 
 .mst_shape_sel div>.selectize-dropdown {
@@ -995,69 +1007,69 @@ button#mst_col_map_menu {
 }
 
 #mst_color_node {
-  margin-top: -10px;
-  margin-bottom: -1px;
+margin-top: -10px;
+margin-bottom: -1px;
 }
 
 #mst_background_color {
-  margin-top: -10px;
+margin-top: -10px;
 }
 
 #mst_shadow {
-  position: relative; 
-  bottom: -1px;
+position: relative; 
+bottom: -1px;
 }
 
 #mst_edge_font_color {
-  margin-top: 17px;
-  margin-bottom: 17px;
+margin-top: 17px;
+margin-bottom: 17px;
 }
 
 #node_font_color {
-  margin-top: 17px
+margin-top: 17px
 }
 
 #scale_nodes {
-  position: relative; 
-  bottom: -1px
+position: relative; 
+bottom: -1px
 }
 
 #tree_mst {
-  border-radius: 10px;
+border-radius: 10px;
 }
 
 #titletree_mst {
-  border-radius: 10px;
-  margin-bottom: 10px;
-  margin-left: 100px;
-  text-align: left !important;
+border-radius: 10px;
+margin-bottom: 10px;
+margin-left: 100px;
+text-align: left !important;
 }
 
 #subtitletree_mst {
-  margin-bottom: 10px;
-  margin-left: 100px;
-  text-align: left !important;
+margin-bottom: 10px;
+margin-left: 100px;
+text-align: left !important;
 }
 
 #footertree_mst {
-  border-radius: 10px;
-  position: relative;
-  top: -10px;
+border-radius: 10px;
+position: relative;
+top: -10px;
 }
 
 #legendtree_mst {
-  border-radius: 10px;
-  position: relative;
-  top: -10px;
+border-radius: 10px;
+position: relative;
+top: -10px;
 }
 
 /* Visualization NJ & UPGMA */
-
-/* Classes*/
-
-.label_sel {
-  margin-bottom: -16px;
-}
+  
+  /* Classes*/
+  
+  .label_sel {
+    margin-bottom: -16px;
+  }
 
 .slider {
   margin-bottom: -6px;
@@ -1145,7 +1157,7 @@ button#mst_col_map_menu {
 
 .material-switch>label.switch:before {
   background: #20e6e559 !important;
-  border-radius: 8px;
+    border-radius: 8px;
   content: "";
   height: 13px;
   margin-top: -10px;
@@ -1159,10 +1171,10 @@ button#mst_col_map_menu {
 .material-switch>label.switch:hover:before {
   border: 1px solid #20e6e5;
 }
-  
+
 .material-switch>input[type=checkbox]:checked+label.switch:before {
   background: #20e6e5 !important;
-  border-radius: 8px;
+    border-radius: 8px;
   content: "";
   height: 13px;
   margin-top: -10px;
@@ -1179,7 +1191,7 @@ button#mst_col_map_menu {
 
 .material-switch>label.switch:after {
   background: #E6E6E6 !important;
-  border-radius: 1pc;
+    border-radius: 1pc;
   box-shadow: 0 0 5px rgba(0,0,0,.3);
   content: "";
   height: 20px;
@@ -1239,178 +1251,178 @@ button#mst_col_map_menu {
 }
 
 #nj_cust_label_save, #upgma_cust_label_save {
-  border-color: white;
-  margin-top: 6px;
-  margin-bottom: 20px;
+border-color: white;
+margin-top: 6px;
+margin-bottom: 20px;
 }
 
 #nj_add_new_label, #upgma_add_new_label {
-  background: green; 
-  height: 35px; 
-  width: 38px;
-  margin-top: 20px;
+background: green; 
+height: 35px; 
+width: 38px;
+margin-top: 20px;
 }
 
 button#nj_del_label, button#upgma_del_label {
-  background: #FF5964; 
+background: #FF5964; 
   height: 35px; 
-  width: 38px;
-  margin-top: 27px;
+width: 38px;
+margin-top: 27px;
 }
 
 #nj_custom_label_select, #upgma_custom_label_select {
-  margin-top: 7px;
-  margin-left: 15px;
+margin-top: 7px;
+margin-left: 15px;
 }
 
 #nj_tiplab_fill, #upgma_tiplab_fill {
-  margin-bottom: 39px;
+margin-bottom: 39px;
 }
-  
+
 #nj_sliderInput_y, #nj_sliderInput_x,
 #upgma_sliderInput_y, #upgma_sliderInput_x{
-  margin-left: 15px;
-  margin-bottom: 10px;
-  margin-right: 15px;
+margin-left: 15px;
+margin-bottom: 10px;
+margin-right: 15px;
 }
 
 #nj_heatmap_sel > div > div > button,
 #upgma_heatmap_sel > div > div > button {
-  background-color: white;
+background-color: white;
 }
 
 #nj_heatmap_sel .filter-option-inner,
 #upgma_heatmap_sel .filter-option-inner {
-  text-align: center;
+text-align: center;
 }
 
 #nj_clade_scale, #upgma_clade_scale {
-  margin-bottom:; 1px;
+margin-bottom:; 1px;
 }
 
 #nj_parentnode, #upgma_parentnode {
-  margin-left: 38px;
-  margin-top: -10px;
+margin-left: 38px;
+margin-top: -10px;
 }
 
 #nj_layout_ctrl, #nj_label_ctrl, #nj_elements_ctrl,
 #upgma_layout_ctrl, #upgma_label_ctrl, #upgma_elements_ctrl {
-    width: 134px;
-    margin-left: 25px;
-    margin-bottom: 5px;
-    margin-top: 10px;
-    height: 40px;
-    text-align-last: justify;
-    font-size: larger;
+width: 134px;
+margin-left: 25px;
+margin-bottom: 5px;
+margin-top: 10px;
+height: 40px;
+text-align-last: justify;
+font-size: larger;
 }
 
 #nj_layout_ctrl, #upgma_layout_ctrl {
-  margin-top: 20px !important;
+margin-top: 20px !important;
 }
 
 #nj_field img,
 #upgma_field img{
-  border-radius: 10px;
+border-radius: 10px;
 }
 
 button#save_plot_jpeg {
-  font-size: 14px; 
-  height: 34px; 
-  background: #282F38;
+font-size: 14px; 
+height: 34px; 
+background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-  position: relative; 
-  top: 10px; 
-  right: 20px
+position: relative; 
+top: 10px; 
+right: 20px
 }
 
 button#save_plot_png {
-  font-size: 14px; 
-  height: 34px; 
-  background: #282F38;
+font-size: 14px; 
+height: 34px; 
+background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-  position: relative; 
-  top: 10px; 
-  right: 20px
+position: relative; 
+top: 10px; 
+right: 20px
 }
 
 button#save_plot_bmp {
-  font-size: 14px; 
-  height: 34px; 
-  background: #282F38;
+font-size: 14px; 
+height: 34px; 
+background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-  position: relative; 
-  top: 10px; 
-  right: 20px;
+position: relative; 
+top: 10px; 
+right: 20px;
 }
 
 button#save_plot_html_bttn {
-  font-size: 14px; 
-  height: 34px; 
-  position: relative; 
-  top: 10px; 
-  right: 20px;
-  background: #282F38;
+font-size: 14px; 
+height: 34px; 
+position: relative; 
+top: 10px; 
+right: 20px;
+background: #282F38;
   color: #ffffff;
   border: 1px solid white;
 }
 
 button#create_rep.btn.btn-default.action-button.shiny-bound-input {
-  border: 1px solid white;
-  margin-left: 11px;
+border: 1px solid white;
+margin-left: 11px;
 }
 
 button#download_nj_bttn, button#download_upgma_bttn {
-  font-size: 14px; 
-  height: 34px; 
-  position: relative; 
-  top: 10px; 
-  right: 20px;
-  background: #282F38;
+font-size: 14px; 
+height: 34px; 
+position: relative; 
+top: 10px; 
+right: 20px;
+background: #282F38;
   color: #ffffff;
   border: 1px solid white;
 }
 
 #nj_ratio, #upgma_ratio {
-  position: absolute; 
-  right: 36px; 
-  top: 23px;
+position: absolute; 
+right: 36px; 
+top: 23px;
 }
 
 #nj_v, #nj_h, #upgma_h, #upgma_v {
-  padding: initial; 
-  margin-top: 3px; 
-  width: 75px; 
-  text-align: center;
+padding: initial; 
+margin-top: 3px; 
+width: 75px; 
+text-align: center;
 }
 
 #nj_title_color, #upgma_title_color {
-  margin-bottom: -15px;
-  margin-top: -16px;
+margin-bottom: -15px;
+margin-top: -16px;
 }
 
 #nj_bg, #upgma_bg {
-  margin-bottom: 10px;
-  margin-left: 10px;
-  margin-top: -22px;
+margin-bottom: 10px;
+margin-left: 10px;
+margin-top: -22px;
 }
 
 #nj_color, #upgma_color {
-  margin-left: 10px;
+margin-left: 10px;
 }
 
 #nj_branch_label_menu-template > div > div:nth-child(2) > div:nth-child(2),
 #upgma_branch_label_menu-template > div > div:nth-child(2) > div:nth-child(2) {
-  margin-top: 26px;
-  margin-bottom: -10px;
-  margin-left: -10px;
+margin-top: 26px;
+margin-bottom: -10px;
+margin-left: -10px;
 }
 
 #nj_controls, #upgma_controls {
-  margin-left: 25px;
-  margin-top: 35px;
+margin-left: 25px;
+margin-top: 35px;
 }
 
 #nj_controls > div > div:nth-child(1),
@@ -1419,19 +1431,19 @@ button#download_nj_bttn, button#download_upgma_bttn {
 #upgma_controls > div > div:nth-child(2),
 #nj_controls > div > div:nth-child(3),
 #upgma_controls > div > div:nth-child(3) {
-  height: 50px;
-  width: 100px;
+height: 50px;
+width: 100px;
 }
 
 #nj_color_mapping,
 #upgma_color_mapping {
-  margin-top: -7px;
-  margin-bottom: 0px;
-  margin-right: 30px;
+margin-top: -7px;
+margin-bottom: 0px;
+margin-right: 30px;
 }
 
 #nj_heatmap_scale, #nj_tiles_scale_1, #nj_tiles_scale_2, #nj_tiles_scale_3, #nj_tiles_scale_4, #nj_tiles_scale_5, #upgma_heatmap_scale, #upgma_tiles_scale_1, #upgma_tiles_scale_2, #upgma_tiles_scale_3, #upgma_tiles_scale_4, #upgma_tiles_scale_5 {
-  margin-top: -10px;
+margin-top: -10px;
 } 
 
 .heatmap-scale div>.selectize-dropdown {
@@ -1440,344 +1452,344 @@ button#download_nj_bttn, button#download_upgma_bttn {
 }
 
 #nj_branch_label_color, #upgma_branch_label_color {
-  margin-top: -7px;
+margin-top: -7px;
 }
 
 #nj_new_label_name, #upgma_new_label_name {
-  margin-left: 15px;
-  width: 90%;
+margin-left: 15px;
+width: 90%;
 }
 
 .heatmap-picker, {
-    margin-right: 105px
+  margin-right: 105px
 }
 
 button#nj_labeltext_menu, button#upgma_labeltext_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   border-radius: 5px; 
-  margin-top: 20px; 
-  margin-left: -50px
+margin-top: 20px; 
+margin-left: -50px
 }
 
 button#nj_labelformat_menu, button#upgma_labelformat_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   border-radius: 5px; 
-  margin-top: 20px
+margin-top: 20px
 }
 
 button#nj_footer_menu, button#upgma_footer_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 20px; 
-  border-radius: 5px
+border-radius: 5px
 }
 
 button#nj_title_menu, button#upgma_title_menu {
-  height: 34px;
-  background: #20E6E5;
+height: 34px;
+background: #20E6E5;
   color: #000000;
   margin-top: 4px;
-  border-radius: 5px;
-  margin-bottom: -24px;
+border-radius: 5px;
+margin-bottom: -24px;
 }
 
 button#nj_size_menu, button#upgma_size_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 0px; 
-  border-radius: 5px;
-  margin-left: -15px;
+border-radius: 5px;
+margin-left: -15px;
 }
 
 button#nj_branch_label_menu, button#upgma_branch_label_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 20px; 
-  border-radius: 5px; 
-  margin-left: -10px
+border-radius: 5px; 
+margin-left: -10px
 }
 
 button#nj_custom_label_menu, button#upgma_custom_label_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 20px; 
-  border-radius: 5px; 
-  margin-left: -20px;
+border-radius: 5px; 
+margin-left: -20px;
 }
 
 button#nj_legend_menu, button#upgma_legend_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 20px; 
-  border-radius: 5px
+border-radius: 5px
 }
 
 button#nj_treescale_menu, button#upgma_treescale_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 20px; 
-  border-radius: 5px
+border-radius: 5px
 }
 
 button#nj_tippoint_menu, button#upgma_tippoint_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 21px; 
-  border-radius: 5px
+border-radius: 5px
 }
 
 button#nj_rootedge_menu, button#upgma_rootedge_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 16px; 
-  border-radius: 5px;
-  margin-right: 10px;
-  margin-bottom: 23px;
+border-radius: 5px;
+margin-right: 10px;
+margin-bottom: 23px;
 }
 
 button#nj_nodepoint_menu, button#upgma_nodepoint_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 21px; 
-  border-radius: 5px
+border-radius: 5px
 }
 
 button#nj_heatmap_menu, button#upgma_heatmap_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 21px; 
-  border-radius: 5px;
-  margin-left: -10px;
+border-radius: 5px;
+margin-left: -10px;
 }
 
 button#nj_clade_menu, button#upgma_clade_menu {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-top: 19px; 
-  border-radius: 5px;
-  margin-bottom: 12px;
+border-radius: 5px;
+margin-bottom: 12px;
 }
 
 button#nj_tile_menu, button#nj_tile_menu_2, button#nj_tile_menu_3, 
 button#nj_tile_menu_4, button#nj_tile_menu_5, button#upgma_tile_menu, 
 button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, button#upgma_tile_menu_5 {
-  height: 34px; 
-  background: #20E6E5; 
+height: 34px; 
+background: #20E6E5; 
   color: #000000; 
   margin-left: 15px; 
-  margin-top: 21px; 
-  border-radius: 5px
+margin-top: 21px; 
+border-radius: 5px
 }
 
 #nj_nodepoint_color, #nj_tippoint_color, #upgma_nodepoint_color, #upgma_tippoint_color {
-  margin-bottom: 10px;
-  margin-top: 6px;
+margin-bottom: 10px;
+margin-top: 6px;
 }
 
 #nj_treescale_show, #upgma_treescale_show {
-  margin-top: 17px;
+margin-top: 17px;
 }
 
 #nj_tiles_show, #nj_tiles_show_2, #nj_tiles_show_3, #nj_tiles_show_4, #nj_tiles_show_5,
 #upgma_tiles_show, #upgma_tiles_show_2, #upgma_tiles_show_3, #upgma_tiles_show_4, #upgma_tiles_show_5 {
-  margin-top: 18px; 
-  margin-left: -5px
+margin-top: 18px; 
+margin-left: -5px
 }
 
 #nj_ladder, #upgma_ladder {
-  margin-top: 8px; 
-  margin-left: -5px
+margin-top: 8px; 
+margin-left: -5px
 }
 
 #nj_align, #upgma_align {
-  margin-top: 10px; 
-  margin-left: -60px
+margin-top: 10px; 
+margin-left: -60px
 }
 
 #nj_rootedge_show, #upgma_rootedge_show {
-  margin-top: 8px;
-  margin-left: -15px;
+margin-top: 8px;
+margin-left: -15px;
 }
 
 #nj_mapping_show, #upgma_mapping_show {
-  margin-top: 13px;
+margin-top: 13px;
 }
 
 #nj_tipcolor_mapping, #nj_tipshape_mapping_show, #upgma_tipcolor_mapping, #upgma_tipshape_mapping_show {
-  margin-top: -10px;
-  margin-right: 30px;
+margin-top: -10px;
+margin-right: 30px;
 }
 
 #nj_tipshape_mapping, #nj_fruit_variable, #nj_fruit_variable2, #nj_fruit_variable3, #nj_fruit_variable4, #nj_fruit_variable5, #upgma_tipshape_mapping, #upgma_fruit_variable, #upgma_fruit_variable2, #upgma_fruit_variable3, #upgma_fruit_variable4, #upgma_fruit_variable5 {
-  margin-top: -10px;
-  margin-right: 30px;
+margin-top: -10px;
+margin-right: 30px;
 }
 
 #nj_tiplab_scale {
-  margin-top: 0px;
-  margin-bottom: -10px;
+margin-top: 0px;
+margin-bottom: -10px;
 }
 
 #upgma_tiplab_scale {
-  margin-top: -6px;
-  margin-bottom: -10px;
+margin-top: -6px;
+margin-bottom: -10px;
 }
 
 #upgma_tippoint_scale {
-  margin-top: -10px;
+margin-top: -10px;
 }
 
 #shiny-tab-visualization > div:nth-child(5) > div > div:nth-child(5) > div > div > div > div > div > div:nth-child(2) > div:nth-child(3) > div > div > div {
-  margin-top: -7px;
+margin-top: -7px;
 }
 
 #shiny-tab-visualization > div:nth-child(5) > div > div:nth-child(5) > div > div > div > div > div > div:nth-child(3) > div:nth-child(3) > div > div > div {
-  margin-top: -10px;
+margin-top: -10px;
 }
 
 #nj_tipcolor_mapping, #upgma_tipcolor_mapping {
-  margin-top: -10px;
+margin-top: -10px;
 }
 
 #nj_geom, #upgma_geom {
-  margin-top: 0px; 
-  margin-left: -5px;
-  margin-bottom: 0px;
+margin-top: 0px; 
+margin-left: -5px;
+margin-bottom: 0px;
 }
 
 #nj_tiplab_color, #upgma_tiplab_color {
-  margin-bottom: 7px;
-  margin-top: -7px;
+margin-bottom: 7px;
+margin-top: -7px;
 }
 
 #nj_show_branch_label, #upgma_show_branch_label {
-  margin-top: 17px; 
-  margin-left: -5px
+margin-top: 17px; 
+margin-left: -5px
 }
 
 #nj_tiplab_show, #upgma_tiplab_show {
-  margin-top: 17px; 
-  margin-left: -5px
+margin-top: 17px; 
+margin-left: -5px
 }
 
 #nj_fruit_offset, #upgma_fruit_offset {
-  position: relative; 
-  top: -20px
+position: relative; 
+top: -20px
 }
 
 #nj_layout .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y,
 #upgma_layout .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y{
-  margin-bottom: 16px
+margin-bottom: 16px
 }
 
 #nj_div_tiles, #upgma_div_tiles {
-  position: absolute; 
-  bottom: 4px; 
-  margin-left: -5px
+position: absolute; 
+bottom: 4px; 
+margin-left: -5px
 }
 
 #nj_fruit_offset_2, #upgma_fruit_offset_2 {
-  position: relative; 
-  top: -20px
+position: relative; 
+top: -20px
 }
 
 #nj_layout_2 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y,
 #upgma_layout_2 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y{
-  margin-bottom: 16px
+margin-bottom: 16px
 }
 
 #nj_div_tiles_2, #upgma_div_tiles_2 {
-  position: absolute; 
-  bottom: 4px; 
-  margin-left: -5px
+position: absolute; 
+bottom: 4px; 
+margin-left: -5px
 }
 
 #nj_fruit_offset_3, #upgma_fruit_offset_3 {
-  position: relative; 
-  top: -20px
+position: relative; 
+top: -20px
 }
 
 #nj_layout_3 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y,
 #upgma_layout_3 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y{
-  margin-bottom: 16px
+margin-bottom: 16px
 }
 
 #nj_div_tiles_3, #upgma_div_tiles_3 {
-  position: absolute; 
-  bottom: 4px; 
-  margin-left: -5px
+position: absolute; 
+bottom: 4px; 
+margin-left: -5px
 }
 
 #nj_fruit_offset_4, #upgma_fruit_offset_4 {
-  position: relative; 
-  top: -20px
+position: relative; 
+top: -20px
 }
 
 #nj_layout_4 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y,
 #upgma_layout_4 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y{
-  margin-bottom: 16px
+margin-bottom: 16px
 }
 
 #nj_div_tiles_4, #upgma_div_tiles_4 {
-  position: absolute; 
-  bottom: 4px; 
-  margin-left: -5px
+position: absolute; 
+bottom: 4px; 
+margin-left: -5px
 }
 
 #nj_fruit_offset_5, #upgma_fruit_offset_5 {
-  position: relative; 
-  top: -20px
+position: relative; 
+top: -20px
 }
 
 #nj_layout_5 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y,
 #upgma_layout_5 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y {
-  margin-bottom: 16px
+margin-bottom: 16px
 }
 
 #nj_div_tiles_5, #upgma_div_tiles_5 {
-  position: absolute; 
-  bottom: 4px; 
-  margin-left: -5px
+position: absolute; 
+bottom: 4px; 
+margin-left: -5px
 }
 
 #nj_heatmap_width, #upgma_heatmap_width {
-  margin-top: 8px;
+margin-top: 8px;
 }
 
 #nj_heatmap_offset, #upgma_heatmap_offset {
-  margin-top: 4px;
-  margin-bottom: 2px;
+margin-top: 4px;
+margin-bottom: 2px;
 }
 
 #nj_fruit_width, #nj_fruit_width2, #nj_fruit_width3, #nj_fruit_width4, #nj_fruit_width5,
 #upgma_fruit_width, #upgma_fruit_width2, #upgma_fruit_width3, #upgma_fruit_width4, #upgma_fruit_width5{
-  margin-top: -5px;
-  margin-bottom: -15px;
+margin-top: -5px;
+margin-bottom: -15px;
 }
 
 #nj_heatmap_show, #upgma_heatmap_show {
-  margin-top: 18px; 
-  margin-left: -5px;
+margin-top: 18px; 
+margin-left: -5px;
 }
 
 #nj_nodepoint_show, #nj_tippoint_show, #upgma_nodepoint_show, #upgma_tippoint_show {
-  margin-top: 18px; 
-  margin-left: -5px
+margin-top: 18px; 
+margin-left: -5px
 }
 
 #nj_tiplab_scale .option[data-value="Set1"],
@@ -1798,10 +1810,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Set1"],
 #upgma_heatmap_scale .option[data-value="Set1"],
 #upgma_clade_scale .option[data-value="Set1"] {
-    background: linear-gradient(to right, #E41A1C 0%, #E41A1C 11%, #377EB8 11%, #377EB8 22%, #4DAF4A 22%, #4DAF4A 33%, #984EA3 33%, #984EA3 44%, #FF7F00 44%, #FF7F00 55%, #FFFF33 55%, #FFFF33 66%, #A65628 66%, #A65628 77%, #F781BF 77%, #F781BF 88%, #999999 88%, #999999 100%);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #E41A1C 0%, #E41A1C 11%, #377EB8 11%, #377EB8 22%, #4DAF4A 22%, #4DAF4A 33%, #984EA3 33%, #984EA3 44%, #FF7F00 44%, #FF7F00 55%, #FFFF33 55%, #FFFF33 66%, #A65628 66%, #A65628 77%, #F781BF 77%, #F781BF 88%, #999999 88%, #999999 100%);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Set2"], 
 #nj_tippoint_scale .option[data-value="Set2"], 
@@ -1821,10 +1833,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Set2"], 
 #upgma_heatmap_scale .option[data-value="Set2"],
 #upgma_clade_scale .option[data-value="Set2"] {
-    background: linear-gradient(to right, #66C2A5 0%, #66C2A5 12.5%, #FC8D62 12.5%, #FC8D62 25%, #8DA0CB 25%, #8DA0CB 37.5%, #E78AC3 37.5%, #E78AC3 50%, #A6D854 50%, #A6D854 62.5%, #FFD92F 62.5%, #FFD92F 75%, #E5C494 75%, #E5C494 87.5%, #B3B3B3 87.5%, #B3B3B3 100%);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #66C2A5 0%, #66C2A5 12.5%, #FC8D62 12.5%, #FC8D62 25%, #8DA0CB 25%, #8DA0CB 37.5%, #E78AC3 37.5%, #E78AC3 50%, #A6D854 50%, #A6D854 62.5%, #FFD92F 62.5%, #FFD92F 75%, #E5C494 75%, #E5C494 87.5%, #B3B3B3 87.5%, #B3B3B3 100%);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Set3"], 
 #nj_tippoint_scale .option[data-value="Set3"], 
@@ -1844,10 +1856,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Set3"], 
 #upgma_heatmap_scale .option[data-value="Set3"],
 #upgma_clade_scale .option[data-value="Set3"] {
-    background: linear-gradient(to right, #8DD3C7 0%, #8DD3C7 8.33333%, #FFFFB3 8.33333%, #FFFFB3 16.6667%, #BEBADA 16.6667%, #BEBADA 25%, #FB8072 25%, #FB8072 33.3333%, #80B1D3 33.3333%, #80B1D3 41.6667%, #FDB462 41.6667%, #FDB462 50%, #B3DE69 50%, #B3DE69 58.3333%, #FCCDE5 58.3333%, #FCCDE5 66.6667%, #D9D9D9 66.6667%, #D9D9D9 75%, #BC80BD 75%, #BC80BD 83.3333%, #CCEBC5 83.3333%, #CCEBC5 91.6667%, #FFED6F 91.6667%, #FFED6F 100%);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #8DD3C7 0%, #8DD3C7 8.33333%, #FFFFB3 8.33333%, #FFFFB3 16.6667%, #BEBADA 16.6667%, #BEBADA 25%, #FB8072 25%, #FB8072 33.3333%, #80B1D3 33.3333%, #80B1D3 41.6667%, #FDB462 41.6667%, #FDB462 50%, #B3DE69 50%, #B3DE69 58.3333%, #FCCDE5 58.3333%, #FCCDE5 66.6667%, #D9D9D9 66.6667%, #D9D9D9 75%, #BC80BD 75%, #BC80BD 83.3333%, #CCEBC5 83.3333%, #CCEBC5 91.6667%, #FFED6F 91.6667%, #FFED6F 100%);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Pastel1"], 
 #nj_tippoint_scale .option[data-value="Pastel1"], 
@@ -1867,10 +1879,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Pastel1"], 
 #upgma_heatmap_scale .option[data-value="Pastel1"],
 #upgma_clade_scale .option[data-value="Pastel1"] {
-    background: linear-gradient(to right, #FBB4AE 0%, #FBB4AE 11.1111%, #B3CDE3 11.1111%, #B3CDE3 22.2222%, #CCEBC5 22.2222%, #CCEBC5 33.3333%, #DECBE4 33.3333%, #DECBE4 44.4444%, #FED9A6 44.4444%, #FED9A6 55.5556%, #FFFFCC 55.5556%, #FFFFCC 66.6667%, #E5D8BD 66.6667%, #E5D8BD 77.7778%, #FDDAEC 77.7778%, #FDDAEC 88.8889%, #F2F2F2 88.8889%, #F2F2F2 100%);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FBB4AE 0%, #FBB4AE 11.1111%, #B3CDE3 11.1111%, #B3CDE3 22.2222%, #CCEBC5 22.2222%, #CCEBC5 33.3333%, #DECBE4 33.3333%, #DECBE4 44.4444%, #FED9A6 44.4444%, #FED9A6 55.5556%, #FFFFCC 55.5556%, #FFFFCC 66.6667%, #E5D8BD 66.6667%, #E5D8BD 77.7778%, #FDDAEC 77.7778%, #FDDAEC 88.8889%, #F2F2F2 88.8889%, #F2F2F2 100%);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Pastel2"], 
 #nj_tippoint_scale .option[data-value="Pastel2"], 
@@ -1890,10 +1902,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Pastel2"], 
 #upgma_heatmap_scale .option[data-value="Pastel2"],
 #upgma_clade_scale .option[data-value="Pastel2"] {
-    background: linear-gradient(to right, #B3E2CD 0%, #B3E2CD 12.5%, #FDCDAC 12.5%, #FDCDAC 25%, #CBD5E8 25%, #CBD5E8 37.5%, #F4CAE4 37.5%, #F4CAE4 50%, #E6F5C9 50%, #E6F5C9 62.5%, #FFF2AE 62.5%, #FFF2AE 75%, #F1E2CC 75%, #F1E2CC 87.5%, #CCCCCC 87.5%, #CCCCCC 100%);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #B3E2CD 0%, #B3E2CD 12.5%, #FDCDAC 12.5%, #FDCDAC 25%, #CBD5E8 25%, #CBD5E8 37.5%, #F4CAE4 37.5%, #F4CAE4 50%, #E6F5C9 50%, #E6F5C9 62.5%, #FFF2AE 62.5%, #FFF2AE 75%, #F1E2CC 75%, #F1E2CC 87.5%, #CCCCCC 87.5%, #CCCCCC 100%);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Paired"], 
 #nj_tippoint_scale .option[data-value="Paired"], 
@@ -1913,10 +1925,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Paired"], 
 #upgma_heatmap_scale .option[data-value="Paired"],
 #upgma_clade_scale .option[data-value="Paired"] {
-    background: linear-gradient(to right, #A6CEE3 0%, #A6CEE3 8.33333%, #1F78B4 8.33333%, #1F78B4 16.6667%, #B2DF8A 16.6667%, #B2DF8A 25%, #33A02C 25%, #33A02C 33.3333%, #FB9A99 33.3333%, #FB9A99 41.6667%, #E31A1C 41.6667%, #E31A1C 50%, #FDBF6F 50%, #FDBF6F 58.3333%, #FF7F00 58.3333%, #FF7F00 66.6667%, #CAB2D6 66.6667%, #CAB2D6 75%, #6A3D9A 75%, #6A3D9A 83.3333%, #FFFF99 83.3333%, #FFFF99 91.6667%, #B15928 91.6667%, #B15928 100%);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #A6CEE3 0%, #A6CEE3 8.33333%, #1F78B4 8.33333%, #1F78B4 16.6667%, #B2DF8A 16.6667%, #B2DF8A 25%, #33A02C 25%, #33A02C 33.3333%, #FB9A99 33.3333%, #FB9A99 41.6667%, #E31A1C 41.6667%, #E31A1C 50%, #FDBF6F 50%, #FDBF6F 58.3333%, #FF7F00 58.3333%, #FF7F00 66.6667%, #CAB2D6 66.6667%, #CAB2D6 75%, #6A3D9A 75%, #6A3D9A 83.3333%, #FFFF99 83.3333%, #FFFF99 91.6667%, #B15928 91.6667%, #B15928 100%);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Dark2"], 
 #nj_tippoint_scale .option[data-value="Dark2"], 
@@ -1936,10 +1948,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Dark2"], 
 #upgma_heatmap_scale .option[data-value="Dark2"],
 #upgma_clade_scale .option[data-value="Dark2"] {
-    background: linear-gradient(to right, #1B9E77 0%, #1B9E77 12.5%, #D95F02 12.5%, #D95F02 25%, #7570B3 25%, #7570B3 37.5%, #E7298A 37.5%, #E7298A 50%, #66A61E 50%, #66A61E 62.5%, #E6AB02 62.5%, #E6AB02 75%, #A6761D 75%, #A6761D 87.5%, #666666 87.5%, #666666 100%);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #1B9E77 0%, #1B9E77 12.5%, #D95F02 12.5%, #D95F02 25%, #7570B3 25%, #7570B3 37.5%, #E7298A 37.5%, #E7298A 50%, #66A61E 50%, #66A61E 62.5%, #E6AB02 62.5%, #E6AB02 75%, #A6761D 75%, #A6761D 87.5%, #666666 87.5%, #666666 100%);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Accent"], 
 #nj_tippoint_scale .option[data-value="Accent"], 
@@ -1959,9 +1971,9 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Accent"], 
 #upgma_heatmap_scale .option[data-value="Accent"],
 #upgma_clade_scale .option[data-value="Accent"]{
-    background: linear-gradient(to right, #7FC97F 0%, #7FC97F 12.5%, #BEAED4 12.5%, #BEAED4 25%, #FDC086 25%, #FDC086 37.5%, #FFFF99 37.5%, #FFFF99 50%, #386CB0 50%, #386CB0 62.5%, #F0027F 62.5%, #F0027F 75%, #BF5B17 75%, #BF5B17 87.5%, #666666 87.5%, #666666 100%);
-    color: black;
-}
+background: linear-gradient(to right, #7FC97F 0%, #7FC97F 12.5%, #BEAED4 12.5%, #BEAED4 25%, #FDC086 25%, #FDC086 37.5%, #FFFF99 37.5%, #FFFF99 50%, #386CB0 50%, #386CB0 62.5%, #F0027F 62.5%, #F0027F 75%, #BF5B17 75%, #BF5B17 87.5%, #666666 87.5%, #666666 100%);
+                            color: black;
+                            }
 
 #nj_tiplab_scale .option[data-value="YlOrRd"], 
 #nj_tippoint_scale .option[data-value="YlOrRd"], 
@@ -1981,10 +1993,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="YlOrRd"], 
 #upgma_heatmap_scale .option[data-value="YlOrRd"],
 #upgma_clade_scale .option[data-value="YlOrRd"] {
-    background: linear-gradient(to right, #FFFFCC 0%, #FFFFCC 11.1111%, #FFEDA0 11.1111%, #FFEDA0 22.2222%, #FED976 22.2222%, #FED976 33.3333%, #FEB24C 33.3333%, #FEB24C 44.4444%, #FD8D3C 44.4444%, #FD8D3C 55.5556%, #FC4E2A 55.5556%, #FC4E2A 66.6667%, #E31A1C 66.6667%, #E31A1C 77.7778%, #BD0026 77.7778%, #BD0026 88.8889%, #800026 88.8889%, #800026 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FFFFCC 0%, #FFFFCC 11.1111%, #FFEDA0 11.1111%, #FFEDA0 22.2222%, #FED976 22.2222%, #FED976 33.3333%, #FEB24C 33.3333%, #FEB24C 44.4444%, #FD8D3C 44.4444%, #FD8D3C 55.5556%, #FC4E2A 55.5556%, #FC4E2A 66.6667%, #E31A1C 66.6667%, #E31A1C 77.7778%, #BD0026 77.7778%, #BD0026 88.8889%, #800026 88.8889%, #800026 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="YlOrBr"], 
 #nj_tippoint_scale .option[data-value="YlOrBr"], 
@@ -2004,10 +2016,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="YlOrBr"], 
 #upgma_heatmap_scale .option[data-value="YlOrBr"],
 #upgma_clade_scale .option[data-value="YlOrBr"] {
-    background: linear-gradient(to right, #FFFFE5 0%, #FFFFE5 11.1111%, #FFF7BC 11.1111%, #FFF7BC 22.2222%, #FEE391 22.2222%, #FEE391 33.3333%, #FEC44F 33.3333%, #FEC44F 44.4444%, #FE9929 44.4444%, #FE9929 55.5556%, #EC7014 55.5556%, #EC7014 66.6667%, #CC4C02 66.6667%, #CC4C02 77.7778%, #993404 77.7778%, #993404 88.8889%, #662506 88.8889%, #662506 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FFFFE5 0%, #FFFFE5 11.1111%, #FFF7BC 11.1111%, #FFF7BC 22.2222%, #FEE391 22.2222%, #FEE391 33.3333%, #FEC44F 33.3333%, #FEC44F 44.4444%, #FE9929 44.4444%, #FE9929 55.5556%, #EC7014 55.5556%, #EC7014 66.6667%, #CC4C02 66.6667%, #CC4C02 77.7778%, #993404 77.7778%, #993404 88.8889%, #662506 88.8889%, #662506 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="YlGnBu"], 
 #nj_tippoint_scale .option[data-value="YlGnBu"], 
@@ -2027,10 +2039,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="YlGnBu"], 
 #upgma_heatmap_scale .option[data-value="YlGnBu"],
 #upgma_clade_scale .option[data-value="YlGnBu"] {
-    background: linear-gradient(to right, #FFFFD9 0%, #FFFFD9 11.1111%, #EDF8B1 11.1111%, #EDF8B1 22.2222%, #C7E9B4 22.2222%, #C7E9B4 33.3333%, #7FCDBB 33.3333%, #7FCDBB 44.4444%, #41B6C4 44.4444%, #41B6C4 55.5556%, #1D91C0 55.5556%, #1D91C0 66.6667%, #225EA8 66.6667%, #225EA8 77.7778%, #253494 77.7778%, #253494 88.8889%, #081D58 88.8889%, #081D58 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FFFFD9 0%, #FFFFD9 11.1111%, #EDF8B1 11.1111%, #EDF8B1 22.2222%, #C7E9B4 22.2222%, #C7E9B4 33.3333%, #7FCDBB 33.3333%, #7FCDBB 44.4444%, #41B6C4 44.4444%, #41B6C4 55.5556%, #1D91C0 55.5556%, #1D91C0 66.6667%, #225EA8 66.6667%, #225EA8 77.7778%, #253494 77.7778%, #253494 88.8889%, #081D58 88.8889%, #081D58 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="YlGn"], 
 #nj_tippoint_scale .option[data-value="YlGn"], 
@@ -2050,10 +2062,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="YlGn"], 
 #upgma_heatmap_scale .option[data-value="YlGn"],
 #upgma_clade_scale .option[data-value="YlGn"]{
-    background: linear-gradient(to right, #FFFFE5 0%, #FFFFE5 11.1111%, #F7FCB9 11.1111%, #F7FCB9 22.2222%, #D9F0A3 22.2222%, #D9F0A3 33.3333%, #ADDD8E 33.3333%, #ADDD8E 44.4444%, #78C679 44.4444%, #78C679 55.5556%, #41AB5D 55.5556%, #41AB5D 66.6667%, #238443 66.6667%, #238443 77.7778%, #006837 77.7778%, #006837 88.8889%, #004529 88.8889%, #004529 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FFFFE5 0%, #FFFFE5 11.1111%, #F7FCB9 11.1111%, #F7FCB9 22.2222%, #D9F0A3 22.2222%, #D9F0A3 33.3333%, #ADDD8E 33.3333%, #ADDD8E 44.4444%, #78C679 44.4444%, #78C679 55.5556%, #41AB5D 55.5556%, #41AB5D 66.6667%, #238443 66.6667%, #238443 77.7778%, #006837 77.7778%, #006837 88.8889%, #004529 88.8889%, #004529 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Reds"], 
 #nj_tippoint_scale .option[data-value="Reds"], 
@@ -2073,10 +2085,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Reds"], 
 #upgma_heatmap_scale .option[data-value="Reds"],
 #upgma_clade_scale .option[data-value="Reds"] {
-    background: linear-gradient(to right, #FFF5F0 0%, #FFF5F0 11.1111%, #FEE0D2 11.1111%, #FEE0D2 22.2222%, #FCBBA1 22.2222%, #FCBBA1 33.3333%, #FC9272 33.3333%, #FC9272 44.4444%, #FB6A4A 44.4444%, #FB6A4A 55.5556%, #EF3B2C 55.5556%, #EF3B2C 66.6667%, #CB181D 66.6667%, #CB181D 77.7778%, #A50F15 77.7778%, #A50F15 88.8889%, #67000D 88.8889%, #67000D 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FFF5F0 0%, #FFF5F0 11.1111%, #FEE0D2 11.1111%, #FEE0D2 22.2222%, #FCBBA1 22.2222%, #FCBBA1 33.3333%, #FC9272 33.3333%, #FC9272 44.4444%, #FB6A4A 44.4444%, #FB6A4A 55.5556%, #EF3B2C 55.5556%, #EF3B2C 66.6667%, #CB181D 66.6667%, #CB181D 77.7778%, #A50F15 77.7778%, #A50F15 88.8889%, #67000D 88.8889%, #67000D 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="RdPu"], 
 #nj_tippoint_scale .option[data-value="RdPu"], 
@@ -2096,10 +2108,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="RdPu"], 
 #upgma_heatmap_scale .option[data-value="RdPu"],
 #upgma_clade_scale .option[data-value="RdPu"] {
-    background: linear-gradient(to right, #FFF7F3 0%, #FFF7F3 11.1111%, #FDE0DD 11.1111%, #FDE0DD 22.2222%, #FCC5C0 22.2222%, #FCC5C0 33.3333%, #FA9FB5 33.3333%, #FA9FB5 44.4444%, #F768A1 44.4444%, #F768A1 55.5556%, #DD3497 55.5556%, #DD3497 66.6667%, #AE017E 66.6667%, #AE017E 77.7778%, #7A0177 77.7778%, #7A0177 88.8889%, #49006A 88.8889%, #49006A 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FFF7F3 0%, #FFF7F3 11.1111%, #FDE0DD 11.1111%, #FDE0DD 22.2222%, #FCC5C0 22.2222%, #FCC5C0 33.3333%, #FA9FB5 33.3333%, #FA9FB5 44.4444%, #F768A1 44.4444%, #F768A1 55.5556%, #DD3497 55.5556%, #DD3497 66.6667%, #AE017E 66.6667%, #AE017E 77.7778%, #7A0177 77.7778%, #7A0177 88.8889%, #49006A 88.8889%, #49006A 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Purples"], 
 #nj_tippoint_scale .option[data-value="Purples"], 
@@ -2119,10 +2131,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Purples"], 
 #upgma_heatmap_scale .option[data-value="Purples"],
 #upgma_clade_scale .option[data-value="Purples"] {
-    background: linear-gradient(to right, #FCFBFD 0%, #FCFBFD 11.1111%, #EFEDF5 11.1111%, #EFEDF5 22.2222%, #DADAEB 22.2222%, #DADAEB 33.3333%, #BCBDDC 33.3333%, #BCBDDC 44.4444%, #9E9AC8 44.4444%, #9E9AC8 55.5556%, #807DBA 55.5556%, #807DBA 66.6667%, #6A51A3 66.6667%, #6A51A3 77.7778%, #54278F 77.7778%, #54278F 88.8889%, #3F007D 88.8889%, #3F007D 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FCFBFD 0%, #FCFBFD 11.1111%, #EFEDF5 11.1111%, #EFEDF5 22.2222%, #DADAEB 22.2222%, #DADAEB 33.3333%, #BCBDDC 33.3333%, #BCBDDC 44.4444%, #9E9AC8 44.4444%, #9E9AC8 55.5556%, #807DBA 55.5556%, #807DBA 66.6667%, #6A51A3 66.6667%, #6A51A3 77.7778%, #54278F 77.7778%, #54278F 88.8889%, #3F007D 88.8889%, #3F007D 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="PuRd"], 
 #nj_tippoint_scale .option[data-value="PuRd"], 
@@ -2142,10 +2154,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="PuRd"], 
 #upgma_heatmap_scale .option[data-value="PuRd"],
 #upgma_clade_scale .option[data-value="PuRd"] {
-    background: linear-gradient(to right, #F7F4F9 0%, #F7F4F9 11.1111%, #E7E1EF 11.1111%, #E7E1EF 22.2222%, #D4B9DA 22.2222%, #D4B9DA 33.3333%, #C994C7 33.3333%, #C994C7 44.4444%, #DF65B0 44.4444%, #DF65B0 55.5556%, #E7298A 55.5556%, #E7298A 66.6667%, #CE1256 66.6667%, #CE1256 77.7778%, #980043 77.7778%, #980043 88.8889%, #67001F 88.8889%, #67001F 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #F7F4F9 0%, #F7F4F9 11.1111%, #E7E1EF 11.1111%, #E7E1EF 22.2222%, #D4B9DA 22.2222%, #D4B9DA 33.3333%, #C994C7 33.3333%, #C994C7 44.4444%, #DF65B0 44.4444%, #DF65B0 55.5556%, #E7298A 55.5556%, #E7298A 66.6667%, #CE1256 66.6667%, #CE1256 77.7778%, #980043 77.7778%, #980043 88.8889%, #67001F 88.8889%, #67001F 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="PuBuGn"], 
 #nj_tippoint_scale .option[data-value="PuBuGn"], 
@@ -2165,10 +2177,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="PuBuGn"], 
 #upgma_heatmap_scale .option[data-value="PuBuGn"],
 #upgma_clade_scale .option[data-value="PuBuGn"] {
-    background: linear-gradient(to right, #FFF7FB 0%, #FFF7FB 11.1111%, #ECE2F0 11.1111%, #ECE2F0 22.2222%, #D0D1E6 22.2222%, #D0D1E6 33.3333%, #A6BDDB 33.3333%, #A6BDDB 44.4444%, #67A9CF 44.4444%, #67A9CF 55.5556%, #3690C0 55.5556%, #3690C0 66.6667%, #02818A 66.6667%, #02818A 77.7778%, #016C59 77.7778%, #016C59 88.8889%, #014636 88.8889%, #014636 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FFF7FB 0%, #FFF7FB 11.1111%, #ECE2F0 11.1111%, #ECE2F0 22.2222%, #D0D1E6 22.2222%, #D0D1E6 33.3333%, #A6BDDB 33.3333%, #A6BDDB 44.4444%, #67A9CF 44.4444%, #67A9CF 55.5556%, #3690C0 55.5556%, #3690C0 66.6667%, #02818A 66.6667%, #02818A 77.7778%, #016C59 77.7778%, #016C59 88.8889%, #014636 88.8889%, #014636 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="PuBu"], 
 #nj_tippoint_scale .option[data-value="PuBu"], 
@@ -2188,10 +2200,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="PuBu"], 
 #upgma_heatmap_scale .option[data-value="PuBu"],
 #upgma_clade_scale .option[data-value="PuBu"] {
-    background: linear-gradient(to right, #FFF7FB 0%, #FFF7FB 11.1111%, #ECE7F2 11.1111%, #ECE7F2 22.2222%, #D0D1E6 22.2222%, #D0D1E6 33.3333%, #A6BDDB 33.3333%, #A6BDDB 44.4444%, #74A9CF 44.4444%, #74A9CF 55.5556%, #3690C0 55.5556%, #3690C0 66.6667%, #0570B0 66.6667%, #0570B0 77.7778%, #045A8D 77.7778%, #045A8D 88.8889%, #023858 88.8889%, #023858 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FFF7FB 0%, #FFF7FB 11.1111%, #ECE7F2 11.1111%, #ECE7F2 22.2222%, #D0D1E6 22.2222%, #D0D1E6 33.3333%, #A6BDDB 33.3333%, #A6BDDB 44.4444%, #74A9CF 44.4444%, #74A9CF 55.5556%, #3690C0 55.5556%, #3690C0 66.6667%, #0570B0 66.6667%, #0570B0 77.7778%, #045A8D 77.7778%, #045A8D 88.8889%, #023858 88.8889%, #023858 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="OrRd"], 
 #nj_tippoint_scale .option[data-value="OrRd"], 
@@ -2211,10 +2223,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="OrRd"], 
 #upgma_heatmap_scale .option[data-value="OrRd"],
 #upgma_clade_scale .option[data-value="OrRd"] {
-    background: linear-gradient(to right, #FFF7EC 0%, #FFF7EC 11.1111%, #FEE8C8 11.1111%, #FEE8C8 22.2222%, #FDD49E 22.2222%, #FDD49E 33.3333%, #FDBB84 33.3333%, #FDBB84 44.4444%, #FC8D59 44.4444%, #FC8D59 55.5556%, #EF6548 55.5556%, #EF6548 66.6667%, #D7301F 66.6667%, #D7301F 77.7778%, #B30000 77.7778%, #B30000 88.8889%, #7F0000 88.8889%, #7F0000 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FFF7EC 0%, #FFF7EC 11.1111%, #FEE8C8 11.1111%, #FEE8C8 22.2222%, #FDD49E 22.2222%, #FDD49E 33.3333%, #FDBB84 33.3333%, #FDBB84 44.4444%, #FC8D59 44.4444%, #FC8D59 55.5556%, #EF6548 55.5556%, #EF6548 66.6667%, #D7301F 66.6667%, #D7301F 77.7778%, #B30000 77.7778%, #B30000 88.8889%, #7F0000 88.8889%, #7F0000 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Oranges"], 
 #nj_tippoint_scale .option[data-value="Oranges"], 
@@ -2234,10 +2246,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Oranges"], 
 #upgma_heatmap_scale .option[data-value="Oranges"],
 #upgma_clade_scale .option[data-value="Oranges"] {
-    background: linear-gradient(to right, #FFF5EB 0%, #FFF5EB 11.1111%, #FEE6CE 11.1111%, #FEE6CE 22.2222%, #FDD0A2 22.2222%, #FDD0A2 33.3333%, #FDAE6B 33.3333%, #FDAE6B 44.4444%, #FD8D3C 44.4444%, #FD8D3C 55.5556%, #F16913 55.5556%, #F16913 66.6667%, #D94801 66.6667%, #D94801 77.7778%, #A63603 77.7778%, #A63603 88.8889%, #7F2704 88.8889%, #7F2704 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #FFF5EB 0%, #FFF5EB 11.1111%, #FEE6CE 11.1111%, #FEE6CE 22.2222%, #FDD0A2 22.2222%, #FDD0A2 33.3333%, #FDAE6B 33.3333%, #FDAE6B 44.4444%, #FD8D3C 44.4444%, #FD8D3C 55.5556%, #F16913 55.5556%, #F16913 66.6667%, #D94801 66.6667%, #D94801 77.7778%, #A63603 77.7778%, #A63603 88.8889%, #7F2704 88.8889%, #7F2704 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Greys"], 
 #nj_tippoint_scale .option[data-value="Greys"], 
@@ -2257,9 +2269,9 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Greys"], 
 #upgma_heatmap_scale .option[data-value="Greys"],
 #upgma_clade_scale .option[data-value="Greys"] {
-    background: linear-gradient(to right, #FFFFFF 0%, #FFFFFF 11.1111%, #F0F0F0 11.1111%, #F0F0F0 22.2222%, #D9D9D9 22.2222%, #D9D9D9 33.3333%, #BDBDBD 33.3333%, #BDBDBD 44.4444%, #969696 44.4444%, #969696 55.5556%, #737373 55.5556%, #737373 66.6667%, #525252 66.6667%, #525252 77.7778%, #252525 77.7778%, #252525 88.8889%, #000000 88.8889%, #000000 100%);
-    color: white;
-}
+background: linear-gradient(to right, #FFFFFF 0%, #FFFFFF 11.1111%, #F0F0F0 11.1111%, #F0F0F0 22.2222%, #D9D9D9 22.2222%, #D9D9D9 33.3333%, #BDBDBD 33.3333%, #BDBDBD 44.4444%, #969696 44.4444%, #969696 55.5556%, #737373 55.5556%, #737373 66.6667%, #525252 66.6667%, #525252 77.7778%, #252525 77.7778%, #252525 88.8889%, #000000 88.8889%, #000000 100%);
+                            color: white;
+                            }
 
 #nj_tiplab_scale .option[data-value="Greens"], 
 #nj_tippoint_scale .option[data-value="Greens"], 
@@ -2279,10 +2291,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Greens"], 
 #upgma_heatmap_scale .option[data-value="Greens"],
 #upgma_clade_scale .option[data-value="Greens"] {
-    background: linear-gradient(to right, #F7FCF5 0%, #F7FCF5 11.1111%, #E5F5E0 11.1111%, #E5F5E0 22.2222%, #C7E9C0 22.2222%, #C7E9C0 33.3333%, #A1D99B 33.3333%, #A1D99B 44.4444%, #74C476 44.4444%, #74C476 55.5556%, #41AB5D 55.5556%, #41AB5D 66.6667%, #238B45 66.6667%, #238B45 77.7778%, #006D2C 77.7778%, #006D2C 88.8889%, #00441B 88.8889%, #00441B 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #F7FCF5 0%, #F7FCF5 11.1111%, #E5F5E0 11.1111%, #E5F5E0 22.2222%, #C7E9C0 22.2222%, #C7E9C0 33.3333%, #A1D99B 33.3333%, #A1D99B 44.4444%, #74C476 44.4444%, #74C476 55.5556%, #41AB5D 55.5556%, #41AB5D 66.6667%, #238B45 66.6667%, #238B45 77.7778%, #006D2C 77.7778%, #006D2C 88.8889%, #00441B 88.8889%, #00441B 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="GnBu"], 
 #nj_tippoint_scale .option[data-value="GnBu"], 
@@ -2302,10 +2314,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="GnBu"], 
 #upgma_heatmap_scale .option[data-value="GnBu"],
 #upgma_clade_scale .option[data-value="GnBu"] {
-    background: linear-gradient(to right, #F7FCF0 0%, #F7FCF0 11.1111%, #E0F3DB 11.1111%, #E0F3DB 22.2222%, #CCEBC5 22.2222%, #CCEBC5 33.3333%, #A8DDB5 33.3333%, #A8DDB5 44.4444%, #7BCCC4 44.4444%, #7BCCC4 55.5556%, #4EB3D3 55.5556%, #4EB3D3 66.6667%, #2B8CBE 66.6667%, #2B8CBE 77.7778%, #0868AC 77.7778%, #0868AC 88.8889%, #084081 88.8889%, #084081 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #F7FCF0 0%, #F7FCF0 11.1111%, #E0F3DB 11.1111%, #E0F3DB 22.2222%, #CCEBC5 22.2222%, #CCEBC5 33.3333%, #A8DDB5 33.3333%, #A8DDB5 44.4444%, #7BCCC4 44.4444%, #7BCCC4 55.5556%, #4EB3D3 55.5556%, #4EB3D3 66.6667%, #2B8CBE 66.6667%, #2B8CBE 77.7778%, #0868AC 77.7778%, #0868AC 88.8889%, #084081 88.8889%, #084081 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="BuPu"], 
 #nj_tippoint_scale .option[data-value="BuPu"], 
@@ -2325,10 +2337,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="BuPu"], 
 #upgma_heatmap_scale .option[data-value="BuPu"],
 #upgma_clade_scale .option[data-value="BuPu"] {
-    background: linear-gradient(to right, #F7FCFD 0%, #F7FCFD 11.1111%, #E0ECF4 11.1111%, #E0ECF4 22.2222%, #BFD3E6 22.2222%, #BFD3E6 33.3333%, #9EBCDA 33.3333%, #9EBCDA 44.4444%, #8C96C6 44.4444%, #8C96C6 55.5556%, #8C6BB1 55.5556%, #8C6BB1 66.6667%, #88419D 66.6667%, #88419D 77.7778%, #810F7C 77.7778%, #810F7C 88.8889%, #4D004B 88.8889%, #4D004B 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #F7FCFD 0%, #F7FCFD 11.1111%, #E0ECF4 11.1111%, #E0ECF4 22.2222%, #BFD3E6 22.2222%, #BFD3E6 33.3333%, #9EBCDA 33.3333%, #9EBCDA 44.4444%, #8C96C6 44.4444%, #8C96C6 55.5556%, #8C6BB1 55.5556%, #8C6BB1 66.6667%, #88419D 66.6667%, #88419D 77.7778%, #810F7C 77.7778%, #810F7C 88.8889%, #4D004B 88.8889%, #4D004B 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="BuGn"], 
 #nj_tippoint_scale .option[data-value="BuGn"], 
@@ -2348,10 +2360,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="BuGn"], 
 #upgma_heatmap_scale .option[data-value="BuGn"],
 #upgma_clade_scale .option[data-value="BuGn"] {
-    background: linear-gradient(to right, #F7FCFD 0%, #F7FCFD 11.1111%, #E5F5F9 11.1111%, #E5F5F9 22.2222%, #CCECE6 22.2222%, #CCECE6 33.3333%, #99D8C9 33.3333%, #99D8C9 44.4444%, #66C2A4 44.4444%, #66C2A4 55.5556%, #41AE76 55.5556%, #41AE76 66.6667%, #238B45 66.6667%, #238B45 77.7778%, #006D2C 77.7778%, #006D2C 88.8889%, #00441B 88.8889%, #00441B 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #F7FCFD 0%, #F7FCFD 11.1111%, #E5F5F9 11.1111%, #E5F5F9 22.2222%, #CCECE6 22.2222%, #CCECE6 33.3333%, #99D8C9 33.3333%, #99D8C9 44.4444%, #66C2A4 44.4444%, #66C2A4 55.5556%, #41AE76 55.5556%, #41AE76 66.6667%, #238B45 66.6667%, #238B45 77.7778%, #006D2C 77.7778%, #006D2C 88.8889%, #00441B 88.8889%, #00441B 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="Blues"], 
 #nj_tippoint_scale .option[data-value="Blues"], 
@@ -2371,10 +2383,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_5 .option[data-value="Blues"], 
 #upgma_heatmap_scale .option[data-value="Blues"],
 #upgma_clade_scale .option[data-value="Blues"] {
-    background: linear-gradient(to right, #F7FBFF 0%, #F7FBFF 11.1111%, #DEEBF7 11.1111%, #DEEBF7 22.2222%, #C6DBEF 22.2222%, #C6DBEF 33.3333%, #9ECAE1 33.3333%, #9ECAE1 44.4444%, #6BAED6 44.4444%, #6BAED6 55.5556%, #4292C6 55.5556%, #4292C6 66.6667%, #2171B5 66.6667%, #2171B5 77.7778%, #08519C 77.7778%, #08519C 88.8889%, #08306B 88.8889%, #08306B 100%);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #F7FBFF 0%, #F7FBFF 11.1111%, #DEEBF7 11.1111%, #DEEBF7 22.2222%, #C6DBEF 22.2222%, #C6DBEF 33.3333%, #9ECAE1 33.3333%, #9ECAE1 44.4444%, #6BAED6 44.4444%, #6BAED6 55.5556%, #4292C6 55.5556%, #4292C6 66.6667%, #2171B5 66.6667%, #2171B5 77.7778%, #08519C 77.7778%, #08519C 88.8889%, #08306B 88.8889%, #08306B 100%);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="magma"], 
 #nj_tippoint_scale .option[data-value="magma"], 
@@ -2392,10 +2404,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="magma"], 
 #upgma_tiles_scale_5 .option[data-value="magma"], 
 #upgma_heatmap_scale .option[data-value="magma"] {
-    background: linear-gradient(to right, #000004FF, #07071DFF, #160F3BFF, #29115AFF, #400F73FF, #56147DFF, #6B1D81FF, #802582FF, #952C80FF, #AB337CFF, #C03A76FF, #D6456CFF, #E85362FF, #F4685CFF, #FA815FFF, #FD9A6AFF, #FEB37BFF, #FECC8FFF, #FDE4A6FF, #FCFDBFFF);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #000004FF, #07071DFF, #160F3BFF, #29115AFF, #400F73FF, #56147DFF, #6B1D81FF, #802582FF, #952C80FF, #AB337CFF, #C03A76FF, #D6456CFF, #E85362FF, #F4685CFF, #FA815FFF, #FD9A6AFF, #FEB37BFF, #FECC8FFF, #FDE4A6FF, #FCFDBFFF);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="inferno"], 
 #nj_tippoint_scale .option[data-value="inferno"], 
@@ -2413,10 +2425,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="inferno"], 
 #upgma_tiles_scale_5 .option[data-value="inferno"], 
 #upgma_heatmap_scale .option[data-value="inferno"] {
-    background: linear-gradient(to right, #000004FF, #08051EFF, #190C3EFF, #300A5BFF, #460B6AFF, #5C126EFF, #711A6EFF, #87216BFF, #9C2964FF, #B1325AFF, #C43C4EFF, #D64B40FF, #E55C30FF, #F17020FF, #F8870EFF, #FCA007FF, #FBB91FFF, #F7D340FF, #F1ED6FFF, #FCFFA4FF);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #000004FF, #08051EFF, #190C3EFF, #300A5BFF, #460B6AFF, #5C126EFF, #711A6EFF, #87216BFF, #9C2964FF, #B1325AFF, #C43C4EFF, #D64B40FF, #E55C30FF, #F17020FF, #F8870EFF, #FCA007FF, #FBB91FFF, #F7D340FF, #F1ED6FFF, #FCFFA4FF);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="plasma"], 
 #nj_tippoint_scale .option[data-value="plasma"], 
@@ -2434,10 +2446,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="plasma"], 
 #upgma_tiles_scale_5 .option[data-value="plasma"], 
 #upgma_heatmap_scale .option[data-value="plasma"] {
-    background: linear-gradient(to right, #0D0887FF, #2D0594FF, #44039EFF, #5901A5FF, #6F00A8FF, #8305A7FF, #9512A1FF, #A72197FF, #B6308BFF, #C5407EFF, #D14E72FF, #DD5E66FF, #E76E5BFF, #EF7F4FFF, #F79044FF, #FBA238FF, #FEB72DFF, #FDCB26FF, #F7E225FF, #F0F921FF);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #0D0887FF, #2D0594FF, #44039EFF, #5901A5FF, #6F00A8FF, #8305A7FF, #9512A1FF, #A72197FF, #B6308BFF, #C5407EFF, #D14E72FF, #DD5E66FF, #E76E5BFF, #EF7F4FFF, #F79044FF, #FBA238FF, #FEB72DFF, #FDCB26FF, #F7E225FF, #F0F921FF);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="viridis"], 
 #nj_tippoint_scale .option[data-value="viridis"], 
@@ -2455,10 +2467,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="viridis"], 
 #upgma_tiles_scale_5 .option[data-value="viridis"], 
 #upgma_heatmap_scale .option[data-value="viridis"] {
-    background: linear-gradient(to right, #440154FF, #481568FF, #482677FF, #453781FF, #3F4788FF, #39558CFF, #32648EFF, #2D718EFF, #287D8EFF, #238A8DFF, #1F968BFF, #20A386FF, #29AF7FFF, #3CBC75FF, #56C667FF, #74D055FF, #94D840FF, #B8DE29FF, #DCE318FF, #FDE725FF);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #440154FF, #481568FF, #482677FF, #453781FF, #3F4788FF, #39558CFF, #32648EFF, #2D718EFF, #287D8EFF, #238A8DFF, #1F968BFF, #20A386FF, #29AF7FFF, #3CBC75FF, #56C667FF, #74D055FF, #94D840FF, #B8DE29FF, #DCE318FF, #FDE725FF);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="cividis"], 
 #nj_tippoint_scale .option[data-value="cividis"], 
@@ -2476,10 +2488,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="cividis"], 
 #upgma_tiles_scale_5 .option[data-value="cividis"], 
 #upgma_heatmap_scale .option[data-value="cividis"] {
-    background: linear-gradient(to right, #00204DFF, #002A64FF, #00336FFF, #1F3C6DFF, #35466BFF, #444F6BFF, #53596CFF, #5F636EFF, #6B6C71FF, #777776FF, #838079FF, #908B79FF, #9D9677FF, #ABA074FF, #B9AC70FF, #C7B76BFF, #D7C463FF, #E5D05AFF, #F5DD4DFF, #FFEA46FF);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #00204DFF, #002A64FF, #00336FFF, #1F3C6DFF, #35466BFF, #444F6BFF, #53596CFF, #5F636EFF, #6B6C71FF, #777776FF, #838079FF, #908B79FF, #9D9677FF, #ABA074FF, #B9AC70FF, #C7B76BFF, #D7C463FF, #E5D05AFF, #F5DD4DFF, #FFEA46FF);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="rocket"], 
 #nj_tippoint_scale .option[data-value="rocket"], 
@@ -2497,10 +2509,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="rocket"], 
 #upgma_tiles_scale_5 .option[data-value="rocket"], 
 #upgma_heatmap_scale .option[data-value="rocket"] {
-    background: linear-gradient(to right, #03051AFF, #150E26FF, #281535FF, #3C1A42FF, #511E4DFF, #661F54FF, #7C1F5AFF, #931C5BFF, #AA185AFF, #C11754FF, #D3214BFF, #E33541FF, #ED4E3EFF, #F26847FF, #F4815AFF, #F5986FFF, #F6AE86FF, #F7C2A2FF, #F8D7BFFF, #FAEBDDFF);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #03051AFF, #150E26FF, #281535FF, #3C1A42FF, #511E4DFF, #661F54FF, #7C1F5AFF, #931C5BFF, #AA185AFF, #C11754FF, #D3214BFF, #E33541FF, #ED4E3EFF, #F26847FF, #F4815AFF, #F5986FFF, #F6AE86FF, #F7C2A2FF, #F8D7BFFF, #FAEBDDFF);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="mako"], 
 #nj_tippoint_scale .option[data-value="mako"], 
@@ -2518,10 +2530,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="mako"], 
 #upgma_tiles_scale_5 .option[data-value="mako"], 
 #upgma_heatmap_scale .option[data-value="mako"]{
-    background: linear-gradient(to right, #0B0405FF, #190E19FF, #27182DFF, #312142FF, #3A2C59FF, #3F3770FF, #414388FF, #3C5397FF, #38639DFF, #3573A1FF, #3482A4FF, #3491A8FF, #35A0ABFF, #3AAEADFF, #46BEADFF, #5ACCADFF, #7ED7AFFF, #A4E0BBFF, #C3E9CEFF, #DEF5E5FF);
-    color: white;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #0B0405FF, #190E19FF, #27182DFF, #312142FF, #3A2C59FF, #3F3770FF, #414388FF, #3C5397FF, #38639DFF, #3573A1FF, #3482A4FF, #3491A8FF, #35A0ABFF, #3AAEADFF, #46BEADFF, #5ACCADFF, #7ED7AFFF, #A4E0BBFF, #C3E9CEFF, #DEF5E5FF);
+                            color: white;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="turbo"], 
 #nj_tippoint_scale .option[data-value="turbo"], 
@@ -2539,9 +2551,9 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="turbo"], 
 #upgma_tiles_scale_5 .option[data-value="turbo"], 
 #upgma_heatmap_scale .option[data-value="turbo"] {
-    background: linear-gradient(to right, #30123BFF, #3F3994FF, #455ED2FF, #4681F7FF, #3AA2FCFF, #23C3E4FF, #18DEC1FF, #2CF09EFF, #5BFB72FF, #8EFF49FF, #B5F836FF, #D6E635FF, #EFCD3AFF, #FCB036FF, #FD8A26FF, #F36215FF, #E14209FF, #C82803FF, #A51301FF, #7A0403FF);
-    color: white;
-}
+background: linear-gradient(to right, #30123BFF, #3F3994FF, #455ED2FF, #4681F7FF, #3AA2FCFF, #23C3E4FF, #18DEC1FF, #2CF09EFF, #5BFB72FF, #8EFF49FF, #B5F836FF, #D6E635FF, #EFCD3AFF, #FCB036FF, #FD8A26FF, #F36215FF, #E14209FF, #C82803FF, #A51301FF, #7A0403FF);
+                            color: white;
+                            }
 
 #nj_tiplab_scale .option[data-value="Spectral"], 
 #nj_tippoint_scale .option[data-value="Spectral"], 
@@ -2559,10 +2571,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="Spectral"], 
 #upgma_tiles_scale_5 .option[data-value="Spectral"], 
 #upgma_heatmap_scale .option[data-value="Spectral"]{
-    background: linear-gradient(to right, #9E0142, #D53E4F, #F46D43, #FDAE61, #FEE08B, #FFFFBF, #E6F598, #ABDDA4, #66C2A5, #3288BD, #5E4FA2);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #9E0142, #D53E4F, #F46D43, #FDAE61, #FEE08B, #FFFFBF, #E6F598, #ABDDA4, #66C2A5, #3288BD, #5E4FA2);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="RdYlGn"], 
 #nj_tippoint_scale .option[data-value="RdYlGn"], 
@@ -2580,10 +2592,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="RdYlGn"], 
 #upgma_tiles_scale_5 .option[data-value="RdYlGn"], 
 #upgma_heatmap_scale .option[data-value="RdYlGn"]{
-    background: linear-gradient(to right, #A50026, #D73027, #F46D43, #FDAE61, #FEE08B, #FFFFBF, #D9EF8B, #A6D96A, #66BD63, #1A9850, #006837);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #A50026, #D73027, #F46D43, #FDAE61, #FEE08B, #FFFFBF, #D9EF8B, #A6D96A, #66BD63, #1A9850, #006837);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="RdYlBu"], 
 #nj_tippoint_scale .option[data-value="RdYlBu"], 
@@ -2601,10 +2613,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="RdYlBu"], 
 #upgma_tiles_scale_5 .option[data-value="RdYlBu"], 
 #upgma_heatmap_scale .option[data-value="RdYlBu"]{
-    background: linear-gradient(to right, #A50026, #D73027, #F46D43, #FDAE61, #FEE090, #FFFFBF, #E0F3F8, #ABD9E9, #74ADD1, #4575B4, #313695);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #A50026, #D73027, #F46D43, #FDAE61, #FEE090, #FFFFBF, #E0F3F8, #ABD9E9, #74ADD1, #4575B4, #313695);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="RdGy"], 
 #nj_tippoint_scale .option[data-value="RdGy"], 
@@ -2622,10 +2634,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="RdGy"], 
 #upgma_tiles_scale_5 .option[data-value="RdGy"], 
 #upgma_heatmap_scale .option[data-value="RdGy"] {
-    background: linear-gradient(to right, #67001F, #B2182B, #D6604D, #F4A582, #FDDBC7, #FFFFFF, #E0E0E0, #BABABA, #878787, #4D4D4D, #1A1A1A);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #67001F, #B2182B, #D6604D, #F4A582, #FDDBC7, #FFFFFF, #E0E0E0, #BABABA, #878787, #4D4D4D, #1A1A1A);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="RdBu"], 
 #nj_tippoint_scale .option[data-value="RdBu"], 
@@ -2643,10 +2655,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="RdBu"], 
 #upgma_tiles_scale_5 .option[data-value="RdBu"], 
 #upgma_heatmap_scale .option[data-value="RdBu"] {
-    background: linear-gradient(to right, #67001F, #B2182B, #D6604D, #F4A582, #FDDBC7, #F7F7F7, #D1E5F0, #92C5DE, #4393C3, #2166AC, #053061);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #67001F, #B2182B, #D6604D, #F4A582, #FDDBC7, #F7F7F7, #D1E5F0, #92C5DE, #4393C3, #2166AC, #053061);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="PuOr"], 
 #nj_tippoint_scale .option[data-value="PuOr"], 
@@ -2664,10 +2676,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="PuOr"], 
 #upgma_tiles_scale_5 .option[data-value="PuOr"], 
 #upgma_heatmap_scale .option[data-value="PuOr"] {
-    background: linear-gradient(to right, #7F3B08, #B35806, #E08214, #FDB863, #FEE0B6, #F7F7F7, #D8DAEB, #B2ABD2, #8073AC, #542788, #2D004B);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #7F3B08, #B35806, #E08214, #FDB863, #FEE0B6, #F7F7F7, #D8DAEB, #B2ABD2, #8073AC, #542788, #2D004B);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="PRGn"], 
 #nj_tippoint_scale .option[data-value="PRGn"], 
@@ -2685,10 +2697,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="PRGn"], 
 #upgma_tiles_scale_5 .option[data-value="PRGn"], 
 #upgma_heatmap_scale .option[data-value="PRGn"] {
-    background: linear-gradient(to right, #40004B, #762A83, #9970AB, #C2A5CF, #E7D4E8, #F7F7F7, #D9F0D3, #A6DBA0, #5AAE61, #1B7837, #00441B);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #40004B, #762A83, #9970AB, #C2A5CF, #E7D4E8, #F7F7F7, #D9F0D3, #A6DBA0, #5AAE61, #1B7837, #00441B);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="PiYG"], 
 #nj_tippoint_scale .option[data-value="PiYG"], 
@@ -2706,10 +2718,10 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="PiYG"], 
 #upgma_tiles_scale_5 .option[data-value="PiYG"], 
 #upgma_heatmap_scale .option[data-value="PiYG"] {
-    background: linear-gradient(to right, #8E0152, #C51B7D, #DE77AE, #F1B6DA, #FDE0EF, #F7F7F7, #E6F5D0, #B8E186, #7FBC41, #4D9221, #276419);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #8E0152, #C51B7D, #DE77AE, #F1B6DA, #FDE0EF, #F7F7F7, #E6F5D0, #B8E186, #7FBC41, #4D9221, #276419);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 #nj_tiplab_scale .option[data-value="BrBG"], 
 #nj_tippoint_scale .option[data-value="BrBG"], 
@@ -2727,44 +2739,44 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #upgma_tiles_scale_4 .option[data-value="BrBG"], 
 #upgma_tiles_scale_5 .option[data-value="BrBG"], 
 #upgma_heatmap_scale .option[data-value="BrBG"] {
-    background: linear-gradient(to right, #543005, #8C510A, #BF812D, #DFC27D, #F6E8C3, #F5F5F5, #C7EAE5, #80CDC1, #35978F, #01665E, #003C30);
-    color: black;
-    margin-bottom: 2px;
-}
+background: linear-gradient(to right, #543005, #8C510A, #BF812D, #DFC27D, #F6E8C3, #F5F5F5, #C7EAE5, #80CDC1, #35978F, #01665E, #003C30);
+                            color: black;
+                            margin-bottom: 2px;
+                            }
 
 /* Report */
-
-#shiny-modal > div > div > div.modal-body > div > div > div:nth-child(5) > div > div > div > div > button {
+  
+  #shiny-modal > div > div > div.modal-body > div > div > div:nth-child(5) > div > div > div > div > button {
   border: 1px solid black;
 }
 
 #rep_general {
-  position: absolute;
-  top: -10px;
-  left: -110px;
+position: absolute;
+top: -10px;
+left: -110px;
 }
 
 #rep_entrytable {
-    position: relative;
-    top: -10px;
-    left: -96px;
+position: relative;
+top: -10px;
+left: -96px;
 }
 
 #rep_plot_report {
-    position: relative;
-    top: -15px;
-    left: -96px;
+position: relative;
+top: -15px;
+left: -96px;
 }
 
 #rep_analysis {
-    position: relative;
-    top: -10px;
-    left: -45px;
+position: relative;
+top: -10px;
+left: -45px;
 }
 
 #mst_date_general_select {
-    margin-top: -14px;
-    width: 100px;
+margin-top: -14px;
+width: 100px;
 }
 
 .datepicker { z-index: 99999 !important; }
@@ -2783,48 +2795,48 @@ button#upgma_tile_menu_2, button#upgma_tile_menu_3, button#upgma_tile_menu_4, bu
 #rep_missval,
 #rep_version,
 #rep_plot_report {
-  margin-top: 10px;
+margin-top: 10px;
 }
 
 #mst_date_general_select .form-control {
-  height: 28px; 
-  position: relative; 
-  right: -22px;
-  margin-top: 7px;
+height: 28px; 
+position: relative; 
+right: -22px;
+margin-top: 7px;
 }
 
 #mst_operator_general_select {
-    height: 28px;
-    margin-top: -8px;
-    position: relative;
-    right: -22px;
-    width: 250px;
+height: 28px;
+margin-top: -8px;
+position: relative;
+right: -22px;
+width: 250px;
 }
 
 #mst_institute_general_select {
-    height: 28px;
-    margin-top: -8px;
-    position: relative;
-    right: -22px;
-    width: 250px;
+height: 28px;
+margin-top: -8px;
+position: relative;
+right: -22px;
+width: 250px;
 }
 
 #mst_comm_general_select {
-    margin-top: -8px;
-    border-radius: 5px;
-    position: relative;
-    right: -22px;
-    border-color: black;
+margin-top: -8px;
+border-radius: 5px;
+position: relative;
+right: -22px;
+border-color: black;
 }
 
 button#download_report_bttn {
-    font-size: 14px;
-    height: 36px;
-    background: #282F38;
-    color: #ffffff;
-    border: 1px solid white;
-    position: relative;
-    top: 1px;
-    border-radius: 6px;
-    margin-left: 10px;
+font-size: 14px;
+height: 36px;
+background: #282F38;
+  color: #ffffff;
+  border: 1px solid white;
+position: relative;
+top: 1px;
+border-radius: 6px;
+margin-left: 10px;
 }
diff --git a/www/head.css b/www/head.css
index 63ff266..5efe422 100644
--- a/www/head.css
+++ b/www/head.css
@@ -113,12 +113,14 @@ div#bs-select-12::-webkit-scrollbar-thumb,
 #mst_comm_general_select::-webkit-scrollbar-thumb {
 background: #bcbcbc;
   border: 2px solid #F0F0F0;
+min-width: 100px;
 }
 
 *::-webkit-scrollbar-thumb {
   background-color: #F0F0F0;
     border-radius: 10px;
   border: 2px solid #282F38;
+  min-width: 100px;
 } 
 
 *::-webkit-scrollbar-corner {
@@ -130,4 +132,27 @@ background: #bcbcbc;
   padding: 50px;
 position: relative;
 top: 15px;
+}
+
+#statustext {
+position: fixed;
+top: 15px;
+left: 400px;
+}
+
+#databasetext {
+position: fixed;
+top: 15px;
+left: 800px;
+}
+
+.main-header {
+  position: relative;
+  max-height: 100px;
+  z-index: 1030;
+  box-shadow: 0px 4px 5px #080c12;
+}
+
+.img_logo {
+  margin-top: -4px;
 }
\ No newline at end of file

From 5c11e2abeb3928d958a432209c381a199dd44307 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Fri, 26 Jul 2024 11:13:20 +0200
Subject: [PATCH 10/75] Moved scheme select to statusbar; small fixes

---
 App.R                       | 167 +++++++++++++++++-------------------
 execute/multi_eval.R        |   2 -
 www/body.css                |  19 ++--
 www/head.css                |  44 ++++++----
 www/javascript_functions.js |  17 ++++
 5 files changed, 133 insertions(+), 116 deletions(-)

diff --git a/App.R b/App.R
index 0649108..09a67d1 100644
--- a/App.R
+++ b/App.R
@@ -280,6 +280,7 @@ ui <- dashboardPage(
         )
       )
     ),
+    uiOutput("loaded_scheme"),
     uiOutput("databasetext"),
     uiOutput("statustext"),
     tags$li(class = "dropdown", 
@@ -304,10 +305,8 @@ ui <- dashboardPage(
           animation: none;
         }")),
     br(), br(),
-    uiOutput("loaded_scheme"),
     sidebarMenu(
       id = "tabs",
-      uiOutput("menu_sep1"),
       sidebarMenuOutput("menu"),
       uiOutput("menu_sep2"),
       conditionalPanel(
@@ -6115,8 +6114,61 @@ server <- function(input, output, session) {
     
     log_print("Input load")
     
+    if(Typing$status == "Finalized") {Typing$status <- "Inactive"}
+    
+    #### Render status bar ----
+    observe({
+      req(DB$scheme)
+      
+      if(is.null(input$scheme_position)) {
+        output$loaded_scheme <- renderUI({
+          fluidRow(
+            tags$li(
+              class = "dropdown", 
+              tags$span(HTML(
+                paste('<i class="fa-solid fa-table"></i>', 
+                      "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
+                      DB$scheme,
+                      "</i>")), 
+                style = "color:white;")
+            )
+          )
+        })
+      } 
+      
+      if(!is.null(input$scheme_position)) {
+        output$loaded_scheme <- renderUI({
+          fluidRow(
+            tags$li(
+              class = "dropdown", 
+              tags$span(HTML(
+                paste('<i class="fa-solid fa-table"></i>', 
+                      "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
+                      DB$scheme,
+                      "</i>")), 
+                style = "color:white;"),
+              div(
+                class = "reload-bttn",
+                style = paste0("margin-left:", 30 + input$scheme_position, "px; position: relative; top: -24px;"),
+                actionButton(
+                  "reload_db",
+                  label = "",
+                  icon = icon("rotate")
+                )
+              )
+            )
+          )
+        })
+      }
+    })
+    
     observe({
       if(!is.null(DB$database)){
+        if(nchar(DB$database) > 60) {
+          database <- paste0(substring(DB$database, first = 1, last = 60), "...")
+        } else {
+          database <- DB$database
+        }
         output$databasetext <- renderUI({
           fluidRow(
             tags$li(
@@ -6124,10 +6176,14 @@ server <- function(input, output, session) {
               tags$span(HTML(
                 paste('<i class="fa-solid fa-folder-open"></i>', 
                       "Database:&nbsp;&nbsp;&nbsp;<i>",
-                      DB$database,
+                      database,
                       "</i>")), 
                 style = "color:white;")
-            )
+            ),
+            if(nchar(database) > 60) {bsTooltip("databasetext", 
+                                                HTML(DB$database), 
+                                                placement = "bottom", 
+                                                trigger = "hover")}
           )
         })
       }
@@ -6217,6 +6273,21 @@ server <- function(input, output, session) {
       }
     }
     
+    shinyjs::runjs(
+      'if(document.querySelector("#loaded_scheme > div > li > span") !== null) {
+          // Select the span element
+          let spanElement = document.querySelector("#loaded_scheme > div > li > span");
+                    
+          // Get the bounding rectangle of the span element
+          let rect = spanElement.getBoundingClientRect();
+          
+          // Extract the width
+          let width = rect.width;
+          
+          Shiny.setInputValue("scheme_position", width);            
+        }'
+    )
+    
     # Load app elements based on database availability and missing value presence
     if(!is.null(DB$select_new)) {
       if(DB$select_new & (paste0(DB$new_database, "/Database") %in% dir_ls(DB$new_database))) {
@@ -6274,7 +6345,6 @@ server <- function(input, output, session) {
         Startup$sidebar <- FALSE
         Startup$header <- FALSE
         
-        output$menu_sep1 <- renderUI(hr())
         output$menu_sep2 <- renderUI(hr())
         
         # Hide start message
@@ -6402,7 +6472,6 @@ server <- function(input, output, session) {
         Startup$sidebar <- FALSE
         Startup$header <- FALSE
         
-        output$menu_sep1 <- renderUI(hr())
         output$menu_sep2 <- renderUI(hr())
         
         # Hide start message
@@ -6625,44 +6694,6 @@ server <- function(input, output, session) {
             )
             
           } else {
-            # Render scheme selector in sidebar
-            output$loaded_scheme <- renderUI({
-              fluidRow(
-                column(width = 2),
-                column(
-                  width = 6,
-                  div(
-                    class = "scheme_start",
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 14px;', strong("Selected scheme:"))
-                        )
-                      )
-                    ),
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 13px; font-style: italic', DB$scheme)
-                        )
-                      )
-                    )
-                  )
-                ),
-                column(
-                  width = 2,
-                  div(
-                    class = "reload-bttn",
-                    actionButton(
-                      "reload_db",
-                      label = "",
-                      icon = icon("rotate")
-                    )
-                  )
-                )
-              )
-            })
-            
             # Produce Scheme Info Table
             schemeinfo <-
               read_html(paste0(
@@ -7340,44 +7371,6 @@ server <- function(input, output, session) {
                   } 
                 })
                 
-                # Render scheme selector in sidebar
-                output$loaded_scheme <- renderUI({
-                  fluidRow(
-                    column(width = 2),
-                    column(
-                      width = 6,
-                      div(
-                        class = "scheme_start",
-                        p(
-                          HTML(
-                            paste(
-                              tags$span(style='color: white; font-size: 14px;', strong("Selected scheme:"))
-                            )
-                          )
-                        ),
-                        p(
-                          HTML(
-                            paste(
-                              tags$span(style='color: white; font-size: 13px; font-style: italic', DB$scheme)
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    column(
-                      width = 2,
-                      div(
-                        class = "reload-bttn",
-                        actionButton(
-                          "reload_db",
-                          label = "",
-                          icon = icon("rotate")
-                        )
-                      )
-                    )
-                  )
-                })
-                
                 # Render missing values sidebar elements
                 output$missing_values_sidebar <- renderUI({
                   column(
@@ -8977,7 +8970,7 @@ server <- function(input, output, session) {
                                 HTML(
                                   paste(
                                     "<span style='color: white;'>",
-                                    "No Entries for this scheme available.",
+                                    "No Entries for this scheme available.\n",
                                     "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
                                     sep = '<br/>'
                                   )
@@ -9087,12 +9080,6 @@ server <- function(input, output, session) {
     
   })
   
-  # _______________________ ####
-  
-  ## Status ----
-  
-  
-  
   # _______________________ ####
   
   ## Database ----
@@ -22796,6 +22783,8 @@ server <- function(input, output, session) {
   observeEvent(input$reset_single_typing, {
     log_print("Reset single typing")
     
+    Typing$status <- "Inactive"
+    
     Typing$progress <- 0
     
     Typing$progress_format <- 900000
diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index 3dc5277..d2c19f3 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -155,8 +155,6 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
   
   saveRDS(event_list, "execute/event_list.rds")
   
-  allele_vector <- as.integer(allele_vector)
-  
   # Find Alleles folder in directory
   allele_folder <- list.files(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing)), full.names = TRUE)[grep("_alleles", list.files(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing))))]
   
diff --git a/www/body.css b/www/body.css
index 50e3583..5f6be8f 100644
--- a/www/body.css
+++ b/www/body.css
@@ -1,15 +1,20 @@
 /* CSS Styling for PhyloTrace */
   
-  /* General */
+/* General */
   
-  h1, h2, h3, h4, h5, p, body {
+h1, h2, h3, h4, h5, p, body {
     font-family: 'Liberation Sans', sans-serif;
-  }
+}
 
 label {
   color: white;
 }
 
+.tooltip-inner {
+      white-space: normal;
+      max-width: 800px; /* Adjust the width as needed */
+    }
+
 .btn-default:active:hover.
 .btn-primary:active:hover{
   color: white !important;
@@ -207,13 +212,13 @@ font-size: 12px;
 
 #reload_db i.fas.fa-rotate {
 position: relative; 
-left: -5px;
-top: -2px;
+left: -6px;
+top: -3px;
 }
 
 button#reload_db.btn.btn-default.action-button.shiny-bound-input {
-height: 30px; 
-width: 30px; 
+height: 27px; 
+width: 27px; 
 position: relative; 
 left: -20px;
 border: 1px solid white;
diff --git a/www/head.css b/www/head.css
index 5efe422..1825811 100644
--- a/www/head.css
+++ b/www/head.css
@@ -1,12 +1,12 @@
 /* Entry table legend */
-  .rectangle-orange {
-    width: 75px;
-    height: 23px;
-    margin-top: 10px;
-    margin-left: 10px;
-    border: 1px solid #BCBCBC;
-    background-color: #DEB200;
-  }
+.rectangle-orange {
+  width: 75px;
+  height: 23px;
+  margin-top: 10px;
+  margin-left: 10px;
+  border: 1px solid #BCBCBC;
+  background-color: #DEB200;
+}
 
 .rectangle-green {
   width: 75px;
@@ -111,16 +111,18 @@ div#bs-select-12::-webkit-scrollbar-thumb,
 #logTextFull::-webkit-scrollbar-thumb,
 .selectize-dropdown-content::-webkit-scrollbar-thumb,
 #mst_comm_general_select::-webkit-scrollbar-thumb {
-background: #bcbcbc;
+  background: #bcbcbc;
   border: 2px solid #F0F0F0;
-min-width: 100px;
+  min-width: 100px;
+  min-height: 100px;
 }
 
 *::-webkit-scrollbar-thumb {
   background-color: #F0F0F0;
-    border-radius: 10px;
+  border-radius: 10px;
   border: 2px solid #282F38;
   min-width: 100px;
+  overflow-y: scroll;
 } 
 
 *::-webkit-scrollbar-corner {
@@ -135,15 +137,21 @@ top: 15px;
 }
 
 #statustext {
-position: fixed;
-top: 15px;
-left: 400px;
+  position: absolute;
+  top: 15px;
+  left: 600px;
 }
 
 #databasetext {
-position: fixed;
-top: 15px;
-left: 800px;
+  position: absolute;
+  top: 15px;
+  left: 900px;
+}
+
+#loaded_scheme {
+  position: absolute;
+  top: 15px;
+  left: 150px;
 }
 
 .main-header {
@@ -154,5 +162,5 @@ left: 800px;
 }
 
 .img_logo {
-  margin-top: -4px;
+  margin-top: -3px;
 }
\ No newline at end of file
diff --git a/www/javascript_functions.js b/www/javascript_functions.js
index 1b9aef6..fdc3cf4 100644
--- a/www/javascript_functions.js
+++ b/www/javascript_functions.js
@@ -15,6 +15,23 @@ function getCurrentDate() {
   return year + '-' + month + '-' + day; // Formats the date as "YYYY-MM-DD"
 };
 
+function checkAndExecute() {
+  if(document.querySelector("#loaded_scheme > div > li > span") !== null) {
+    // Select the span element
+    let spanElement = document.querySelector("#loaded_scheme > div > li > span");
+              
+    // Get the bounding rectangle of the span element
+    let rect = spanElement.getBoundingClientRect();
+    
+    // Extract the width
+    let width = rect.width;
+    
+    Shiny.setInputValue("scheme_position", width);            
+  }
+}
+setInterval(checkAndExecute, 1000);
+checkAndExecute();
+
 // Get time
 function updateTime() {
   var options = {

From 947b1dad21484445b51c166500e3acc0087f6a11 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Fri, 26 Jul 2024 13:22:06 +0200
Subject: [PATCH 11/75] Updated partners

---
 README.md                   |   2 +-
 www/partners_logo_round.svg | 296 ++++++++++++++++++++++--------------
 2 files changed, 182 insertions(+), 116 deletions(-)

diff --git a/README.md b/README.md
index c92687e..db61444 100644
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ working on achieving that.
 ![PartnerLogos](www/partners_logo_round.svg)
 
 <sup><sup> Developed in collaboration with Hochschule Furtwangen University (HFU) and Medical
-University of Graz (MUG). Featured on ShinyConf 2024. </sup> </sup>
+University of Graz (MUG). Featured on ShinyConf 2024 and R/Medicine 2024. </sup> </sup>
 
 [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.10996423-00e896?labelColor=gray&color=2500ba&logoColor=black)](https://doi.org/10.5281/zenodo.10996423)
 [![License: GPL
diff --git a/www/partners_logo_round.svg b/www/partners_logo_round.svg
index a9a13da..457f64a 100644
--- a/www/partners_logo_round.svg
+++ b/www/partners_logo_round.svg
@@ -1,6 +1,34 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<svg version="1.2" width="228.62mm" height="31.77mm" viewBox="2270 7649 22862 3177" preserveAspectRatio="xMidYMid" fill-rule="evenodd" stroke-width="28.222" stroke-linejoin="round" xmlns="http://www.w3.org/2000/svg" xmlns:ooo="http://xml.openoffice.org/svg/export" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:presentation="http://sun.com/xmlns/staroffice/presentation" xmlns:smil="http://www.w3.org/2001/SMIL20/" xmlns:anim="urn:oasis:names:tc:opendocument:xmlns:animation:1.0" xmlns:svg="urn:oasis:names:tc:opendocument:xmlns:svg-compatible:1.0" xml:space="preserve">
+<svg version="1.2" width="279.4mm" height="215.9mm" viewBox="0 0 27940 21590" preserveAspectRatio="xMidYMid" fill-rule="evenodd" stroke-width="28.222" stroke-linejoin="round" xmlns="http://www.w3.org/2000/svg" xmlns:ooo="http://xml.openoffice.org/svg/export" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:presentation="http://sun.com/xmlns/staroffice/presentation" xmlns:smil="http://www.w3.org/2001/SMIL20/" xmlns:anim="urn:oasis:names:tc:opendocument:xmlns:animation:1.0" xmlns:svg="urn:oasis:names:tc:opendocument:xmlns:svg-compatible:1.0" xml:space="preserve">
+ <defs class="ClipPathGroup">
+  <clipPath id="presentation_clip_path" clipPathUnits="userSpaceOnUse">
+   <rect x="0" y="0" width="27940" height="21590"/>
+  </clipPath>
+  <clipPath id="presentation_clip_path_shrink" clipPathUnits="userSpaceOnUse">
+   <rect x="27" y="21" width="27885" height="21547"/>
+  </clipPath>
+ </defs>
+ <defs>
+  <font id="EmbeddedFont_1" horiz-adv-x="2048">
+   <font-face font-family="Liberation Sans embedded" units-per-em="2048" font-weight="bold" font-style="normal" ascent="1852" descent="423"/>
+   <missing-glyph horiz-adv-x="2048" d="M 0,0 L 2047,0 2047,2047 0,2047 0,0 Z"/>
+   <glyph unicode="n" horiz-adv-x="986" d="M 844,0 L 844,607 C 844,797 780,892 651,892 583,892 528,863 487,805 445,746 424,671 424,580 L 424,0 143,0 143,840 C 143,898 142,946 141,983 139,1020 137,1053 135,1082 L 403,1082 C 405,1069 408,1036 411,981 414,926 416,888 416,867 L 420,867 C 458,950 506,1010 563,1047 620,1084 689,1103 768,1103 883,1103 971,1068 1032,997 1093,926 1124,823 1124,687 L 1124,0 844,0 Z"/>
+   <glyph unicode="i" horiz-adv-x="281" d="M 143,1277 L 143,1484 424,1484 424,1277 143,1277 Z M 143,0 L 143,1082 424,1082 424,0 143,0 Z"/>
+   <glyph unicode="e" horiz-adv-x="986" d="M 586,-20 C 423,-20 298,28 211,125 124,221 80,361 80,546 80,725 124,862 213,958 302,1054 427,1102 590,1102 745,1102 864,1051 946,948 1028,845 1069,694 1069,495 L 1069,487 375,487 C 375,382 395,302 434,249 473,195 528,168 600,168 699,168 762,211 788,297 L 1053,274 C 976,78 821,-20 586,-20 Z M 586,925 C 520,925 469,902 434,856 398,810 379,746 377,663 L 797,663 C 792,750 771,816 734,860 697,903 648,925 586,925 Z"/>
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From 3dd450afb821ec7514b77bbb01f06f3bd05c8978 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Fri, 26 Jul 2024 13:23:38 +0200
Subject: [PATCH 12/75] Updated partners

---
 www/partners_logo_round.svg | 305 +++++++++++++++++-------------------
 1 file changed, 140 insertions(+), 165 deletions(-)

diff --git a/www/partners_logo_round.svg b/www/partners_logo_round.svg
index 457f64a..73082ab 100644
--- a/www/partners_logo_round.svg
+++ b/www/partners_logo_round.svg
@@ -1,14 +1,6 @@
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 <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
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-   <rect x="0" y="0" width="27940" height="21590"/>
-  </clipPath>
-  <clipPath id="presentation_clip_path_shrink" clipPathUnits="userSpaceOnUse">
-   <rect x="27" y="21" width="27885" height="21547"/>
-  </clipPath>
- </defs>
+<svg version="1.2" width="228.62mm" height="24.32mm" viewBox="2370 8200 22862 2432" preserveAspectRatio="xMidYMid" fill-rule="evenodd" stroke-width="28.222" stroke-linejoin="round" xmlns="http://www.w3.org/2000/svg" xmlns:ooo="http://xml.openoffice.org/svg/export" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:presentation="http://sun.com/xmlns/staroffice/presentation" xmlns:smil="http://www.w3.org/2001/SMIL20/" xmlns:anim="urn:oasis:names:tc:opendocument:xmlns:animation:1.0" xmlns:svg="urn:oasis:names:tc:opendocument:xmlns:svg-compatible:1.0" xml:space="preserve">
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@@ -26,9 +18,6 @@
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@@ -61,160 +50,146 @@
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- <g>
-  <g id="id2" class="Master_Slide">
-   <g id="bg-id2" class="Background"/>
-   <g id="bo-id2" class="BackgroundObjects"/>
+ <g class="Page">
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+   <g id="id3">
+    <rect class="BoundingBox" stroke="none" fill="none" x="2370" y="8200" width="22862" height="2432"/>
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     </g>
    </g>
   </g>

From 582a0a5224b3815c31cd91c0d5e80ebe70c02518 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Fri, 26 Jul 2024 13:44:54 +0200
Subject: [PATCH 13/75] Changed selected scheme icon

---
 App.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/App.R b/App.R
index 09a67d1..514e7ae 100644
--- a/App.R
+++ b/App.R
@@ -6126,7 +6126,7 @@ server <- function(input, output, session) {
             tags$li(
               class = "dropdown", 
               tags$span(HTML(
-                paste('<i class="fa-solid fa-table"></i>', 
+                paste('<i class="fa-solid fa-layer-group"></i>', 
                       "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
                       DB$scheme,
                       "</i>")), 
@@ -6142,7 +6142,7 @@ server <- function(input, output, session) {
             tags$li(
               class = "dropdown", 
               tags$span(HTML(
-                paste('<i class="fa-solid fa-table"></i>', 
+                paste('<i class="fa-solid fa-layer-group"></i>', 
                       "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
                       DB$scheme,
                       "</i>")), 

From 2324e61d5ac6e5d6fb831bc7d9b8c86b6d3dff23 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Fri, 26 Jul 2024 17:22:37 +0200
Subject: [PATCH 14/75] Initial clustering module

---
 App.R | 228 ++++++++++++++++++++++++++++++++++++++++++++++++++--------
 1 file changed, 200 insertions(+), 28 deletions(-)

diff --git a/App.R b/App.R
index 514e7ae..50d4ce2 100644
--- a/App.R
+++ b/App.R
@@ -1502,7 +1502,7 @@ ui <- dashboardPage(
                 hr(style = "margin-top: 3px !important"),
                 fluidRow(
                   column(
-                    width = 12,
+                    width = 6,
                     fluidRow(
                       column(
                         width = 12,
@@ -1511,7 +1511,7 @@ ui <- dashboardPage(
                       )
                     ),
                     column(
-                      width = 6,
+                      width = 12,
                       align = "left",
                       br(),
                       div(
@@ -1577,7 +1577,49 @@ ui <- dashboardPage(
                         )
                       )
                     )
-                  )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Clustering"), style = "color:white; text-align: left;")
+                      )
+                    ),
+                    br(),
+                    fluidRow(
+                      div(
+                        class = "switch-clusters",
+                        materialSwitch(
+                          "mst_show_clusters",
+                          h5(p("Show Clusters"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                          value = FALSE,
+                          right = TRUE
+                        )
+                      )
+                    ),
+                    column(
+                      width = 3,
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; text-align: left; font-size: 14px; margin: 10px', 'Threshold')
+                        )
+                      )
+                    ),
+                    column(
+                      width = 9,
+                      sliderInput(
+                        inputId = "mst_cluster_threshold",
+                        label = NULL,
+                        min = 0,
+                        max = 10, 
+                        value = 4,
+                        ticks = FALSE
+                      )
+                    )
+                  ),
+                  br(),
                 )
               ), br(), br(), br(), br(), br(), br()
             )
@@ -5407,6 +5449,42 @@ ui <- dashboardPage(
           ),
           br(), br(), br(), br(), br(), br()
         )
+      ),
+      tabItem(
+        tabName = "utilities",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Utilities"), style = "color:white")
+          )
+        ),
+        br(),
+        hr(),
+        column(
+          width = 5,
+          align = "left",
+          shinyDirButton(
+            "hash_dir",
+            "Hash folder with loci",
+            title = "Locate the folder with loci",
+            buttonType = "default",
+            root = path_home(),
+            style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
+          ),
+          br(),
+          actionButton(
+            "backup_database",
+            "Create backup",
+            style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
+          ),
+          br(),
+          actionButton(
+            "import_db_backup",
+            "Restore backup",
+            style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
+          )
+        )
       )
     ) # End tabItems
   ) # End dashboardPage
@@ -5699,6 +5777,37 @@ server <- function(input, output, session) {
     close(locus_file)
   }
   
+  # Compute clusters to use in visNetwork
+  compute_clusters <- function(nodes, edges, threshold) {
+    groups <- rep(0, length(nodes$id))
+    
+    edges_table <- data.frame(
+      from = edges$from,
+      to = edges$to,
+      weight = edges$weight
+    )
+    
+    count <- 0
+    while (any(groups == 0)) {
+      group_na <- groups == 0
+      labels <- nodes$id[group_na]
+      
+      cluster <- nodes$id[group_na][1] # Initialize with 1 label
+      while (!is_empty(labels)) {
+        sub_tb <- edges_table[(edges_table$from %in% cluster | edges_table$to %in% cluster) & edges_table$weight <= threshold,]
+        
+        if (nrow(sub_tb) == 0 | length(unique(c(sub_tb$from, sub_tb$to))) == length(cluster)) {
+          count <- count + 1
+          groups[nodes$id %in% cluster] <- paste("Group", count)
+          break
+        } else {
+          cluster <- unique(c(sub_tb$from, sub_tb$to))
+        }
+      }
+    }
+    groups
+  }
+  
   # Function to check single typing log file
   check_new_entry <- reactive({
     
@@ -6399,6 +6508,11 @@ server <- function(input, output, session) {
               text = "Visualization",
               tabName = "visualization",
               icon = icon("chart-line")
+            ),
+            menuItem(
+              text = "Utilities",
+              tabName = "utilities",
+              icon = icon("screwdriver-wrench")
             )
           )
         )
@@ -6545,6 +6659,11 @@ server <- function(input, output, session) {
                   text = "Visualization",
                   tabName = "visualization",
                   icon = icon("chart-line")
+                ),
+                menuItem(
+                  text = "Utilities",
+                  tabName = "utilities",
+                  icon = icon("screwdriver-wrench")
                 )
               )
             )
@@ -6616,6 +6735,11 @@ server <- function(input, output, session) {
                   text = "Visualization",
                   tabName = "visualization",
                   icon = icon("chart-line")
+                ),
+                menuItem(
+                  text = "Utilities",
+                  tabName = "utilities",
+                  icon = icon("screwdriver-wrench")
                 )
               )
             )
@@ -6689,6 +6813,11 @@ server <- function(input, output, session) {
                   text = "Visualization",
                   tabName = "visualization",
                   icon = icon("chart-line")
+                ),
+                menuItem(
+                  text = "Utilities",
+                  tabName = "utilities",
+                  icon = icon("screwdriver-wrench")
                 )
               )
             )
@@ -6791,6 +6920,11 @@ server <- function(input, output, session) {
                     text = "Visualization",
                     tabName = "visualization",
                     icon = icon("chart-line")
+                  ),
+                  menuItem(
+                    text = "Utilities",
+                    tabName = "utilities",
+                    icon = icon("screwdriver-wrench")
                   )
                 )
               )
@@ -6955,6 +7089,11 @@ server <- function(input, output, session) {
                         text = "Visualization",
                         tabName = "visualization",
                         icon = icon("chart-line")
+                      ),
+                      menuItem(
+                        text = "Utilities",
+                        tabName = "utilities",
+                        icon = icon("screwdriver-wrench")
                       )
                     )
                   )
@@ -7003,6 +7142,11 @@ server <- function(input, output, session) {
                         text = "Visualization",
                         tabName = "visualization",
                         icon = icon("chart-line")
+                      ),
+                      menuItem(
+                        text = "Utilities",
+                        tabName = "utilities",
+                        icon = icon("screwdriver-wrench")
                       )
                     )
                   )
@@ -8924,6 +9068,11 @@ server <- function(input, output, session) {
                       text = "Visualization",
                       tabName = "visualization",
                       icon = icon("chart-line")
+                    ),
+                    menuItem(
+                      text = "Utilities",
+                      tabName = "utilities",
+                      icon = icon("screwdriver-wrench")
                     )
                   )
                 )
@@ -9263,6 +9412,11 @@ server <- function(input, output, session) {
                 text = "Visualization",
                 tabName = "visualization",
                 icon = icon("chart-line")
+              ),
+              menuItem(
+                text = "Utilities",
+                tabName = "utilities",
+                icon = icon("screwdriver-wrench")
               )
             )
           )
@@ -9307,6 +9461,11 @@ server <- function(input, output, session) {
               text = "Visualization",
               tabName = "visualization",
               icon = icon("chart-line")
+            ),
+            menuItem(
+              text = "Utilities",
+              tabName = "utilities",
+              icon = icon("screwdriver-wrench")
             )
           )
         )
@@ -17510,31 +17669,44 @@ server <- function(input, output, session) {
                          label = as.character(data$edges$weight),
                          opacity = mst_edge_opacity())
     
-    visNetwork(data$nodes, data$edges, 
-               main = mst_title(),
-               background = mst_background_color(),
-               submain = mst_subtitle()) %>%
-      visNodes(size = mst_node_size(), 
-               shape = input$mst_node_shape,
-               shadow = input$mst_shadow,
-               color = mst_color_node(),
-               ctxRenderer = ctxRendererJS,
-               scaling = list(min = mst_node_size_min(), 
-                              max = mst_node_size_max()),
-               font = list(color = node_font_color(),
-                           size = input$node_label_fontsize)) %>%
-      visEdges(color = mst_color_edge(), 
-               font = list(color = mst_edge_font_color(),
-                           size = mst_edge_font_size(),
-                           strokeWidth = 4)) %>%
-      visOptions(collapse = TRUE) %>%
-      visInteraction(hover = TRUE) %>%
-      visLayout(randomSeed = 1) %>%
-      visLegend(useGroups = FALSE, 
-                zoom = FALSE,
-                position = input$mst_legend_ori,
-                ncol = legend_col(),
-                addNodes = mst_legend())
+    save(data, file="data.Rdata")
+    
+    visNetwork_graph <- visNetwork(data$nodes, data$edges,
+                                   main = mst_title(),
+                                   background = mst_background_color(),
+                                   submain = mst_subtitle()) %>%
+                          visNodes(size = mst_node_size(),
+                                   shape = input$mst_node_shape,
+                                   shadow = input$mst_shadow,
+                                   color = mst_color_node(),
+                                   ctxRenderer = ctxRendererJS,
+                                   scaling = list(min = mst_node_size_min(),
+                                                  max = mst_node_size_max()),
+                                   font = list(color = node_font_color(),
+                                               size = input$node_label_fontsize)) %>%
+                          visEdges(color = mst_color_edge(),
+                                   font = list(color = mst_edge_font_color(),
+                                               size = mst_edge_font_size(),
+                                               strokeWidth = 4)) %>%
+                          visOptions(collapse = TRUE) %>%
+                          visInteraction(hover = TRUE) %>%
+                          visLayout(randomSeed = 1) %>%
+                          visLegend(useGroups = FALSE,
+                                    zoom = FALSE,
+                                    position = input$mst_legend_ori,
+                                    ncol = legend_col(),
+                                    addNodes = mst_legend())
+
+    if (input$mst_show_clusters) {
+      data$nodes$group <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
+      color_palette <- grDevices::rainbow(length(data$nodes$group))
+
+      for (i in 1:length(unique(data$nodes$group))) {
+        visNetwork_graph <- visNetwork_graph %>% visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
+      }
+    }
+    
+    visNetwork_graph
   })
   
   # MST legend

From 107e5922ca9b53f2e75766866979b1c1a30be250 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Fri, 26 Jul 2024 17:28:13 +0200
Subject: [PATCH 15/75] Small fix

---
 App.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/App.R b/App.R
index 50d4ce2..c160bbe 100644
--- a/App.R
+++ b/App.R
@@ -17669,8 +17669,6 @@ server <- function(input, output, session) {
                          label = as.character(data$edges$weight),
                          opacity = mst_edge_opacity())
     
-    save(data, file="data.Rdata")
-    
     visNetwork_graph <- visNetwork(data$nodes, data$edges,
                                    main = mst_title(),
                                    background = mst_background_color(),

From 74b809934b4451774476842e640e5a6e5de47fa8 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Mon, 29 Jul 2024 15:17:40 +0200
Subject: [PATCH 16/75] Fixed clustering

---
 App.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/App.R b/App.R
index c160bbe..91cd157 100644
--- a/App.R
+++ b/App.R
@@ -17669,6 +17669,8 @@ server <- function(input, output, session) {
                          label = as.character(data$edges$weight),
                          opacity = mst_edge_opacity())
     
+    data$nodes$group <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
+    
     visNetwork_graph <- visNetwork(data$nodes, data$edges,
                                    main = mst_title(),
                                    background = mst_background_color(),
@@ -17695,8 +17697,7 @@ server <- function(input, output, session) {
                                     ncol = legend_col(),
                                     addNodes = mst_legend())
 
-    if (input$mst_show_clusters) {
-      data$nodes$group <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
+    if (TRUE) {
       color_palette <- grDevices::rainbow(length(data$nodes$group))
 
       for (i in 1:length(unique(data$nodes$group))) {

From a15ab92c3aee8bd8f36469ba8143a7d110684a03 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Mon, 29 Jul 2024 17:07:55 +0200
Subject: [PATCH 17/75] Fully implemented clustering

---
 App.R | 111 ++++++++++++++++++++++++++++++++++++++++------------------
 1 file changed, 77 insertions(+), 34 deletions(-)

diff --git a/App.R b/App.R
index 91cd157..acf07a5 100644
--- a/App.R
+++ b/App.R
@@ -1589,33 +1589,58 @@ ui <- dashboardPage(
                     ),
                     br(),
                     fluidRow(
-                      div(
-                        class = "switch-clusters",
+                      column(
+                        width = 9,
                         materialSwitch(
                           "mst_show_clusters",
                           h5(p("Show Clusters"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
                           value = FALSE,
                           right = TRUE
                         )
-                      )
-                    ),
-                    column(
-                      width = 3,
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; text-align: left; font-size: 14px; margin: 10px', 'Threshold')
+                      ),
+                      column(
+                        width = 3,
+                        dropMenu(
+                          actionBttn(
+                            "mst_cluster_col_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          width = 5,
+                          selectInput(
+                            "mst_cluster_col_scale",
+                            label = h5("Color Scale", style = "color:white; margin-bottom: 0px;"),
+                            choices = c("Viridis", "Rainbow"),
+                            width = "150px"
+                          )
                         )
                       )
                     ),
-                    column(
-                      width = 9,
-                      sliderInput(
-                        inputId = "mst_cluster_threshold",
-                        label = NULL,
-                        min = 0,
-                        max = 10, 
-                        value = 4,
-                        ticks = FALSE
+                    br(),
+                    fluidRow(
+                      column(
+                        width = 4,
+                        HTML(
+                          paste(
+                            tags$span(style='color: white; text-align: left; font-size: 14px; margin: 10px', 'Threshold')
+                          )
+                        )
+                      ),
+                      column(
+                        width = 8,
+                        sliderInput(
+                          inputId = "mst_cluster_threshold",
+                          label = NULL,
+                          min = 0,
+                          max = 20,
+                          value = 4,
+                          ticks = FALSE
+                        )
                       )
                     )
                   ),
@@ -5470,20 +5495,22 @@ ui <- dashboardPage(
             title = "Locate the folder with loci",
             buttonType = "default",
             root = path_home(),
+            roots = c(Home = path_home(), Root = "/"),
+            defaultRoot = "Home",
             style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
           ),
-          br(),
-          actionButton(
-            "backup_database",
-            "Create backup",
-            style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
-          ),
-          br(),
-          actionButton(
-            "import_db_backup",
-            "Restore backup",
-            style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
-          )
+          # br(),
+          # actionButton(
+          #   "backup_database",
+          #   "Create backup",
+          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
+          # ),
+          # br(),
+          # actionButton(
+          #   "import_db_backup",
+          #   "Restore backup",
+          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
+          # )
         )
       )
     ) # End tabItems
@@ -11708,6 +11735,13 @@ server <- function(input, output, session) {
     }
   })
   
+  observe({
+    req(DB$schemeinfo)
+    updateSliderInput(session, "mst_cluster_threshold",
+                      max = as.numeric(DB$schemeinfo[[7,2]]) * 2,
+                      value = as.numeric(DB$schemeinfo[[7,2]]))
+  })
+  
   # Custom Labels
   
   # Add custom label
@@ -17669,7 +17703,11 @@ server <- function(input, output, session) {
                          label = as.character(data$edges$weight),
                          opacity = mst_edge_opacity())
     
-    data$nodes$group <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
+    if (input$mst_show_clusters) {
+      data$nodes$group <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
+    }
+    
+    updateSliderInput(session, "mst_cluster_threshold", max = max(data$edges$weight))
     
     visNetwork_graph <- visNetwork(data$nodes, data$edges,
                                    main = mst_title(),
@@ -17697,11 +17735,16 @@ server <- function(input, output, session) {
                                     ncol = legend_col(),
                                     addNodes = mst_legend())
 
-    if (TRUE) {
-      color_palette <- grDevices::rainbow(length(data$nodes$group))
+    if (input$mst_show_clusters) {
+      if (input$mst_cluster_col_scale == "Viridis") {
+        color_palette <- viridis(length(data$nodes$group))
+      } else {
+        color_palette <- rainbow(length(data$nodes$group))
+      }
 
       for (i in 1:length(unique(data$nodes$group))) {
-        visNetwork_graph <- visNetwork_graph %>% visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
+        visNetwork_graph <- visNetwork_graph %>% 
+          visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
       }
     }
     

From 17d90949670cc1c48e137baec548116f4f505ebc Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Mon, 29 Jul 2024 17:38:37 +0200
Subject: [PATCH 18/75] Implemented hashing utility

---
 App.R | 41 +++++++++++++++++++++++++++++++++++++----
 1 file changed, 37 insertions(+), 4 deletions(-)

diff --git a/App.R b/App.R
index acf07a5..60fc22f 100644
--- a/App.R
+++ b/App.R
@@ -5494,10 +5494,7 @@ ui <- dashboardPage(
             "Hash folder with loci",
             title = "Locate the folder with loci",
             buttonType = "default",
-            root = path_home(),
-            roots = c(Home = path_home(), Root = "/"),
-            defaultRoot = "Home",
-            style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
+            style = "border-color: white; margin: 10px; min-width: 200px; text-align: center"
           ),
           # br(),
           # actionButton(
@@ -23947,6 +23944,42 @@ server <- function(input, output, session) {
     }
   })
   
+  observe({
+    # Get selected Genome in Multi Mode
+    shinyDirChoose(input,
+                   "hash_dir",
+                   roots = c(Home = path_home(), Root = "/"),
+                   defaultRoot = "Home",
+                   session = session,
+                   filetypes = c('', 'fasta', 'fna', 'fa'))
+    
+    dir_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$hash_dir)
+    req(dir_path)
+    output$statustext <- renderUI(
+      fluidRow(
+        tags$li(
+          class = "dropdown", 
+          tags$span(HTML(
+            paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                  "Status:&nbsp;&nbsp;&nbsp; <i>hashing directory</i>")),
+            style = "color:white;")
+        )
+      )
+    )
+    hash_database(dir_path)
+    output$statustext <- renderUI(
+      fluidRow(
+        tags$li(
+          class = "dropdown", 
+          tags$span(HTML(
+            paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                  "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
+            style = "color:white;")
+        )
+      )
+    )
+  })
+  
   
   
 } # end server

From 8a324acdb746da3c6b8488b5240914f1aabc670f Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Mon, 29 Jul 2024 18:20:29 +0200
Subject: [PATCH 19/75] Enviroment updates for packages xfun, yaml, tinytex and
 knitr

---
 PhyloTrace.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/PhyloTrace.yml b/PhyloTrace.yml
index 47e2911..daaacbd 100644
--- a/PhyloTrace.yml
+++ b/PhyloTrace.yml
@@ -92,7 +92,7 @@ dependencies:
   - r-jquerylib=0.1.4
   - r-jsonlite=1.8.8
   - r-kableExtra=1.3.4
-  - r-knitr=1.47
+  - r-knitr=1.48
   - r-labeling=0.4.3
   - r-later=1.3.1
   - r-lattice=0.22_5
@@ -159,7 +159,7 @@ dependencies:
   - r-tidytree=0.4.5
   - r-tidyverse=2.0.0
   - r-timechange=0.2.0
-  - r-tinytex=0.51
+  - r-tinytex=0.52
   - r-tzdb=0.4.0
   - r-utf8=1.2.3
   - r-uuid=1.1_1
@@ -169,9 +169,9 @@ dependencies:
   - r-vroom=1.6.4
   - r-webshot=0.5.5
   - r-withr=2.5.1
-  - r-xfun=0.45
+  - r-xfun=0.46
   - r-xml2=1.3.5
   - r-xtable=1.8_4
-  - r-yaml=2.3.8
+  - r-yaml=2.3.10
   - r-yulab.utils=0.1.0
   - r-zoo=1.8_12

From d3aef4965e20219fe1bd1db346215af8788ec2fd Mon Sep 17 00:00:00 2001
From: Marian Freisleben <115372379+infinity-a11y@users.noreply.github.com>
Date: Wed, 31 Jul 2024 12:05:12 +0200
Subject: [PATCH 20/75] Reload bttn icon position change

---
 www/body.css | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/www/body.css b/www/body.css
index 5f6be8f..c197353 100644
--- a/www/body.css
+++ b/www/body.css
@@ -212,7 +212,7 @@ font-size: 12px;
 
 #reload_db i.fas.fa-rotate {
 position: relative; 
-left: -6px;
+left: -7px;
 top: -3px;
 }
 

From e0f55818a2669cc406003b554d463809fd8a2539 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Wed, 31 Jul 2024 18:24:26 +0200
Subject: [PATCH 21/75] Fixed color palette for visNetwork

---
 App.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/App.R b/App.R
index 60fc22f..f369e32 100644
--- a/App.R
+++ b/App.R
@@ -17734,9 +17734,9 @@ server <- function(input, output, session) {
 
     if (input$mst_show_clusters) {
       if (input$mst_cluster_col_scale == "Viridis") {
-        color_palette <- viridis(length(data$nodes$group))
+        color_palette <- viridis(length(unique(data$nodes$group)))
       } else {
-        color_palette <- rainbow(length(data$nodes$group))
+        color_palette <- rainbow(length(unique(data$nodes$group)))
       }
 
       for (i in 1:length(unique(data$nodes$group))) {

From 7ff2ec2b8af4b5dff3f55165d0dec28ad3686314 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Wed, 31 Jul 2024 18:49:33 +0200
Subject: [PATCH 22/75] Created Tab for Gene Screening

---
 App.R       | 700 ++++++++++++++++++++++++++++++++--------------------
 resources.R | 231 +++++++++++++++++
 2 files changed, 670 insertions(+), 261 deletions(-)
 create mode 100644 resources.R

diff --git a/App.R b/App.R
index 60fc22f..dfe1984 100644
--- a/App.R
+++ b/App.R
@@ -44,222 +44,7 @@ library(treeio)
 library(ggtree)
 library(ggtreeExtra)
 
-schemes <- c("Acinetobacter_baumanii", "Bacillus_anthracis", "Bordetella_pertussis", 
-             "Brucella_melitensis", "Brucella_spp", "Burkholderia_mallei_FLI", 
-             "Burkholderia_mallei_RKI", "Burkholderia_pseudomallei", "Campylobacter_jejuni_coli", 
-             "Clostridioides_difficile", "Clostridium_perfringens", "Corynebacterium_diphtheriae",
-             "Cronobacter_sakazakii_malonaticus", "Enterococcus_faecalis", "Enterococcus_faecium", 
-             "Escherichia_coli", "Francisella_tularensis", "Klebsiella_oxytoca_sensu_lato", "Klebsiella_pneumoniae_sensu_lato", 
-             "Legionella_pneumophila", "Listeria_monocytogenes", "Mycobacterium_tuberculosis_complex", 
-             "Mycobacteroides_abscessus", "Mycoplasma_gallisepticum", "Paenibacillus_larvae",
-             "Pseudomonas_aeruginosa", "Salmonella_enterica", "Serratia_marcescens", 
-             "Staphylococcus_aureus", "Staphylococcus_capitis", "Streptococcus_pyogenes"
-)
-
-country_names <- c(
-  "Afghanistan",
-  "Albania",
-  "Algeria",
-  "Andorra",
-  "Angola",
-  "Antigua and Barbuda",
-  "Argentina",
-  "Armenia",
-  "Australia",
-  "Austria",
-  "Azerbaijan",
-  "Bahamas",
-  "Bahrain",
-  "Bangladesh",
-  "Barbados",
-  "Belarus",
-  "Belgium",
-  "Belize",
-  "Benin",
-  "Bhutan",
-  "Bolivia",
-  "Bosnia and Herzegovina",
-  "Botswana",
-  "Brazil",
-  "Brunei",
-  "Bulgaria",
-  "Burkina Faso",
-  "Burundi",
-  "Côte d'Ivoire",
-  "Cabo Verde",
-  "Cambodia",
-  "Cameroon",
-  "Canada",
-  "Central African Republic",
-  "Chad",
-  "Chile",
-  "China",
-  "Colombia",
-  "Comoros",
-  "Congo (Congo-Brazzaville)",
-  "Costa Rica",
-  "Croatia",
-  "Cuba",
-  "Cyprus",
-  "Czechia (Czech Republic)",
-  "Democratic Republic of the Congo",
-  "Denmark",
-  "Djibouti",
-  "Dominica",
-  "Dominican Republic",
-  "Ecuador",
-  "Egypt",
-  "El Salvador",
-  "Equatorial Guinea",
-  "Eritrea",
-  "Estonia",
-  'Eswatini (fmr. "Swaziland")',
-  "Ethiopia",
-  "Fiji",
-  "Finland",
-  "France",
-  "Gabon",
-  "Gambia",
-  "Georgia",
-  "Germany",
-  "Ghana",
-  "Greece",
-  "Grenada",
-  "Guatemala",
-  "Guinea",
-  "Guinea-Bissau",
-  "Guyana",
-  "Haiti",
-  "Holy See",
-  "Honduras",
-  "Hungary",
-  "Iceland",
-  "India",
-  "Indonesia",
-  "Iran",
-  "Iraq",
-  "Ireland",
-  "Israel",
-  "Italy",
-  "Jamaica",
-  "Japan",
-  "Jordan",
-  "Kazakhstan",
-  "Kenya",
-  "Kiribati",
-  "Kuwait",
-  "Kyrgyzstan",
-  "Laos",
-  "Latvia",
-  "Lebanon",
-  "Lesotho",
-  "Liberia",
-  "Libya",
-  "Liechtenstein",
-  "Lithuania",
-  "Luxembourg",
-  "Madagascar",
-  "Malawi",
-  "Malaysia",
-  "Maldives",
-  "Mali",
-  "Malta",
-  "Marshall Islands",
-  "Mauritania",
-  "Mauritius",
-  "Mexico",
-  "Micronesia",
-  "Moldova",
-  "Monaco",
-  "Mongolia",
-  "Montenegro",
-  "Morocco",
-  "Mozambique",
-  "Myanmar (formerly Burma)",
-  "Namibia",
-  "Nauru",
-  "Nepal",
-  "Netherlands",
-  "New Zealand",
-  "Nicaragua",
-  "Niger",
-  "Nigeria",
-  "North Korea",
-  "North Macedonia (formerly Macedonia)",
-  "Norway",
-  "Oman",
-  "Pakistan",
-  "Palau",
-  "Palestine State",
-  "Panama",
-  "Papua New Guinea",
-  "Paraguay",
-  "Peru",
-  "Philippines",
-  "Poland",
-  "Portugal",
-  "Qatar",
-  "Romania",
-  "Russia",
-  "Rwanda",
-  "Saint Kitts and Nevis",
-  "Saint Lucia",
-  "Saint Vincent and the Grenadines",
-  "Samoa",
-  "San Marino",
-  "Sao Tome and Principe",
-  "Saudi Arabia",
-  "Senegal",
-  "Serbia",
-  "Seychelles",
-  "Sierra Leone",
-  "Singapore",
-  "Slovakia",
-  "Slovenia",
-  "Solomon Islands",
-  "Somalia",
-  "South Africa",
-  "South Korea",
-  "South Sudan",
-  "Spain",
-  "Sri Lanka",
-  "Sudan",
-  "Suriname",
-  "Sweden",
-  "Switzerland",
-  "Syria",
-  "Tajikistan",
-  "Tanzania",
-  "Thailand",
-  "Timor-Leste",
-  "Togo",
-  "Tonga",
-  "Trinidad and Tobago",
-  "Tunisia",
-  "Turkey",
-  "Turkmenistan",
-  "Tuvalu",
-  "Uganda",
-  "Ukraine",
-  "United Arab Emirates",
-  "United Kingdom",
-  "United States of America",
-  "Uruguay",
-  "Uzbekistan",
-  "Vanuatu",
-  "Venezuela",
-  "Vietnam",
-  "Yemen",
-  "Zambia",
-  "Zimbabwe"
-)
-
-sel_countries <-
-  c("Austria",
-    "Germany",
-    "Switzerland",
-    "United Kingdom",
-    "United States of America")
+source("resources.R")
 
 options(ignore.negative.edge=TRUE)
 
@@ -5475,6 +5260,9 @@ ui <- dashboardPage(
           br(), br(), br(), br(), br(), br()
         )
       ),
+      
+      ## Tab Utilities -------------------------------------------------------
+      
       tabItem(
         tabName = "utilities",
         fluidRow(
@@ -5509,6 +5297,53 @@ ui <- dashboardPage(
           #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
           # )
         )
+      ),
+      
+      
+      ## Tab Gene Screening -------------------------------------------------------
+      
+      tabItem(
+        tabName = "gs_screening",
+        fluidRow(
+          column(1),
+          column(
+            width = 3,
+            align = "left",
+            h2(p("Gene Screening"), style = "color:white")
+          ),
+          column(
+            width = 7,
+            uiOutput("gene_screening_info")
+          )
+        ),
+        br(),
+        hr(),
+        uiOutput("screening_interface")
+      ),
+      
+      ## Tab Resistance Profile -------------------------------------------------------
+      
+      tabItem(
+        tabName = "gs_profile",
+        fluidRow(
+          column(1),
+          column(
+            width = 3,
+            align = "left",
+            h2(p("Resistance Profiles"), style = "color:white")
+          ),
+          column(
+            width = 7,
+            uiOutput("gene_resistance_info")
+          )
+        ),
+        br(),
+        hr(),
+        column(
+          width = 12,
+          align = "left",
+          
+        )
       )
     ) # End tabItems
   ) # End dashboardPage
@@ -5938,6 +5773,8 @@ server <- function(input, output, session) {
                            result_list = NULL,
                            status = "") # reactive variables related to typing process
   
+  Screening <- reactiveValues()
+  
   Vis <- reactiveValues(cluster = NULL, 
                         metadata = list(),
                         custom_label_nj = data.frame(),
@@ -6526,12 +6363,26 @@ server <- function(input, output, session) {
             menuItem(
               text = "Allelic Typing",
               tabName = "typing",
-              icon = icon("dna")
+              icon = icon("gears")
+            ),
+            menuItem(
+              text = "Gene Screening",
+              tabName = "gene_screening",
+              icon = icon("dna"),
+              startExpanded = FALSE,
+              menuSubItem(
+                text = "Screen Assembly",
+                tabName = "gs_screening"
+              ),
+              menuSubItem(
+                text = "Resistance Profile",
+                tabName = "gs_profile"
+              )
             ),
             menuItem(
               text = "Visualization",
               tabName = "visualization",
-              icon = icon("chart-line")
+              icon = icon("circle-nodes")
             ),
             menuItem(
               text = "Utilities",
@@ -6677,12 +6528,26 @@ server <- function(input, output, session) {
                 menuItem(
                   text = "Allelic Typing",
                   tabName = "typing",
-                  icon = icon("dna")
+                  icon = icon("gears")
+                ),
+                menuItem(
+                  text = "Gene Screening",
+                  tabName = "gene_screening",
+                  icon = icon("dna"),
+                  startExpanded = FALSE,
+                  menuSubItem(
+                    text = "Screen Assembly",
+                    tabName = "gs_screening"
+                  ),
+                  menuSubItem(
+                    text = "Resistance Profile",
+                    tabName = "gs_profile"
+                  )
                 ),
                 menuItem(
                   text = "Visualization",
                   tabName = "visualization",
-                  icon = icon("chart-line")
+                  icon = icon("circle-nodes")
                 ),
                 menuItem(
                   text = "Utilities",
@@ -6753,12 +6618,26 @@ server <- function(input, output, session) {
                 menuItem(
                   text = "Allelic Typing",
                   tabName = "typing",
-                  icon = icon("dna")
+                  icon = icon("gears")
+                ),
+                menuItem(
+                  text = "Gene Screening",
+                  tabName = "gene_screening",
+                  icon = icon("dna"),
+                  startExpanded = FALSE,
+                  menuSubItem(
+                    text = "Screen Assembly",
+                    tabName = "gs_screening"
+                  ),
+                  menuSubItem(
+                    text = "Resistance Profile",
+                    tabName = "gs_profile"
+                  )
                 ),
                 menuItem(
                   text = "Visualization",
                   tabName = "visualization",
-                  icon = icon("chart-line")
+                  icon = icon("circle-nodes")
                 ),
                 menuItem(
                   text = "Utilities",
@@ -6831,12 +6710,26 @@ server <- function(input, output, session) {
                 menuItem(
                   text = "Allelic Typing",
                   tabName = "typing",
-                  icon = icon("dna")
+                  icon = icon("gears")
+                ),
+                menuItem(
+                  text = "Gene Screening",
+                  tabName = "gene_screening",
+                  icon = icon("dna"),
+                  startExpanded = FALSE,
+                  menuSubItem(
+                    text = "Screen Assembly",
+                    tabName = "gs_screening"
+                  ),
+                  menuSubItem(
+                    text = "Resistance Profile",
+                    tabName = "gs_profile"
+                  )
                 ),
                 menuItem(
                   text = "Visualization",
                   tabName = "visualization",
-                  icon = icon("chart-line")
+                  icon = icon("circle-nodes")
                 ),
                 menuItem(
                   text = "Utilities",
@@ -6938,12 +6831,26 @@ server <- function(input, output, session) {
                   menuItem(
                     text = "Allelic Typing",
                     tabName = "typing",
-                    icon = icon("dna")
+                    icon = icon("gears")
+                  ),
+                  menuItem(
+                    text = "Gene Screening",
+                    tabName = "gene_screening",
+                    icon = icon("dna"),
+                    startExpanded = FALSE,
+                    menuSubItem(
+                      text = "Screen Assembly",
+                      tabName = "gs_screening"
+                    ),
+                    menuSubItem(
+                      text = "Resistance Profile",
+                      tabName = "gs_profile"
+                    )
                   ),
                   menuItem(
                     text = "Visualization",
                     tabName = "visualization",
-                    icon = icon("chart-line")
+                    icon = icon("circle-nodes")
                   ),
                   menuItem(
                     text = "Utilities",
@@ -7107,12 +7014,26 @@ server <- function(input, output, session) {
                       menuItem(
                         text = "Allelic Typing",
                         tabName = "typing",
-                        icon = icon("dna")
+                        icon = icon("gears")
+                      ),
+                      menuItem(
+                        text = "Gene Screening",
+                        tabName = "gene_screening",
+                        icon = icon("dna"),
+                        startExpanded = FALSE,
+                        menuSubItem(
+                          text = "Screen Assembly",
+                          tabName = "gs_screening"
+                        ),
+                        menuSubItem(
+                          text = "Resistance Profile",
+                          tabName = "gs_profile"
+                        )
                       ),
                       menuItem(
                         text = "Visualization",
                         tabName = "visualization",
-                        icon = icon("chart-line")
+                        icon = icon("circle-nodes")
                       ),
                       menuItem(
                         text = "Utilities",
@@ -7160,12 +7081,26 @@ server <- function(input, output, session) {
                       menuItem(
                         text = "Allelic Typing",
                         tabName = "typing",
-                        icon = icon("dna")
+                        icon = icon("gears")
+                      ),
+                      menuItem(
+                        text = "Gene Screening",
+                        tabName = "gene_screening",
+                        icon = icon("dna"),
+                        startExpanded = TRUE,
+                        menuSubItem(
+                          text = "Screen Assembly",
+                          tabName = "gs_screening"
+                        ),
+                        menuSubItem(
+                          text = "Resistance Profile",
+                          tabName = "gs_profile"
+                        )
                       ),
                       menuItem(
                         text = "Visualization",
                         tabName = "visualization",
-                        icon = icon("chart-line")
+                        icon = icon("circle-nodes")
                       ),
                       menuItem(
                         text = "Utilities",
@@ -9086,12 +9021,26 @@ server <- function(input, output, session) {
                     menuItem(
                       text = "Allelic Typing",
                       tabName = "typing",
-                      icon = icon("dna")
+                      icon = icon("gears")
+                    ),
+                    menuItem(
+                      text = "Gene Screening",
+                      tabName = "gene_screening",
+                      icon = icon("dna"),
+                      startExpanded = TRUE,
+                      menuSubItem(
+                        text = "Screen Assembly",
+                        tabName = "gs_screening"
+                      ),
+                      menuSubItem(
+                        text = "Resistance Profile",
+                        tabName = "gs_profile"
+                      )
                     ),
                     menuItem(
                       text = "Visualization",
                       tabName = "visualization",
-                      icon = icon("chart-line")
+                      icon = icon("circle-nodes")
                     ),
                     menuItem(
                       text = "Utilities",
@@ -9430,12 +9379,26 @@ server <- function(input, output, session) {
               menuItem(
                 text = "Allelic Typing",
                 tabName = "typing",
-                icon = icon("dna")
+                icon = icon("gears")
+              ),
+              menuItem(
+                text = "Gene Screening",
+                tabName = "gene_screening",
+                icon = icon("dna"),
+                startExpanded = TRUE,
+                menuSubItem(
+                  text = "Screen Assembly",
+                  tabName = "gs_screening"
+                ),
+                menuSubItem(
+                  text = "Resistance Profile",
+                  tabName = "gs_profile"
+                )
               ),
               menuItem(
                 text = "Visualization",
                 tabName = "visualization",
-                icon = icon("chart-line")
+                icon = icon("circle-nodes")
               ),
               menuItem(
                 text = "Utilities",
@@ -9479,12 +9442,26 @@ server <- function(input, output, session) {
             menuItem(
               text = "Allelic Typing",
               tabName = "typing",
-              icon = icon("dna")
+              icon = icon("gears")
+            ),
+            menuItem(
+              text = "Gene Screening",
+              tabName = "gene_screening",
+              icon = icon("dna"),
+              startExpanded = TRUE,
+              menuSubItem(
+                text = "Screen Assembly",
+                tabName = "gs_screening"
+              ),
+              menuSubItem(
+                text = "Resistance Profile",
+                tabName = "gs_profile"
+              )
             ),
             menuItem(
               text = "Visualization",
               tabName = "visualization",
-              icon = icon("chart-line")
+              icon = icon("circle-nodes")
             ),
             menuItem(
               text = "Utilities",
@@ -9635,6 +9612,8 @@ server <- function(input, output, session) {
   # Change scheme
   observeEvent(input$reload_db, {
     
+    test <<- DB$scheme
+    
     log_print("Input reload_db")
     
     if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
@@ -17565,12 +17544,12 @@ server <- function(input, output, session) {
   #### MST ----
   
   mst_tree <- reactive({
-    data <- toVisNetworkData(Vis$ggraph_1)
-    data$nodes <- mutate(data$nodes, 
+    Typing$data <- toVisNetworkData(Vis$ggraph_1)
+    Typing$data$nodes <- mutate(Typing$data$nodes, 
                          label = label_mst(),
                          value = mst_node_scaling(),
                          opacity = node_opacity())
-    
+    test <<- Typing$data
     ctxRendererJS <- htmlwidgets::JS("({ctx, id, x, y, state: { selected, hover }, style, font, label, metadata}) => {
                             var pieData = JSON.parse(metadata);
                             var radius = style.size;
@@ -17652,10 +17631,10 @@ server <- function(input, output, session) {
         group[i] <- unique(Vis$meta_mst[[input$mst_col_var]])[i]
       }
       
-      data$nodes <- cbind(data$nodes, data.frame(metadata = character(nrow(data$nodes))))
+      Typing$data$nodes <- cbind(Typing$data$nodes, data.frame(metadata = character(nrow(Typing$data$nodes))))
       
-      if(length(which(data$nodes$group == "")) != 0) {
-        data$nodes$group[which(data$nodes$group == "")] <- data$nodes$group[1]
+      if(length(which(Typing$data$nodes$group == "")) != 0) {
+        Typing$data$nodes$group[which(Typing$data$nodes$group == "")] <- Typing$data$nodes$group[1]
       }
       
       if(is.null(input$mst_col_scale)) {
@@ -17669,9 +17648,9 @@ server <- function(input, output, session) {
                                       color = viridis(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
       }
       
-      for(i in 1:nrow(data$nodes)) {
+      for(i in 1:nrow(Typing$data$nodes)) {
         
-        iso_subset <- strsplit(data$nodes$label[i], split = "\n")[[1]]
+        iso_subset <- strsplit(Typing$data$nodes$label[i], split = "\n")[[1]]
         variable <- Vis$meta_mst[[input$mst_col_var]]
         values <- variable[which(Vis$meta_mst$`Assembly Name` %in% iso_subset)]
         
@@ -17687,26 +17666,26 @@ server <- function(input, output, session) {
           }
         }
         
-        data$nodes$metadata[i] <- paste0('[', pie_vec, ']')
+        Typing$data$nodes$metadata[i] <- paste0('[', pie_vec, ']')
       }
     }
     
-    data$edges <- mutate(data$edges,
+    Typing$data$edges <- mutate(Typing$data$edges,
                          length = if(input$mst_scale_edges == FALSE) {
                            input$mst_edge_length
                          } else {
-                           data$edges$weight * input$mst_edge_length_scale
+                           Typing$data$edges$weight * input$mst_edge_length_scale
                          },
-                         label = as.character(data$edges$weight),
-                         opacity = mst_edge_opacity())
+                         label = as.character(Typing$data$edges$weight),
+                         opacity = input$mst_edge_opacity)
     
     if (input$mst_show_clusters) {
-      data$nodes$group <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
+      Typing$data$nodes$group <- compute_clusters(Typing$data$nodes, Typing$data$edges, input$mst_cluster_threshold)
     }
     
-    updateSliderInput(session, "mst_cluster_threshold", max = max(data$edges$weight))
+    updateSliderInput(session, "mst_cluster_threshold", max = max(Typing$data$edges$weight))
     
-    visNetwork_graph <- visNetwork(data$nodes, data$edges,
+    visNetwork_graph <- visNetwork(Typing$data$nodes, Typing$data$edges,
                                    main = mst_title(),
                                    background = mst_background_color(),
                                    submain = mst_subtitle()) %>%
@@ -17727,7 +17706,8 @@ server <- function(input, output, session) {
                           visInteraction(hover = TRUE) %>%
                           visLayout(randomSeed = 1) %>%
                           visLegend(useGroups = FALSE,
-                                    zoom = FALSE,
+                                    zoom = TRUE,
+                                    width = legend_width(),
                                     position = input$mst_legend_ori,
                                     ncol = legend_col(),
                                     addNodes = mst_legend())
@@ -17767,13 +17747,22 @@ server <- function(input, output, session) {
     } else {
       legend <- Typing$var_cols
       names(legend)[1] <- "label"
-      mutate(legend, shape = "dot",
+      legend <- mutate(legend, shape = "dot",
              font.color = input$mst_legend_color,
              size = input$mst_symbol_size,
              font.size = input$mst_font_size)
+      
+      legend1 <<- legend
+      dnode <<- Typing$data$nodes
+      legend
     }
   })
   
+  # Set MST legend width
+  legend_width <- reactive({
+    0.2
+  })
+  
   # Set MST node shape
   mst_node_shape <- reactive({
     if(input$mst_node_shape == "Pie Nodes"){
@@ -17886,11 +17875,6 @@ server <- function(input, output, session) {
     }
   })
   
-  # Edge Opacity
-  mst_edge_opacity <- reactive({
-    input$mst_edge_opacity
-  })
-  
   # Edge font color
   mst_edge_font_color <- reactive({
     input$mst_edge_font_color
@@ -22237,6 +22221,202 @@ server <- function(input, output, session) {
     }
   )
   
+  
+  # _______________________ ####
+  
+  ## Gene Screening  ----
+  
+  ### Render UI Elements ----
+  
+  # Availablity feedback
+  output$gene_screening_info <- renderUI({
+    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
+      fluidRow(
+        column(
+          width = 11,
+          align = "left",
+          p(
+            HTML(
+              paste(
+                '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
+                tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                          paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
+              )
+            )
+          )
+        )
+      )
+    } else {
+      fluidRow(
+        column(
+          width = 11,
+          align = "left",
+          p(
+            HTML(
+              paste(
+                '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
+                tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                          paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
+              )
+            )
+          )
+        )
+      )
+    }
+  })
+  
+  output$gene_resistance_info <- renderUI({
+    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
+      fluidRow(
+        column(
+          width = 11,
+          align = "left",
+          p(
+            HTML(
+              paste(
+                '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
+                tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                          paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
+              )
+            )
+          )
+        )
+      )
+    } else {
+      fluidRow(
+        column(
+          width = 11,
+          align = "left",
+          p(
+            HTML(
+              paste(
+                '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
+                tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                          paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
+              )
+            )
+          )
+        )
+      )
+    }
+  })
+  
+  # Screening Interface
+  
+  output$screening_interface <- renderUI({
+    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
+      fluidRow(
+        column(1),
+        column(
+          width = 3,
+          align = "center",
+          br(),
+          br(),
+          p(
+            HTML(
+              paste(
+                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Assembly File (FASTA)')
+              )
+            )
+          ),
+          shinyFilesButton(
+            "genome_file_gs",
+            "Browse" ,
+            icon = icon("file"),
+            title = "Select the assembly in .fasta/.fna/.fa format:",
+            multiple = FALSE,
+            buttonType = "default",
+            class = NULL,
+            root = path_home()
+          ),
+          br(), br(),
+          uiOutput("genome_path_gs"),
+          br(), br(), br(), hr(), br(), br(),
+          uiOutput("screening_start")
+        )
+      )
+    }
+  })
+  
+  ### Screening Events ----
+  
+  # Get selected Genome in Single Mode
+  
+  observe({
+    shinyFileChoose(input,
+                    "genome_file_gs",
+                    roots = c(Home = path_home(), Root = "/"),
+                    defaultRoot = "Home",
+                    session = session,
+                    filetypes = c('', 'fasta', 'fna', 'fa'))
+    Screening$single_path <- parseFilePaths(roots = c(Home = path_home(), Root = "/"), input$genome_file_gs)
+    
+  })
+  
+  # Get selected assembly
+  
+  observe({
+    if (nrow(Screening$single_path) < 1) {
+      output$genome_path_gs <- renderUI(HTML(
+        paste("<span style='color: white;'>", "No file selected.")
+      ))
+      
+      output$screening_start <- NULL
+      
+    } else if (nrow(Screening$single_path) > 0) {
+      
+      if (str_detect(str_sub(Screening$single_path$name, start = -6), ".fasta") | 
+          str_detect(str_sub(Screening$single_path$name, start = -6), ".fna") | 
+          str_detect(str_sub(Screening$single_path$name, start = -6), ".fa")) {
+        
+        # Render selected assembly path
+        output$genome_path_gs <- renderUI({
+          HTML(
+            paste(
+              "<span style='color: white; font-weight: bolder'>",
+              as.character(Screening$single_path$name)
+            )
+          )
+        })
+        
+        output$screening_start <- renderUI(
+          actionButton(
+            inputId = "screening_start_button",
+            label = "Start",
+            icon = icon("circle-play")
+          )
+        )
+      } else {
+        show_toast(
+          title = "Wrong file type (only fasta/fna/fa)",
+          type = "error",
+          position = "bottom-end",
+          width = "500px",
+          timer = 6000
+        )
+        
+      }
+    }
+  })
+  
+  #### Running Screening ----
+  
+  observeEvent(input$screening_start_button, {
+    
+  })
+  
+  ### Screening Feedback ----
+  
+  # # Set the path to your .got file
+  # file_path <- "test_dna.got"
+  # 
+  # # Read the .got file into a data frame
+  # amrfinder_data <- read.delim(file_path, header = TRUE, sep = "\t")
+  # 
+  # # Check the first few rows of the data
+  # head(amrfinder_data)
+  
+  
   # _______________________ ####
   
   ## Typing  ----
@@ -22627,8 +22807,6 @@ server <- function(input, output, session) {
   
   # Get genome datapath
   
-  volumes = getVolumes()
-  
   observe({
     # Get selected Genome in Single Mode
     shinyFileChoose(input,
diff --git a/resources.R b/resources.R
new file mode 100644
index 0000000..162cba1
--- /dev/null
+++ b/resources.R
@@ -0,0 +1,231 @@
+# Resources
+
+amrfinder_species <- c(
+  "Acinetobacter_baumannii", "Burkholderia_cepacia", "Burkholderia_mallei_FLI", 
+  "Burkholderia_mallei_RKI", "Burkholderia_pseudomallei", "Campylobacter_jejuni_coli",
+  "Citrobacter_freundii", "Clostridioides_difficile", "Corynebacterium_diphtheriae", 
+  "Enterobacter_asburiae", "Enterobacter_cloacae", "Enterococcus_faecalis", 
+  "Enterococcus_faecium", "Escherichia_coli", "Klebsiella_oxytoca_sensu_lato", 
+  "Klebsiella_pneumoniae_sensu_lato", "Neisseria_gonorrhoeae", "Neisseria_meningitidis", 
+  "Pseudomonas_aeruginosa", "Salmonella_enterica", "Serratia_marcescens", 
+  "Staphylococcus_aureus", "Staphylococcus_pseudintermedius", "Streptococcus_agalactiae", 
+  "Streptococcus_pneumoniae", "Streptococcus_pyogenes", "Vibrio_cholerae", 
+  "Vibrio_parahaemolyticus", "Vibrio_vulnificus"
+  )
+
+schemes <- c("Acinetobacter_baumanii", "Bacillus_anthracis", "Bordetella_pertussis", 
+             "Brucella_melitensis", "Brucella_spp", "Burkholderia_mallei_FLI", 
+             "Burkholderia_mallei_RKI", "Burkholderia_pseudomallei", "Campylobacter_jejuni_coli", 
+             "Clostridioides_difficile", "Clostridium_perfringens", "Corynebacterium_diphtheriae",
+             "Cronobacter_sakazakii_malonaticus", "Enterococcus_faecalis", "Enterococcus_faecium", 
+             "Escherichia_coli", "Francisella_tularensis", "Klebsiella_oxytoca_sensu_lato", "Klebsiella_pneumoniae_sensu_lato", 
+             "Legionella_pneumophila", "Listeria_monocytogenes", "Mycobacterium_tuberculosis_complex", 
+             "Mycobacteroides_abscessus", "Mycoplasma_gallisepticum", "Paenibacillus_larvae",
+             "Pseudomonas_aeruginosa", "Salmonella_enterica", "Serratia_marcescens", 
+             "Staphylococcus_aureus", "Staphylococcus_capitis", "Streptococcus_pyogenes"
+)
+
+country_names <- c(
+  "Afghanistan",
+  "Albania",
+  "Algeria",
+  "Andorra",
+  "Angola",
+  "Antigua and Barbuda",
+  "Argentina",
+  "Armenia",
+  "Australia",
+  "Austria",
+  "Azerbaijan",
+  "Bahamas",
+  "Bahrain",
+  "Bangladesh",
+  "Barbados",
+  "Belarus",
+  "Belgium",
+  "Belize",
+  "Benin",
+  "Bhutan",
+  "Bolivia",
+  "Bosnia and Herzegovina",
+  "Botswana",
+  "Brazil",
+  "Brunei",
+  "Bulgaria",
+  "Burkina Faso",
+  "Burundi",
+  "Côte d'Ivoire",
+  "Cabo Verde",
+  "Cambodia",
+  "Cameroon",
+  "Canada",
+  "Central African Republic",
+  "Chad",
+  "Chile",
+  "China",
+  "Colombia",
+  "Comoros",
+  "Congo (Congo-Brazzaville)",
+  "Costa Rica",
+  "Croatia",
+  "Cuba",
+  "Cyprus",
+  "Czechia (Czech Republic)",
+  "Democratic Republic of the Congo",
+  "Denmark",
+  "Djibouti",
+  "Dominica",
+  "Dominican Republic",
+  "Ecuador",
+  "Egypt",
+  "El Salvador",
+  "Equatorial Guinea",
+  "Eritrea",
+  "Estonia",
+  'Eswatini (fmr. "Swaziland")',
+  "Ethiopia",
+  "Fiji",
+  "Finland",
+  "France",
+  "Gabon",
+  "Gambia",
+  "Georgia",
+  "Germany",
+  "Ghana",
+  "Greece",
+  "Grenada",
+  "Guatemala",
+  "Guinea",
+  "Guinea-Bissau",
+  "Guyana",
+  "Haiti",
+  "Holy See",
+  "Honduras",
+  "Hungary",
+  "Iceland",
+  "India",
+  "Indonesia",
+  "Iran",
+  "Iraq",
+  "Ireland",
+  "Israel",
+  "Italy",
+  "Jamaica",
+  "Japan",
+  "Jordan",
+  "Kazakhstan",
+  "Kenya",
+  "Kiribati",
+  "Kuwait",
+  "Kyrgyzstan",
+  "Laos",
+  "Latvia",
+  "Lebanon",
+  "Lesotho",
+  "Liberia",
+  "Libya",
+  "Liechtenstein",
+  "Lithuania",
+  "Luxembourg",
+  "Madagascar",
+  "Malawi",
+  "Malaysia",
+  "Maldives",
+  "Mali",
+  "Malta",
+  "Marshall Islands",
+  "Mauritania",
+  "Mauritius",
+  "Mexico",
+  "Micronesia",
+  "Moldova",
+  "Monaco",
+  "Mongolia",
+  "Montenegro",
+  "Morocco",
+  "Mozambique",
+  "Myanmar (formerly Burma)",
+  "Namibia",
+  "Nauru",
+  "Nepal",
+  "Netherlands",
+  "New Zealand",
+  "Nicaragua",
+  "Niger",
+  "Nigeria",
+  "North Korea",
+  "North Macedonia (formerly Macedonia)",
+  "Norway",
+  "Oman",
+  "Pakistan",
+  "Palau",
+  "Palestine State",
+  "Panama",
+  "Papua New Guinea",
+  "Paraguay",
+  "Peru",
+  "Philippines",
+  "Poland",
+  "Portugal",
+  "Qatar",
+  "Romania",
+  "Russia",
+  "Rwanda",
+  "Saint Kitts and Nevis",
+  "Saint Lucia",
+  "Saint Vincent and the Grenadines",
+  "Samoa",
+  "San Marino",
+  "Sao Tome and Principe",
+  "Saudi Arabia",
+  "Senegal",
+  "Serbia",
+  "Seychelles",
+  "Sierra Leone",
+  "Singapore",
+  "Slovakia",
+  "Slovenia",
+  "Solomon Islands",
+  "Somalia",
+  "South Africa",
+  "South Korea",
+  "South Sudan",
+  "Spain",
+  "Sri Lanka",
+  "Sudan",
+  "Suriname",
+  "Sweden",
+  "Switzerland",
+  "Syria",
+  "Tajikistan",
+  "Tanzania",
+  "Thailand",
+  "Timor-Leste",
+  "Togo",
+  "Tonga",
+  "Trinidad and Tobago",
+  "Tunisia",
+  "Turkey",
+  "Turkmenistan",
+  "Tuvalu",
+  "Uganda",
+  "Ukraine",
+  "United Arab Emirates",
+  "United Kingdom",
+  "United States of America",
+  "Uruguay",
+  "Uzbekistan",
+  "Vanuatu",
+  "Venezuela",
+  "Vietnam",
+  "Yemen",
+  "Zambia",
+  "Zimbabwe"
+)
+
+sel_countries <-
+  c("Austria",
+    "Germany",
+    "Switzerland",
+    "United Kingdom",
+    "United States of America")
\ No newline at end of file

From 28e15e246a02459ea4f6ef640321744f8cf00064 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Wed, 31 Jul 2024 18:51:14 +0200
Subject: [PATCH 23/75] Changed location for resources.R

---
 resources.R => www/resources.R | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename resources.R => www/resources.R (100%)

diff --git a/resources.R b/www/resources.R
similarity index 100%
rename from resources.R
rename to www/resources.R

From 5de2c48e7d9779eb699f5df2eae509912dde2111 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Wed, 31 Jul 2024 19:48:38 +0200
Subject: [PATCH 24/75] Added log messages

---
 App.R | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/App.R b/App.R
index f369e32..65f5d86 100644
--- a/App.R
+++ b/App.R
@@ -6880,7 +6880,7 @@ server <- function(input, output, session) {
             )
             
             # Check if number of loci/fastq-files of alleles is coherent with number of targets in scheme
-            if(DB$number_loci != length(dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")))) {
+            if(DB$number_loci > length(dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")))) {
               
               log_print(paste0("Loci files are missing in the local ", DB$scheme, " folder"))
               
@@ -11394,13 +11394,11 @@ server <- function(input, output, session) {
     
     # Check if .downloaded_schemes folder exists and if not create it
     if (!dir.exists(file.path(DB$database, ".downloaded_schemes"))) {
-      print("Creating download schemes folder")
       dir.create(file.path(DB$database, ".downloaded_schemes"), recursive = TRUE)
     }
     
     # Check if remains of old temporary folder exists and remove them
     if (dir.exists(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")))) {
-      print("Deleting old temporary folder")
       unlink(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")), recursive = TRUE)
     }
     
@@ -11415,7 +11413,6 @@ server <- function(input, output, session) {
       paste("Error: ", e$message)
     })
     
-    print("Unzipping the scheme")
     # Unzip the scheme in temporary folder
     unzip(
       zipfile = file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")),
@@ -11425,7 +11422,7 @@ server <- function(input, output, session) {
       )
     )
     
-    print("Producing hashes for the database")
+    log_print("Hashing downloaded database")
     # Hash temporary folder
     hash_database(file.path(DB$database, 
                             Scheme$folder_name, 
@@ -11436,7 +11433,6 @@ server <- function(input, output, session) {
                                               Scheme$folder_name, 
                                               paste0(Scheme$folder_name, "_alleles")))
     if (!is_empty(local_db_filelist)) {
-      print("Old database is not empty, resolving the files!")
       # Get list from temporary database
       tmp_db_filelist <- list.files(file.path(DB$database,
                                               Scheme$folder_name,
@@ -11493,11 +11489,9 @@ server <- function(input, output, session) {
       }
     }
     
-    print("Delete old alleles folder")
     unlink(file.path(DB$database, Scheme$folder_name, 
                      paste0(Scheme$folder_name, "_alleles")), recursive = TRUE)
     
-    print("Overwriting old alleles directory with temporary directory")
     file.rename(file.path(DB$database, Scheme$folder_name,
                           paste0(Scheme$folder_name, ".tmp")),
                 file.path(DB$database, Scheme$folder_name,
@@ -11547,7 +11541,6 @@ server <- function(input, output, session) {
       width = "400px"
     )
     
-    # TODO Add log message regarding the update of the scheme
     log_print("Download successful")
     
     showModal(
@@ -17565,6 +17558,7 @@ server <- function(input, output, session) {
   #### MST ----
   
   mst_tree <- reactive({
+    log_print("Generating visNetwork")
     data <- toVisNetworkData(Vis$ggraph_1)
     data$nodes <- mutate(data$nodes, 
                          label = label_mst(),
@@ -17744,7 +17738,7 @@ server <- function(input, output, session) {
           visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
       }
     }
-    
+    log_print("Plotting MST graph")
     visNetwork_graph
   })
   
@@ -23955,6 +23949,7 @@ server <- function(input, output, session) {
     
     dir_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$hash_dir)
     req(dir_path)
+    log_print("Hashing directory using utilities")
     output$statustext <- renderUI(
       fluidRow(
         tags$li(

From efc90a34aee9c31c6a36fe9b240f557df16efd81 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Wed, 31 Jul 2024 20:15:20 +0200
Subject: [PATCH 25/75] Added AMRFinder, first implementation of shell script

---
 App.R                 | 41 ++++++++++++++++++++++++++++++++++-------
 PhyloTrace.yml        |  1 +
 execute/screening.sh  | 39 +++++++++++++++++++++++++++++++++++++++
 install_phylotrace.sh |  3 +++
 4 files changed, 77 insertions(+), 7 deletions(-)
 create mode 100755 execute/screening.sh

diff --git a/App.R b/App.R
index dfe1984..baa406e 100644
--- a/App.R
+++ b/App.R
@@ -44,7 +44,7 @@ library(treeio)
 library(ggtree)
 library(ggtreeExtra)
 
-source("resources.R")
+source("www/resources.R")
 
 options(ignore.negative.edge=TRUE)
 
@@ -9612,7 +9612,7 @@ server <- function(input, output, session) {
   # Change scheme
   observeEvent(input$reload_db, {
     
-    test <<- DB$scheme
+    test <<- Screening$single_path$datapath
     
     log_print("Input reload_db")
     
@@ -22331,7 +22331,7 @@ server <- function(input, output, session) {
           ),
           br(), br(),
           uiOutput("genome_path_gs"),
-          br(), br(), br(), hr(), br(), br(),
+          br(), br(), br(), 
           uiOutput("screening_start")
         )
       )
@@ -22380,10 +22380,20 @@ server <- function(input, output, session) {
         })
         
         output$screening_start <- renderUI(
-          actionButton(
-            inputId = "screening_start_button",
-            label = "Start",
-            icon = icon("circle-play")
+          fluidRow(
+            hr(), br(), br(),
+            column(
+              width = 8,
+              actionButton(
+                inputId = "screening_start_button",
+                label = "Start",
+                icon = icon("circle-play")
+              )
+            ),
+            column(
+              width = 4,
+              uiOutput("screening_progress")
+            )
           )
         )
       } else {
@@ -22403,6 +22413,23 @@ server <- function(input, output, session) {
   
   observeEvent(input$screening_start_button, {
     
+    # Start spinner
+    output$screening_progress <- renderUI(
+      HTML('<i class="fa-solid fa-spinner"></i>')
+    )
+    
+    screening_df <- data.frame(wd = getwd(),
+                               assembly_path = Screening$single_path$datapath,
+                               assembly = as.character(basename(Screening$single_path$name)),
+                               species = gsub(" ", "_", DB$scheme))
+    
+    saveRDS(screening_df, paste0(getwd(), "/execute/screening_meta.rds"))
+    
+    # System execution screening.sh
+    system(paste("bash", paste0(getwd(), "/execute/screening.sh")), wait = TRUE)
+    
+    # Stop spinner
+    output$screening_progress <- NULL
   })
   
   ### Screening Feedback ----
diff --git a/PhyloTrace.yml b/PhyloTrace.yml
index daaacbd..8bd2b59 100644
--- a/PhyloTrace.yml
+++ b/PhyloTrace.yml
@@ -7,6 +7,7 @@ dependencies:
   - r-base=4.3.2
   - r-remotes=2.5.0
   - kma=1.4.14
+  - ncbi-amrfinderplus=3.12.8
   - parallel=20240522
   - pblat=2.5.1
   - r-bh=1.81.0-1
diff --git a/execute/screening.sh b/execute/screening.sh
new file mode 100755
index 0000000..856c36d
--- /dev/null
+++ b/execute/screening.sh
@@ -0,0 +1,39 @@
+#!/bin/bash
+
+cd execute
+source ~/miniconda3/etc/profile.d/conda.sh
+conda activate PhyloTrace
+unset R_HOME
+
+# Set base path
+base_path=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'wd'])")
+path_assembly=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'assembly_path'])")
+assembly=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'assembly'])")
+species=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'species'])")
+
+cat "$path_assembly"
+
+# Remove the existing directory (if it exists)
+if [ -d "$base_path/execute/screening" ]; then
+    rm -r "$base_path/execute/screening"
+fi
+
+mkdir "$base_path/execute/screening"
+
+# Directory name
+results="$base_path/execute/screening/results"
+
+# Remove the existing directory (if it exists)
+if [ -d "$results" ]; then
+    rm -r "$results"
+fi
+
+# Create a new directory
+mkdir "$results"
+
+# Get cores
+coresall=$(nproc --all)
+cores=$((num_processors - 2))
+
+amrfinder -n "$path_assembly" --threads $cores #--organism "Klebsiella_oxytoca" 
+
diff --git a/install_phylotrace.sh b/install_phylotrace.sh
index f392816..8239529 100755
--- a/install_phylotrace.sh
+++ b/install_phylotrace.sh
@@ -36,6 +36,9 @@ else
 fi
 EOF
 
+# Download AMRFinder Database
+amrfinder -u
+
 # Install visNetwork modification
 Rscript -e "remotes::install_github('fpaskali/visNetwork', force = TRUE)"
 

From 77b74c7f03f8122ed1e7996ba800a05d4086022a Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Wed, 31 Jul 2024 21:56:04 +0200
Subject: [PATCH 26/75] added hash formating in tables

---
 App.R | 101 +++++++++++++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 89 insertions(+), 12 deletions(-)

diff --git a/App.R b/App.R
index 65f5d86..07d717b 100644
--- a/App.R
+++ b/App.R
@@ -8947,7 +8947,17 @@ server <- function(input, output, session) {
                                   td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
                                 }
                               }
-                            }") 
+                            }") %>%
+                            hot_col(3:ncol(DB$na_table), renderer = htmlwidgets::JS(
+                              "function(instance, td, row, col, prop, value, cellProperties) {
+                                if (value.length > 8) {
+                                  value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                                }
+                                td.innerHTML = value;
+                                td.style.textAlign = 'center';
+                                return td;
+                               }"
+                            ))
                         })
                       } else {
                         output$table_missing_values <- renderRHandsontable({
@@ -8974,7 +8984,17 @@ server <- function(input, output, session) {
                                   td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
                                 }
                               }
-                            }") 
+                            }") %>%
+                            hot_col(3:ncol(DB$na_table), renderer = htmlwidgets::JS(
+                              "function(instance, td, row, col, prop, value, cellProperties) {
+                                if (value.length > 8) {
+                                  value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                                }
+                                td.innerHTML = value;
+                                td.style.textAlign = 'center';
+                                return td;
+                               }"
+                            ))
                         })
                       }
                     }
@@ -22318,14 +22338,36 @@ server <- function(input, output, session) {
                               contextMenu = FALSE) %>%
                   hot_cols(columnSorting = TRUE) %>%
                   hot_rows(rowHeights = 25) %>%
-                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter")
+                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter",
+                          cellWidths = list(100, 160, NULL)) %>%
+                  hot_col("Value", renderer=htmlwidgets::JS(
+                    "function(instance, td, row, col, prop, value, cellProperties) {
+                      if (value.length > 8) {
+                        value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                      }
+                      td.innerHTML = value;
+                      td.style.textAlign = 'center';
+                      return td;
+                     }"
+                  ))
               } else {
                 rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
                               stretchH = "all", readOnly = TRUE,
                               contextMenu = FALSE,) %>%
                   hot_cols(columnSorting = TRUE) %>%
                   hot_rows(rowHeights = 25) %>%
-                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter")
+                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter",
+                          cellWidths = list(100, 160, NULL)) %>%
+                  hot_col("Value", renderer=htmlwidgets::JS(
+                    "function(instance, td, row, col, prop, value, cellProperties) {
+                      if (value.length > 8) {
+                        value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                      }
+                      td.innerHTML = value;
+                      td.style.textAlign = 'center';
+                      return td;
+                     }"
+                  ))
               }
             }
           })
@@ -22767,7 +22809,7 @@ server <- function(input, output, session) {
               ),
               column(1),
               column(
-                width = 3,
+                width = 5,
                 br(), br(), br(),
                 uiOutput("single_typing_results")
               )
@@ -23748,7 +23790,19 @@ server <- function(input, output, session) {
                           rowHeaders = NULL, stretchH = "all",
                           readOnly = TRUE, contextMenu = FALSE) %>%
               hot_rows(rowHeights = 25) %>%
-              hot_col(1:3, valign = "htMiddle", halign = "htCenter")})
+              hot_col(1:3, valign = "htMiddle", halign = "htCenter",
+                      cellWidths = list(100, 160, NULL)) %>%
+              hot_col("Value", renderer=htmlwidgets::JS(
+                "function(instance, td, row, col, prop, value, cellProperties) {
+                  if (value.length > 8) {
+                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                  }
+                  td.innerHTML = value;
+                  td.style.textAlign = 'center';
+                  return td;
+                 }"
+              ))
+            })
           
         } else {
           if(Typing$multi_table_length > 15) {
@@ -23757,15 +23811,38 @@ server <- function(input, output, session) {
                             stretchH = "all", height = 500,
                             readOnly = TRUE, contextMenu = FALSE) %>%
                 hot_rows(rowHeights = 25) %>%
-                hot_col(1:3, valign = "htMiddle", halign = "htCenter")})
+                hot_col(1:3, valign = "htMiddle", halign = "htCenter",
+                        cellWidths = list(100, 160, NULL)) %>%
+                hot_col("Value", renderer=htmlwidgets::JS(
+                  "function(instance, td, row, col, prop, value, cellProperties) {
+                  if (value.length > 8) {
+                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                  }
+                  td.innerHTML = value;
+                  td.style.textAlign = 'center';
+                  return td;
+                 }"
+                ))
+              })
           } else {
             output$multi_typing_result_table <- renderRHandsontable({
               rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
                             stretchH = "all", readOnly = TRUE,
                             contextMenu = FALSE) %>%
                 hot_rows(rowHeights = 25) %>%
-                hot_col(1:3, valign = "htMiddle", halign = "htCenter")})
-            
+                hot_col(1:3, valign = "htMiddle", halign = "htCenter",
+                        cellWidths = list(100, 160, NULL)) %>%
+                hot_col("Value", renderer=htmlwidgets::JS(
+                  "function(instance, td, row, col, prop, value, cellProperties) {
+                  if (value.length > 8) {
+                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                  }
+                  td.innerHTML = value;
+                  td.style.textAlign = 'center';
+                  return td;
+                 }"
+                ))
+              })
           }
         }
       } else {
@@ -23813,10 +23890,10 @@ server <- function(input, output, session) {
                     selected = names(Typing$result_list)[length(names(Typing$result_list))],
                   )
                 ),
-                br(), br(), 
-                rHandsontableOutput("multi_typing_result_table")
+                br(), br()
               )
-            )
+            ),
+            rHandsontableOutput("multi_typing_result_table")
           )
         })
       }

From 0c9c6825100b6629010a431470207edf6b9adace Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Wed, 31 Jul 2024 23:25:19 +0200
Subject: [PATCH 27/75] Implementation of AMRFinder, Set up reactive UI

---
 App.R                | 107 +++++++++++++++++++++++++++++++++++--------
 execute/screening.sh |  36 +++++++++------
 www/resources.R      |   6 +--
 3 files changed, 113 insertions(+), 36 deletions(-)

diff --git a/App.R b/App.R
index baa406e..29a028c 100644
--- a/App.R
+++ b/App.R
@@ -5755,6 +5755,11 @@ server <- function(input, output, session) {
   
   log_print("Session started")
   
+  # Clear screening file
+  if(file.exists(paste0(getwd(), "/execute/screening/output_file.tsv"))) {
+    file.remove(paste0(getwd(), "/execute/screening/output_file.tsv"))
+  }
+  
   # Declare reactive variables
   Startup <- reactiveValues(sidebar = TRUE, 
                             header = TRUE) # reactive variables related to startup process
@@ -22228,6 +22233,46 @@ server <- function(input, output, session) {
   
   ### Render UI Elements ----
   
+  output$screening_results <- renderUI({
+    if(!is.null(Screening$results)) {
+      dataTableOutput("screening_table")
+    }
+  })
+  
+  observe({
+    if(!is.null(Screening$results)) {
+      output$screening_reset <- renderUI(
+        actionButton(
+          "screening_reset_bttn",
+          "Reset"
+        )
+      )
+      
+      output$screening_table <- renderDataTable(
+        select(Screening$results, c(6, 7, 8, 9, 11)),
+        selection = "single",
+        options = list(pageLength = 10,
+                       columnDefs = list(list(searchable = TRUE,
+                                              targets = "_all")),
+                       initComplete = DT::JS(
+                         "function(settings, json) {",
+                         "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                         "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                         "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                         "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                         "}"
+                       ),
+                       drawCallback = DT::JS(
+                         "function(settings) {",
+                         "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                         "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                         "}"
+                       )))
+    } else {
+      output$screening_reset <- NULL
+    }
+  })
+  
   # Availablity feedback
   output$gene_screening_info <- renderUI({
     if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
@@ -22310,8 +22355,7 @@ server <- function(input, output, session) {
         column(
           width = 3,
           align = "center",
-          br(),
-          br(),
+          br(), br(),
           p(
             HTML(
               paste(
@@ -22332,7 +22376,15 @@ server <- function(input, output, session) {
           br(), br(),
           uiOutput("genome_path_gs"),
           br(), br(), br(), 
-          uiOutput("screening_start")
+          uiOutput("screening_start"),
+          br(), br(), br(), 
+          uiOutput("screening_reset")
+        ),
+        column(1),
+        column(
+          width = 6,
+          br(), br(),
+          uiOutput("screening_results")
         )
       )
     }
@@ -22340,6 +22392,13 @@ server <- function(input, output, session) {
   
   ### Screening Events ----
   
+  # Reset screening 
+  observeEvent(input$screening_reset_bttn, {
+    Screening$status <- "idle"
+    file.remove(paste0(getwd(), "/execute/screening/output_file.tsv"))
+    Screening$results <- NULL
+  })
+  
   # Get selected Genome in Single Mode
   
   observe({
@@ -22413,10 +22472,7 @@ server <- function(input, output, session) {
   
   observeEvent(input$screening_start_button, {
     
-    # Start spinner
-    output$screening_progress <- renderUI(
-      HTML('<i class="fa-solid fa-spinner"></i>')
-    )
+    Screening$status <- "started"
     
     screening_df <- data.frame(wd = getwd(),
                                assembly_path = Screening$single_path$datapath,
@@ -22426,24 +22482,37 @@ server <- function(input, output, session) {
     saveRDS(screening_df, paste0(getwd(), "/execute/screening_meta.rds"))
     
     # System execution screening.sh
-    system(paste("bash", paste0(getwd(), "/execute/screening.sh")), wait = TRUE)
-    
-    # Stop spinner
-    output$screening_progress <- NULL
+    system(paste("bash", paste0(getwd(), "/execute/screening.sh")), wait = FALSE)
   })
   
   ### Screening Feedback ----
   
-  # # Set the path to your .got file
-  # file_path <- "test_dna.got"
-  # 
-  # # Read the .got file into a data frame
-  # amrfinder_data <- read.delim(file_path, header = TRUE, sep = "\t")
-  # 
-  # # Check the first few rows of the data
-  # head(amrfinder_data)
+  observe({
+    req(Screening$status)
+    if(Screening$status == "started") {
+      # Start spinner
+      output$screening_progress <- renderUI(
+        HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px;color:white"></i>'))
+      )
+      
+      check_screening()
+      
+    } else if (Screening$status == "finished") {
+      output$screening_progress <- NULL
+    }
+  })
   
+  check_screening <- reactive({
+    invalidateLater(2000, session)
+    if(Screening$status == "started"){
+      if(file.exists(paste0(getwd(), "/execute/screening/output_file.tsv"))) {
+        Screening$results <- read.delim(paste0(getwd(), "/execute/screening/output_file.tsv"))
+        Screening$status <- "finished"
+      }
+    }
+  })
   
+
   # _______________________ ####
   
   ## Typing  ----
diff --git a/execute/screening.sh b/execute/screening.sh
index 856c36d..87fe552 100755
--- a/execute/screening.sh
+++ b/execute/screening.sh
@@ -11,29 +11,39 @@ path_assembly=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'assembly_path'])
 assembly=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'assembly'])")
 species=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'species'])")
 
-cat "$path_assembly"
+if [ "$species" = "Escherichia_coli" ]; then
+  species="Escherichia"
+fi
 
-# Remove the existing directory (if it exists)
-if [ -d "$base_path/execute/screening" ]; then
-    rm -r "$base_path/execute/screening"
+if [ "$species" = "Burkholderia_mallei_FLI" ] || [ "$species" = "Burkholderia_mallei_RKI" ]; then
+species="Burkholderia_mallei"
 fi
 
-mkdir "$base_path/execute/screening"
+if [ "$species" = "Klebsiella_oxytoca_sensu_lato" ]; then
+  species="Klebsiella_oxytoca"
+fi
 
-# Directory name
-results="$base_path/execute/screening/results"
+if [ "$species" = "Salmonella_enterica" ]; then
+  species="Salmonella"
+fi
+
+if [ "$species" = "Campylobacter_jejuni_coli" ]; then
+  species="Campylobacter"
+fi
+
+if [ "$species" = "Klebsiella_pneumoniae_sensu_lato" ]; then
+  species="Klebsiella_pneumoniae"
+fi
 
 # Remove the existing directory (if it exists)
-if [ -d "$results" ]; then
-    rm -r "$results"
+if [ -d "$base_path/execute/screening" ]; then
+    rm -r "$base_path/execute/screening"
 fi
 
-# Create a new directory
-mkdir "$results"
+mkdir "$base_path/execute/screening"
 
 # Get cores
 coresall=$(nproc --all)
 cores=$((num_processors - 2))
 
-amrfinder -n "$path_assembly" --threads $cores #--organism "Klebsiella_oxytoca" 
-
+amrfinder -n "$path_assembly" --threads $cores --plus --organism $species -o "screening/output_file.tsv"
diff --git a/www/resources.R b/www/resources.R
index 162cba1..fc46c7f 100644
--- a/www/resources.R
+++ b/www/resources.R
@@ -10,8 +10,7 @@ amrfinder_species <- c(
   "Pseudomonas_aeruginosa", "Salmonella_enterica", "Serratia_marcescens", 
   "Staphylococcus_aureus", "Staphylococcus_pseudintermedius", "Streptococcus_agalactiae", 
   "Streptococcus_pneumoniae", "Streptococcus_pyogenes", "Vibrio_cholerae", 
-  "Vibrio_parahaemolyticus", "Vibrio_vulnificus"
-  )
+  "Vibrio_parahaemolyticus", "Vibrio_vulnificus")
 
 schemes <- c("Acinetobacter_baumanii", "Bacillus_anthracis", "Bordetella_pertussis", 
              "Brucella_melitensis", "Brucella_spp", "Burkholderia_mallei_FLI", 
@@ -22,8 +21,7 @@ schemes <- c("Acinetobacter_baumanii", "Bacillus_anthracis", "Bordetella_pertuss
              "Legionella_pneumophila", "Listeria_monocytogenes", "Mycobacterium_tuberculosis_complex", 
              "Mycobacteroides_abscessus", "Mycoplasma_gallisepticum", "Paenibacillus_larvae",
              "Pseudomonas_aeruginosa", "Salmonella_enterica", "Serratia_marcescens", 
-             "Staphylococcus_aureus", "Staphylococcus_capitis", "Streptococcus_pyogenes"
-)
+             "Staphylococcus_aureus", "Staphylococcus_capitis", "Streptococcus_pyogenes")
 
 country_names <- c(
   "Afghanistan",

From c5ff229e66ea3a1efc2c76b8987f9c01094db907 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Thu, 1 Aug 2024 11:35:09 +0200
Subject: [PATCH 28/75] Improvements of screening functionality and feedback

---
 App.R                | 253 ++++++++++++++++++++++++++++++-------------
 execute/screening.sh |  20 +++-
 www/body.css         |  11 ++
 www/head.css         |   2 +
 4 files changed, 209 insertions(+), 77 deletions(-)

diff --git a/App.R b/App.R
index 29a028c..ac7e57f 100644
--- a/App.R
+++ b/App.R
@@ -5778,7 +5778,7 @@ server <- function(input, output, session) {
                            result_list = NULL,
                            status = "") # reactive variables related to typing process
   
-  Screening <- reactiveValues()
+  Screening <- reactiveValues(status = "idle") # reactive variables related to gene screening
   
   Vis <- reactiveValues(cluster = NULL, 
                         metadata = list(),
@@ -6202,6 +6202,42 @@ server <- function(input, output, session) {
               )
             )
           )
+        } else if(Screening$status == "started") {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> running gene screening</i>")), 
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(Screening$status == "finished") {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> gene screening finalized</i>")), 
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(isTRUE(Screening$fail)) {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:red !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> gene screening failed</i>")), 
+                  style = "color:white;")
+              )
+            )
+          )
         } else {
           output$statustext <- renderUI(
             fluidRow(
@@ -22239,14 +22275,20 @@ server <- function(input, output, session) {
     }
   })
   
+  observe({
+    if(isTRUE(Screening$fail)) {
+      output$screening_fail <- renderPrint({
+        readLines(paste0(getwd(), "/execute/screening/error.txt"))
+      })
+    } else {
+      output$screening_fail <- NULL
+    }
+  })
+  
+  
   observe({
     if(!is.null(Screening$results)) {
-      output$screening_reset <- renderUI(
-        actionButton(
-          "screening_reset_bttn",
-          "Reset"
-        )
-      )
+      req(Screening$results)
       
       output$screening_table <- renderDataTable(
         select(Screening$results, c(6, 7, 8, 9, 11)),
@@ -22268,8 +22310,6 @@ server <- function(input, output, session) {
                          "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
                          "}"
                        )))
-    } else {
-      output$screening_reset <- NULL
     }
   })
   
@@ -22350,41 +22390,48 @@ server <- function(input, output, session) {
   
   output$screening_interface <- renderUI({
     if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
-      fluidRow(
-        column(1),
-        column(
-          width = 3,
-          align = "center",
-          br(), br(),
-          p(
-            HTML(
-              paste(
-                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Assembly File (FASTA)')
+      column(
+        width = 12,
+        fluidRow(
+          column(1),
+          column(
+            width = 3,
+            align = "center",
+            br(), br(),
+            p(
+              HTML(
+                paste(
+                  tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Assembly File (FASTA)')
+                )
               )
-            )
-          ),
-          shinyFilesButton(
-            "genome_file_gs",
-            "Browse" ,
-            icon = icon("file"),
-            title = "Select the assembly in .fasta/.fna/.fa format:",
-            multiple = FALSE,
-            buttonType = "default",
-            class = NULL,
-            root = path_home()
+            ),
+            shinyFilesButton(
+              "genome_file_gs",
+              "Browse" ,
+              icon = icon("file"),
+              title = "Select the assembly in .fasta/.fna/.fa format:",
+              multiple = FALSE,
+              buttonType = "default",
+              class = NULL,
+              root = path_home()
+            ),
+            br(), br(),
+            uiOutput("genome_path_gs")
           ),
-          br(), br(),
-          uiOutput("genome_path_gs"),
-          br(), br(), br(), 
-          uiOutput("screening_start"),
-          br(), br(), br(), 
-          uiOutput("screening_reset")
+          column(1),
+          column(
+            width = 2,
+            uiOutput("screening_start")
+          )
         ),
-        column(1),
-        column(
-          width = 6,
-          br(), br(),
-          uiOutput("screening_results")
+        fluidRow(
+          column(1),
+          column(
+            width = 10,
+            br(), br(), br(), br(),
+            uiOutput("screening_results"),
+            verbatimTextOutput("screening_fail")
+          )
         )
       )
     }
@@ -22394,9 +22441,13 @@ server <- function(input, output, session) {
   
   # Reset screening 
   observeEvent(input$screening_reset_bttn, {
+    log_print("Reset gene screening")
     Screening$status <- "idle"
     file.remove(paste0(getwd(), "/execute/screening/output_file.tsv"))
+    file.remove(paste0(getwd(), "/execute/screening/error.txt"))
     Screening$results <- NULL
+    Screening$single_path <- data.frame()
+    Screening$fail <- NULL
   })
   
   # Get selected Genome in Single Mode
@@ -22438,23 +22489,31 @@ server <- function(input, output, session) {
           )
         })
         
-        output$screening_start <- renderUI(
+        output$screening_start <- renderUI({
+          
           fluidRow(
-            hr(), br(), br(),
             column(
               width = 8,
-              actionButton(
-                inputId = "screening_start_button",
-                label = "Start",
-                icon = icon("circle-play")
-              )
-            ),
-            column(
-              width = 4,
-              uiOutput("screening_progress")
+              br(), br(), 
+              if(Screening$status == "finished") {
+                actionButton(
+                  "screening_reset_bttn",
+                  "Reset",
+                  icon = icon("arrows-rotate")
+                )
+              } else if(Screening$status == "idle") {
+                actionButton(
+                  inputId = "screening_start_button",
+                  label = "Start",
+                  icon = icon("circle-play")
+                )
+              } else if(Screening$status == "started") {
+                HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:22px;color:white;margin-top:37px;position:relative;left:20px"></i>'))
+              }
             )
           )
-        )
+        })
+        
       } else {
         show_toast(
           title = "Wrong file type (only fasta/fna/fa)",
@@ -22472,17 +22531,47 @@ server <- function(input, output, session) {
   
   observeEvent(input$screening_start_button, {
     
-    Screening$status <- "started"
-    
-    screening_df <- data.frame(wd = getwd(),
-                               assembly_path = Screening$single_path$datapath,
-                               assembly = as.character(basename(Screening$single_path$name)),
-                               species = gsub(" ", "_", DB$scheme))
-    
-    saveRDS(screening_df, paste0(getwd(), "/execute/screening_meta.rds"))
-    
-    # System execution screening.sh
-    system(paste("bash", paste0(getwd(), "/execute/screening.sh")), wait = FALSE)
+    if(tail(readLogFile(), 1) != "0") {
+      show_toast(
+        title = "Pending Multi Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000,
+        width = "500px"
+      )
+    } else if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000,
+        width = "500px"
+      )
+    } else {
+      
+      log_print("Started gene screening")
+      
+      Screening$status <- "started"
+      
+      show_toast(
+        title = "Gene screening started",
+        type = "success",
+        position = "bottom-end",
+        width = "500px",
+        timer = 6000
+      )
+      
+      screening_df <- data.frame(wd = getwd(),
+                                 assembly_path = Screening$single_path$datapath,
+                                 assembly = as.character(basename(Screening$single_path$name)),
+                                 species = gsub(" ", "_", DB$scheme))
+      
+      saveRDS(screening_df, paste0(getwd(), "/execute/screening_meta.rds"))
+      
+      # System execution screening.sh
+      system(paste("bash", paste0(getwd(), "/execute/screening.sh")), wait = FALSE)
+      
+    }
   })
   
   ### Screening Feedback ----
@@ -22490,15 +22579,10 @@ server <- function(input, output, session) {
   observe({
     req(Screening$status)
     if(Screening$status == "started") {
-      # Start spinner
-      output$screening_progress <- renderUI(
-        HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px;color:white"></i>'))
-      )
-      
+      shinyjs::disable("genome_file_gs") 
       check_screening()
-      
-    } else if (Screening$status == "finished") {
-      output$screening_progress <- NULL
+    } else if(Screening$status == "idle") {
+      shinyjs::enable("genome_file_gs") 
     }
   })
   
@@ -22508,6 +22592,11 @@ server <- function(input, output, session) {
       if(file.exists(paste0(getwd(), "/execute/screening/output_file.tsv"))) {
         Screening$results <- read.delim(paste0(getwd(), "/execute/screening/output_file.tsv"))
         Screening$status <- "finished"
+        log_print("Finalized gene screening")
+      } else if(file.exists(paste0(getwd(), "/execute/screening/error.txt"))) {
+        Screening$status <- "finished"
+        log_print("Failed gene screening")
+        Screening$fail <- TRUE
       }
     }
   })
@@ -22896,7 +22985,6 @@ server <- function(input, output, session) {
           width = "500px",
           timer = 6000
         )
-        
       }
     }
   })
@@ -22922,8 +23010,6 @@ server <- function(input, output, session) {
     log_print("Input typing_start")
     
     if(tail(readLogFile(), 1) != "0") {
-      log_print("Pending multi typing")
-      
       show_toast(
         title = "Pending Multi Typing",
         type = "warning",
@@ -22931,6 +23017,14 @@ server <- function(input, output, session) {
         timer = 6000,
         width = "500px"
       )
+    } else if (Screening$status == "started") {
+      show_toast(
+        title = "Pending Gene Screening",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000,
+        width = "500px"
+      )
     } else {
       
       if(!is.null(DB$data)) {
@@ -23842,7 +23936,6 @@ server <- function(input, output, session) {
     log_print("Initiate multi typing")
     
     if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
-      log_print("Pending Single Typing")
       show_toast(
         title = "Pending Single Typing",
         type = "warning",
@@ -23850,6 +23943,14 @@ server <- function(input, output, session) {
         timer = 6000,
         width = "500px"
       )
+    } else if (Screening$status == "started") {
+      show_toast(
+        title = "Pending Gene Screening",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000,
+        width = "500px"
+      )
     } else {
       if (any(!grepl("\\.fasta|\\.fna|\\.fa", str_sub(Typing$genome_selected$Files[which(Typing$genome_selected$Include == TRUE)], start = -6)))) {
         
diff --git a/execute/screening.sh b/execute/screening.sh
index 87fe552..f0ed3d0 100755
--- a/execute/screening.sh
+++ b/execute/screening.sh
@@ -11,6 +11,8 @@ path_assembly=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'assembly_path'])
 assembly=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'assembly'])")
 species=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'species'])")
 
+error_file="screening/error.txt"
+
 if [ "$species" = "Escherichia_coli" ]; then
   species="Escherichia"
 fi
@@ -46,4 +48,20 @@ mkdir "$base_path/execute/screening"
 coresall=$(nproc --all)
 cores=$((num_processors - 2))
 
-amrfinder -n "$path_assembly" --threads $cores --plus --organism $species -o "screening/output_file.tsv"
+amrfinder -n "$path_assembly" --threads $cores --plus --organism $species -o "screening/output_file.tsv" > amrfinder_stdout.txt 2> amrfinder_stderr.txt
+status=$?
+
+# Check if status variable is set and is an integer
+if [ -z "$status" ]; then
+  echo "AMRFinder execution did not set an exit status." > "$base_path/execute/$error_file"
+  exit 1
+fi
+
+if [ "$status" -ne 0 ]; then
+  echo "AMRFinder failed with status $status" > "$base_path/execute/$error_file"
+  echo "Error details:" >> "$base_path/execute/$error_file"
+  cat amrfinder_stderr.txt >> "$base_path/execute/$error_file"
+  exit $status
+fi
+
+echo "AMRFinder completed successfully"
diff --git a/www/body.css b/www/body.css
index c197353..28d78c4 100644
--- a/www/body.css
+++ b/www/body.css
@@ -2845,3 +2845,14 @@ top: 1px;
 border-radius: 6px;
 margin-left: 10px;
 }
+
+/* Gene Screening */
+
+#screening_start_button,
+#screening_reset_bttn {
+  margin-top: 31px;
+}
+
+#screening_fail {
+  max-width: 1000px;
+}
\ No newline at end of file
diff --git a/www/head.css b/www/head.css
index 1825811..2aa66d2 100644
--- a/www/head.css
+++ b/www/head.css
@@ -89,6 +89,7 @@ div#bs-select-11::-webkit-scrollbar-track,
 div#bs-select-12::-webkit-scrollbar-track,
 #logText::-webkit-scrollbar-track, 
 #logTextFull::-webkit-scrollbar-track,
+#screening_fail::-webkit-scrollbar-track,
 .selectize-dropdown-content::-webkit-scrollbar-track,
 #mst_comm_general_select::-webkit-scrollbar-track {
 background: #F0F0F0;
@@ -109,6 +110,7 @@ div#bs-select-11::-webkit-scrollbar-thumb,
 div#bs-select-12::-webkit-scrollbar-thumb,
 #logText::-webkit-scrollbar-thumb, 
 #logTextFull::-webkit-scrollbar-thumb,
+#screening_fail::-webkit-scrollbar-thumb,
 .selectize-dropdown-content::-webkit-scrollbar-thumb,
 #mst_comm_general_select::-webkit-scrollbar-thumb {
   background: #bcbcbc;

From cba86073176e742fde811e394f86335abbf3285d Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Fri, 2 Aug 2024 11:17:25 +0200
Subject: [PATCH 29/75] Fixes in fasta formatting; assembly file saving

---
 App.R                            | 287 +++++++++++++++++++------------
 execute/check_duplicate_multi.R  |  92 ++++++----
 execute/check_duplicate_single.R |  88 +++++++---
 execute/multi_eval.R             |  63 +++++--
 execute/screening.sh             |   6 +-
 execute/single_eval.R            |  67 ++++++--
 execute/single_typing.sh         |   2 +-
 execute/variant_validation.R     |   2 +-
 www/body.css                     |  10 +-
 9 files changed, 418 insertions(+), 199 deletions(-)

diff --git a/App.R b/App.R
index ac7e57f..ecdf699 100644
--- a/App.R
+++ b/App.R
@@ -44,7 +44,7 @@ library(treeio)
 library(ggtree)
 library(ggtreeExtra)
 
-source("www/resources.R")
+source(paste0(getwd(), "/www/resources.R"))
 
 options(ignore.negative.edge=TRUE)
 
@@ -5339,10 +5339,14 @@ ui <- dashboardPage(
         ),
         br(),
         hr(),
-        column(
-          width = 12,
-          align = "left",
-          
+        br(), br(),
+        fluidRow(
+          column(1),
+          column(
+            width = 10,
+            div(class = "loci_table",
+                dataTableOutput("gs_isolate_table"))
+          )
         )
       )
     ) # End tabItems
@@ -5357,12 +5361,12 @@ server <- function(input, output, session) {
   
   phylotraceVersion <- paste("1.4.1")
   
-  # TODO Enable this, or leave disabled
-  # # Kill server on session end
-  # session$onSessionEnded( function() {
-  #   stopApp()
-  # })
-  
+  #TODO Enable this, or leave disabled
+  # Kill server on session end
+  session$onSessionEnded( function() {
+    stopApp()
+  })
+   
   # Disable various user inputs (visualization control)
   shinyjs::disable('mst_edge_label') 
   
@@ -5760,6 +5764,10 @@ server <- function(input, output, session) {
     file.remove(paste0(getwd(), "/execute/screening/output_file.tsv"))
   }
   
+  if(file.exists(paste0(getwd(), "/execute/screening/error.txt"))) {
+    file.remove(paste0(getwd(), "/execute/screening/error.txt"))
+  }
+  
   # Declare reactive variables
   Startup <- reactiveValues(sidebar = TRUE, 
                             header = TRUE) # reactive variables related to startup process
@@ -6215,29 +6223,31 @@ server <- function(input, output, session) {
             )
           )
         } else if(Screening$status == "finished") {
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp;<i> gene screening finalized</i>")), 
-                  style = "color:white;")
+          if(isTRUE(Screening$fail)) {
+            output$statustext <- renderUI(
+              fluidRow(
+                tags$li(
+                  class = "dropdown", 
+                  tags$span(HTML(
+                    paste('<i class="fa-solid fa-circle-dot" style="color:red !important;"></i>', 
+                          "Status:&nbsp;&nbsp;&nbsp;<i> gene screening failed</i>")), 
+                    style = "color:white;")
+                )
               )
             )
-          )
-        } else if(isTRUE(Screening$fail)) {
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:red !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp;<i> gene screening failed</i>")), 
-                  style = "color:white;")
+          } else {
+            output$statustext <- renderUI(
+              fluidRow(
+                tags$li(
+                  class = "dropdown", 
+                  tags$span(HTML(
+                    paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                          "Status:&nbsp;&nbsp;&nbsp;<i> gene screening finalized</i>")), 
+                    style = "color:white;")
+                )
               )
             )
-          )
+          }
         } else {
           output$statustext <- renderUI(
             fluidRow(
@@ -6322,6 +6332,8 @@ server <- function(input, output, session) {
         
         DB$data <- NULL
         
+        DB$meta_gs <- NULL
+        
         DB$meta <- NULL
         
         DB$meta_true <- NULL
@@ -6398,7 +6410,7 @@ server <- function(input, output, session) {
             menuItem(
               text = "Manage Schemes",
               tabName = "init",
-              icon = icon("plus"),
+              icon = icon("layer-group"),
               selected = TRUE
             ),
             menuItem(
@@ -6468,6 +6480,8 @@ server <- function(input, output, session) {
         
         DB$data <- NULL
         
+        DB$meta_gs <- NULL
+        
         DB$meta <- NULL
         
         DB$meta_true <- NULL
@@ -6563,7 +6577,7 @@ server <- function(input, output, session) {
                 menuItem(
                   text = "Manage Schemes",
                   tabName = "init",
-                  icon = icon("plus"),
+                  icon = icon("layer-group"),
                   selected = TRUE
                 ),
                 menuItem(
@@ -6653,7 +6667,7 @@ server <- function(input, output, session) {
                 menuItem(
                   text = "Manage Schemes",
                   tabName = "init",
-                  icon = icon("plus"),
+                  icon = icon("layer-group"),
                   selected = TRUE
                 ),
                 menuItem(
@@ -6745,7 +6759,7 @@ server <- function(input, output, session) {
                 menuItem(
                   text = "Manage Schemes",
                   tabName = "init",
-                  icon = icon("plus"),
+                  icon = icon("layer-group"),
                   selected = TRUE
                 ),
                 menuItem(
@@ -6866,7 +6880,7 @@ server <- function(input, output, session) {
                   menuItem(
                     text = "Manage Schemes",
                     tabName = "init",
-                    icon = icon("plus"),
+                    icon = icon("layer-group"),
                     selected = TRUE
                   ),
                   menuItem(
@@ -6919,8 +6933,8 @@ server <- function(input, output, session) {
                 DB$data <- Database[["Typing"]]
                 
                 if(!is.null(DB$data)){
-                  if ((ncol(DB$data)-12) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-                    cust_var <- select(DB$data, 13:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+                  if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+                    cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
                     DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
                   } else {
                     DB$cust_var <- data.frame()
@@ -6929,11 +6943,13 @@ server <- function(input, output, session) {
                 
                 DB$change <- FALSE
                 
-                DB$meta <- select(DB$data, 1:(12 + nrow(DB$cust_var)))
+                DB$meta_gs <- select(DB$data, c(1, 3:13))
+                
+                DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
                 
                 DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
                 
-                DB$allelic_profile <- select(DB$data, -(1:(12 + nrow(DB$cust_var))))
+                DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
                 
                 DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
                 
@@ -7050,7 +7066,7 @@ server <- function(input, output, session) {
                       menuItem(
                         text = "Manage Schemes",
                         tabName = "init",
-                        icon = icon("plus")
+                        icon = icon("layer-group")
                       ),
                       menuItem(
                         text = "Allelic Typing",
@@ -7117,7 +7133,7 @@ server <- function(input, output, session) {
                       menuItem(
                         text = "Manage Schemes",
                         tabName = "init",
-                        icon = icon("plus")
+                        icon = icon("layer-group")
                       ),
                       menuItem(
                         text = "Allelic Typing",
@@ -7724,7 +7740,7 @@ server <- function(input, output, session) {
                         if(!is.null(DB$data) & !is.null(DB$cust_var)) {
                           output$db_entries <- renderRHandsontable({
                             rhandsontable(
-                              select(DB$data, 1:(12 + nrow(DB$cust_var))),
+                              select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
                               error_highlight = err_thresh() - 1,                              
                               rowHeaders = NULL,
                               contextMenu = FALSE,
@@ -7819,7 +7835,7 @@ server <- function(input, output, session) {
                           if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
                             output$db_entries <- renderRHandsontable({
                               rhandsontable(
-                                select(DB$data, 1:(12 + nrow(DB$cust_var)), input$compare_select),
+                                select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)), input$compare_select),
                                 col_highlight = diff_allele() - 1,
                                 dup_names_high = duplicated_names() - 1,
                                 dup_ids_high = duplicated_ids() - 1,
@@ -7978,7 +7994,7 @@ server <- function(input, output, session) {
                           if(!is.null(DB$data) & !is.null(DB$cust_var)) {
                             output$db_entries <- renderRHandsontable({
                               rhandsontable(
-                                select(DB$data, 1:(12 + nrow(DB$cust_var))),
+                                select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
                                 rowHeaders = NULL,
                                 row_highlight = true_rows() - 1,
                                 dup_names_high = duplicated_names()- 1,
@@ -8117,7 +8133,7 @@ server <- function(input, output, session) {
                           if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
                             output$db_entries <- renderRHandsontable({
                               rhandsontable(
-                                select(DB$data, 1:(12 + nrow(DB$cust_var)), input$compare_select),
+                                select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)), input$compare_select),
                                 col_highlight = diff_allele() - 1,
                                 rowHeaders = NULL,
                                 height = table_height(),
@@ -8272,7 +8288,7 @@ server <- function(input, output, session) {
                           if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
                             output$db_entries <- renderRHandsontable({
                               rhandsontable(
-                                select(DB$data, 1:(12 + nrow(DB$cust_var))),
+                                select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
                                 rowHeaders = NULL,
                                 height = table_height(),
                                 dup_names_high = duplicated_names() - 1,
@@ -9022,6 +9038,8 @@ server <- function(input, output, session) {
                 
                 DB$meta <- NULL
                 
+                DB$meta_gs <- NULL
+                
                 DB$meta_true <- NULL
                 
                 DB$allelic_profile <- NULL
@@ -9057,7 +9075,7 @@ server <- function(input, output, session) {
                     menuItem(
                       text = "Manage Schemes",
                       tabName = "init",
-                      icon = icon("plus")
+                      icon = icon("layer-group")
                     ),
                     menuItem(
                       text = "Allelic Typing",
@@ -9415,7 +9433,7 @@ server <- function(input, output, session) {
               menuItem(
                 text = "Manage Schemes",
                 tabName = "init",
-                icon = icon("plus")
+                icon = icon("layer-group")
               ),
               menuItem(
                 text = "Allelic Typing",
@@ -9478,7 +9496,7 @@ server <- function(input, output, session) {
             menuItem(
               text = "Manage Schemes",
               tabName = "init",
-              icon = icon("plus")
+              icon = icon("layer-group")
             ),
             menuItem(
               text = "Allelic Typing",
@@ -9653,8 +9671,6 @@ server <- function(input, output, session) {
   # Change scheme
   observeEvent(input$reload_db, {
     
-    test <<- Screening$single_path$datapath
-    
     log_print("Input reload_db")
     
     if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
@@ -9724,8 +9740,8 @@ server <- function(input, output, session) {
     
     DB$data <- Data[["Typing"]]
     
-    if ((ncol(DB$data)-12) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-      cust_var <- select(DB$data, 13:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+    if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+      cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
       DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
     } else {
       DB$cust_var <- data.frame()
@@ -9737,11 +9753,13 @@ server <- function(input, output, session) {
     
     DB$no_na_switch <- TRUE
     
-    DB$meta <- select(DB$data, 1:(12 + nrow(DB$cust_var)))
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    
+    DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
     
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     
-    DB$allelic_profile <- select(DB$data, -(1:(12 + nrow(DB$cust_var))))
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
     
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
     
@@ -9753,7 +9771,7 @@ server <- function(input, output, session) {
           if(!is.null(DB$data) & !is.null(DB$cust_var)) {
             output$db_entries <- renderRHandsontable({
               rhandsontable(
-                select(DB$data, 1:(12 + nrow(DB$cust_var))),
+                select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
                 error_highlight = err_thresh() - 1,                              
                 rowHeaders = NULL,
                 contextMenu = FALSE,
@@ -9848,7 +9866,7 @@ server <- function(input, output, session) {
             if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
               output$db_entries <- renderRHandsontable({
                 rhandsontable(
-                  select(DB$data, 1:(12 + nrow(DB$cust_var)), input$compare_select),
+                  select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)), input$compare_select),
                   col_highlight = diff_allele() - 1,
                   dup_names_high = duplicated_names() - 1,
                   dup_ids_high = duplicated_ids() - 1,
@@ -10007,7 +10025,7 @@ server <- function(input, output, session) {
             if(!is.null(DB$data) & !is.null(DB$cust_var)) {
               output$db_entries <- renderRHandsontable({
                 rhandsontable(
-                  select(DB$data, 1:(12 + nrow(DB$cust_var))),
+                  select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
                   rowHeaders = NULL,
                   row_highlight = true_rows() - 1,
                   dup_names_high = duplicated_names()- 1,
@@ -10146,7 +10164,7 @@ server <- function(input, output, session) {
             if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
               output$db_entries <- renderRHandsontable({
                 rhandsontable(
-                  select(DB$data, 1:(12 + nrow(DB$cust_var)), input$compare_select),
+                  select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)), input$compare_select),
                   col_highlight = diff_allele() - 1,
                   rowHeaders = NULL,
                   height = table_height(),
@@ -10301,7 +10319,7 @@ server <- function(input, output, session) {
             if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
               output$db_entries <- renderRHandsontable({
                 rhandsontable(
-                  select(DB$data, 1:(12 + nrow(DB$cust_var))),
+                  select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
                   rowHeaders = NULL,
                   height = table_height(),
                   dup_names_high = duplicated_names() - 1,
@@ -10441,8 +10459,8 @@ server <- function(input, output, session) {
   
   observe({
     if(!is.null(DB$data)){
-      if ((ncol(DB$data)-12) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-        cust_var <- select(DB$data, 13:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+      if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+        cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
         DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
         
       } else {
@@ -10519,21 +10537,24 @@ server <- function(input, output, session) {
     
     if(input$new_var_type == "Categorical (character)") {
       DB$data <- DB$data %>%
-        mutate("{name}" := character(nrow(DB$data)), .after = 12)
+        mutate("{name}" := character(nrow(DB$data)), .after = 13)
       
       DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "categ"))
     } else {
       DB$data <- DB$data %>%
-        mutate("{name}" := numeric(nrow(DB$data)), .after = 12)
+        mutate("{name}" := numeric(nrow(DB$data)), .after = 13)
       
       DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "cont"))
     }
     
-    DB$meta <- select(DB$data, 1:(12 + nrow(DB$cust_var)))
+    
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    
+    DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
     
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     
-    DB$allelic_profile <- select(DB$data, -(1:(12 + nrow(DB$cust_var))))
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
     
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
     
@@ -10603,13 +10624,18 @@ server <- function(input, output, session) {
     log_print(paste0("Variable ", input$del_which_var, " removed"))
     
     DB$cust_var <- DB$cust_var[-which(DB$cust_var$Variable == input$del_which_var),]
+    
     DB$data <- select(DB$data, -(input$del_which_var))
-    DB$meta <- select(DB$data, 1:(12 + nrow(DB$cust_var)))
+    
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    
+    DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
+    
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     
-    DB$allelic_profile <- select(DB$data, -(1:(12 + nrow(DB$cust_var))))
-    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
     
+    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
   })
   
   # Select all button
@@ -10818,8 +10844,8 @@ server <- function(input, output, session) {
     DB$data <- Database[["Typing"]]
     
     if(!is.null(DB$data)){
-      if ((ncol(DB$data)-12) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-        cust_var <- select(DB$data, 13:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+      if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+        cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
         DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
       } else {
         DB$cust_var <- data.frame()
@@ -10832,11 +10858,13 @@ server <- function(input, output, session) {
     
     DB$no_na_switch <- TRUE
     
-    DB$meta <- select(DB$data, 1:(12 + nrow(DB$cust_var)))
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    
+    DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
     
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     
-    DB$allelic_profile <- select(DB$data, -(1:(12 + nrow(DB$cust_var))))
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
     
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
     
@@ -10953,11 +10981,13 @@ server <- function(input, output, session) {
     
     DB$data <- DB$data[!(DB$data$Index %in% as.numeric(input$select_delete)),]
     
-    DB$meta <- select(DB$data, 1:(12 + nrow(DB$cust_var)))
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    
+    DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
     
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     
-    DB$allelic_profile <- select(DB$data, -(1:(12 + nrow(DB$cust_var))))
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
     
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
     
@@ -11589,33 +11619,34 @@ server <- function(input, output, session) {
     )
   })
   
-  # Download Target Info (CSV Table)
-  observe({
-    input$download_cgMLST
-    
-    scheme_overview <- read_html(Scheme$link_scheme) %>%
-      html_table(header = FALSE) %>%
-      as.data.frame(stringsAsFactors = FALSE)
-    
-    last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"], 
-                                   format = "%B %d, %Y, %H:%M %p")
-    names(scheme_overview) <- NULL
-    
-    last_file_change <- format(
-      file.info(file.path(DB$database,
-                          ".downloaded_schemes",
-                          paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
-    
-    output$cgmlst_scheme <- renderTable({scheme_overview})
-    output$scheme_update_info <- renderText({
-      req(last_file_change)
-      if (last_file_change < last_scheme_change) {
-        "(Newer scheme available \u274c)"
-      } else {
-        "(Scheme is up-to-date \u2705)"
-      }
-    })
-  })
+  # Download Target Info (CSV Table)#
+  #TODO
+  # observe({
+  #   input$download_cgMLST
+  #   
+  #   scheme_overview <- read_html(Scheme$link_scheme) %>%
+  #     html_table(header = FALSE) %>%
+  #     as.data.frame(stringsAsFactors = FALSE)
+  #   
+  #   last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"], 
+  #                                  format = "%B %d, %Y, %H:%M %p")
+  #   names(scheme_overview) <- NULL
+  #   
+  #   last_file_change <- format(
+  #     file.info(file.path(DB$database,
+  #                         ".downloaded_schemes",
+  #                         paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
+  #   
+  #   output$cgmlst_scheme <- renderTable({scheme_overview})
+  #   output$scheme_update_info <- renderText({
+  #     req(last_file_change)
+  #     if (last_file_change < last_scheme_change) {
+  #       "(Newer scheme available \u274c)"
+  #     } else {
+  #       "(Scheme is up-to-date \u2705)"
+  #     }
+  #   })
+  # })
   
   # _______________________ ####
   
@@ -17590,7 +17621,7 @@ server <- function(input, output, session) {
                          label = label_mst(),
                          value = mst_node_scaling(),
                          opacity = node_opacity())
-    test <<- Typing$data
+    
     ctxRendererJS <- htmlwidgets::JS("({ctx, id, x, y, state: { selected, hover }, style, font, label, metadata}) => {
                             var pieData = JSON.parse(metadata);
                             var radius = style.size;
@@ -17788,14 +17819,10 @@ server <- function(input, output, session) {
     } else {
       legend <- Typing$var_cols
       names(legend)[1] <- "label"
-      legend <- mutate(legend, shape = "dot",
+      mutate(legend, shape = "dot",
              font.color = input$mst_legend_color,
              size = input$mst_symbol_size,
              font.size = input$mst_font_size)
-      
-      legend1 <<- legend
-      dnode <<- Typing$data$nodes
-      legend
     }
   })
   
@@ -22269,6 +22296,32 @@ server <- function(input, output, session) {
   
   ### Render UI Elements ----
   
+  observe({
+    req(DB$meta)
+    output$gs_isolate_table <- renderDataTable(
+      DB$meta_gs,
+      selection = "single",
+      rownames= FALSE,
+      options = list(pageLength = 10,
+                     columnDefs = list(list(searchable = TRUE,
+                                            targets = "_all")),
+                     initComplete = DT::JS(
+                       "function(settings, json) {",
+                       "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                       "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                       "}"
+                     ),
+                     drawCallback = DT::JS(
+                       "function(settings) {",
+                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                       "}"
+                     ))
+    )
+  })
+  
   output$screening_results <- renderUI({
     if(!is.null(Screening$results)) {
       dataTableOutput("screening_table")
@@ -22430,7 +22483,8 @@ server <- function(input, output, session) {
             width = 10,
             br(), br(), br(), br(),
             uiOutput("screening_results"),
-            verbatimTextOutput("screening_fail")
+            verbatimTextOutput("screening_fail"),
+            br(), br(), br(), br(), br(), br()
           )
         )
       )
@@ -22593,10 +22647,24 @@ server <- function(input, output, session) {
         Screening$results <- read.delim(paste0(getwd(), "/execute/screening/output_file.tsv"))
         Screening$status <- "finished"
         log_print("Finalized gene screening")
+        show_toast(
+          title = "Successful gene screening",
+          type = "success",
+          position = "bottom-end",
+          width = "500px",
+          timer = 6000
+        )
       } else if(file.exists(paste0(getwd(), "/execute/screening/error.txt"))) {
         Screening$status <- "finished"
         log_print("Failed gene screening")
         Screening$fail <- TRUE
+        show_toast(
+          title = "Failed gene screening",
+          type = "error",
+          position = "bottom-end",
+          width = "500px",
+          timer = 6000
+        )
       }
     }
   })
@@ -22682,6 +22750,7 @@ server <- function(input, output, session) {
         if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
           output$typing_result_table <- renderRHandsontable({
             Typing$typing_result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
+            Typing$typing_result_table <- mutate_all(Typing$typing_result_table, as.character)
             if(nrow(Typing$typing_result_table) > 0) {
               if(nrow(Typing$typing_result_table) > 15) {
                 rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
diff --git a/execute/check_duplicate_multi.R b/execute/check_duplicate_multi.R
index 21b995e..fe0cf12 100644
--- a/execute/check_duplicate_multi.R
+++ b/execute/check_duplicate_multi.R
@@ -1,35 +1,33 @@
 library(logr)
-# Get the command line arguments
-args <- commandArgs(trailingOnly = TRUE)
-
-# Access the first argument
-base_path <- args[1]
-
-# Get selected assembly file names
-file_names <- list.files(paste0(getwd(), "/selected_genomes"), full.names = T)
-
-# Function to log messages 
-log.message <- function(log_file, message) {
-  cat(format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "-", message, "\n", file = log_file, append = TRUE)
-}
 
-logfile <- file.path(paste0(base_path, "/logs/check_duplicate_multi.log"))
-
-log <- log_open(logfile, logdir = FALSE)
-
-log_print("Initiated multi typing fasta name duplicates check")
-
-# load selected assemblies
-assemblies <- lapply(list.files(paste0(getwd(), "/selected_genomes"), full.names = T), readLines)
-
-# loop through every assembly
-for(i in 1:length(assemblies)){
-  names <- stringr::str_extract(assemblies[[i]][seq(1, length(assemblies[[i]]), by = 3)], "^[^\\s]+")
+process_fasta <- function(fasta_path) {
+  # Read the FASTA file into a data.table
+  dt <- data.table::fread(fasta_path, header = FALSE, sep = "\n", col.names = "line", data.table = TRUE)
+  
+  # Identify headers and sequence lines
+  dt[, is_header := grepl("^>", line)]
+  
+  # Create a group identifier for each sequence based on headers
+  dt[, group := cumsum(is_header)]
+  
+  # Process each group to concatenate sequences, keeping headers as is
+  result <- dt[, .(header = line[1], 
+                   sequence = paste(line[!is_header], collapse = "")), 
+               by = group]
+  
+  # Prepare the final output as a character vector
+  # Ensure exactly one empty line between sequence end and next header
+  output <- unlist(result[, .(output = c(header, sequence, "")), by = group]$output)
+  
+  # Remove the last empty line to avoid trailing empty line in the file
+  output <- output[-length(output)]
+  
+  names <- stringr::str_extract(output[seq(1, length(output), by = 3)], "^[^\\s]+")
   
   # Test if there are duplicates
   if(length(names) != length(unique(names))){
     
-    log_print(paste0("Duplicate(s) present in ", basename(file_names[i])))
+    log_print(paste0("Duplicate(s) present in ", basename(fasta_path)))
     
     # add a number to the duplicates
     for(j in 1:length(names)){
@@ -41,12 +39,46 @@ for(i in 1:length(assemblies)){
     
     # substitute the respective lines in the file with the new names 
     for(k in 1:length(names)){
-      assemblies[[i]][3*k - 2] <- paste0(names[k])
+      output[3*k - 2] <- paste0(names[k])
     }
     
-    # save the new assembly 
-    writeLines(assemblies[[i]], file_names[i])
-  } 
+    # save formatted fasta
+    writeLines(output, fasta_path) 
+    
+    # Return invisible NULL to suppress output
+    invisible(NULL)
+    
+  } else {
+    
+    # save formatted fasta
+    writeLines(output, fasta_path) 
+    
+    # Return invisible NULL to suppress output
+    invisible(NULL)
+  }
 }
 
+# Get the command line arguments
+args <- commandArgs(trailingOnly = TRUE)
+
+# Access the first argument
+base_path <- args[1]
+
+# Get selected assembly file names
+assemblies <- list.files(paste0(getwd(), "/selected_genomes"), full.names = T)
+
+# Function to log messages 
+log.message <- function(log_file, message) {
+  cat(format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "-", message, "\n", file = log_file, append = TRUE)
+}
+
+logfile <- file.path(paste0(base_path, "/logs/check_duplicate_multi.log"))
+
+log <- log_open(logfile, logdir = FALSE)
+
+log_print("Initiated multi typing fasta check and formatting")
+
+# Check and format fasta of assemblies
+invisible(lapply(assemblies, process_fasta))
+
 log_close()
diff --git a/execute/check_duplicate_single.R b/execute/check_duplicate_single.R
index ae111e2..d5ea766 100644
--- a/execute/check_duplicate_single.R
+++ b/execute/check_duplicate_single.R
@@ -1,4 +1,63 @@
 library(logr)
+
+process_fasta <- function(fasta_path) {
+  # Read the FASTA file into a data.table
+  dt <- data.table::fread(fasta_path, header = FALSE, sep = "\n", col.names = "line", data.table = TRUE)
+  
+  # Identify headers and sequence lines
+  dt[, is_header := grepl("^>", line)]
+  
+  # Create a group identifier for each sequence based on headers
+  dt[, group := cumsum(is_header)]
+  
+  # Process each group to concatenate sequences, keeping headers as is
+  result <- dt[, .(header = line[1], 
+                   sequence = paste(line[!is_header], collapse = "")), 
+               by = group]
+  
+  # Prepare the final output as a character vector
+  # Ensure exactly one empty line between sequence end and next header
+  output <- unlist(result[, .(output = c(header, sequence, "")), by = group]$output)
+  
+  # Remove the last empty line to avoid trailing empty line in the file
+  output <- output[-length(output)]
+  
+  names <- stringr::str_extract(output[seq(1, length(output), by = 3)], "^[^\\s]+")
+  
+  # Test if there are duplicates
+  if(length(names) != length(unique(names))){
+    
+    log_print(paste0("Duplicate(s) present in ", basename(fasta_path)))
+    
+    # add a number to the duplicates
+    for(j in 1:length(names)){
+      if(sum(names == names[j]) > 1){
+        indices <- which(names == names[j])
+        names[j] <- paste0(names[j], "_", which(names == names[j]))
+      }
+    }
+    
+    # substitute the respective lines in the file with the new names 
+    for(k in 1:length(names)){
+      output[3*k - 2] <- paste0(names[k])
+    }
+    
+    # save formatted fasta
+    writeLines(output, paste0(getwd(), "/blat_single/", basename(fasta_path))) 
+    
+    # Return invisible NULL to suppress output
+    invisible(NULL)
+    
+  } else {
+    
+    # save formatted fasta
+    writeLines(output, paste0(getwd(), "/blat_single/", basename(fasta_path)))
+    
+    # Return invisible NULL to suppress output
+    invisible(NULL)
+  }
+}
+
 typing_meta <- readRDS(paste0(getwd(), "/single_typing_df.rds"))
 
 # Function to log messages 
@@ -14,32 +73,7 @@ log_print("Initiated single typing fasta name duplicates check")
 
 assembly <- typing_meta$genome
 
-lines <- readLines(assembly)
-
-names <- stringr::str_extract(lines[seq(1, length(lines), by = 3)], "^[^\\s]+")
-
-# Test if there are duplicates
-if(length(names) != length(unique(names))) {
-  
-  log_print(paste0("Duplicate(s) present in ", basename(assembly)))
-  
-  # add a number to the duplicates
-  for(i in 1:length(names)) {
-    if(sum(names == names[i]) > 1) {
-      indices <- which(names == names[i])
-      names[i] <- paste0(names[i], "_", indices[which(indices == i)])
-    }
-  }
-  
-  # substitute the respective lines in the file with the new names 
-  for(i in 1:length(names)) {
-    lines[3*i - 2] <- paste0(names[i])
-  }
-  
-  # save the new assembly to working directory
-  writeLines(lines, paste0(getwd(), "/blat_single/assembly.fasta"))
-} else {
-  writeLines(lines, paste0(getwd(), "/blat_single/assembly.fasta"))
-}
+# Check and format fasta of assemblies
+invisible(lapply(assembly, process_fasta))
 
 log_close()
diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index d2c19f3..6a12612 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -167,7 +167,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
       data.frame(matrix(
         NA,
         nrow = 0,
-        ncol = 12 + length(psl_files)
+        ncol = 13 + length(psl_files)
       ))
     
     metadata <-
@@ -183,7 +183,8 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
         meta_info$append_city,
         as.character(meta_info$append_analysisdate),
         length(allele_vector) - sum(sapply(allele_vector, is.na)),
-        sum(sapply(allele_vector, is.na))
+        sum(sapply(allele_vector, is.na)),
+        "No"
       )
     
     new_row <- c(metadata, allele_vector)
@@ -205,16 +206,17 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
           "City",
           "Typing Date",
           "Successes",
-          "Errors"
+          "Errors",
+          "Screened"
         ),
         gsub(".fasta", "", basename(list.files(allele_folder)))
       )
     
     Database[["Typing"]] <- Typing
     
-    df2 <- dplyr::mutate_all(dplyr::select(Database$Typing, 13:(12+length(list.files(allele_folder)))), function(x) as.character(x))
+    df2 <- dplyr::mutate_all(dplyr::select(Database$Typing, 14:(13+length(list.files(allele_folder)))), function(x) as.character(x))
     
-    df1 <- dplyr::select(Database$Typing, 1:12)
+    df1 <- dplyr::select(Database$Typing, 1:13)
     df1 <- dplyr::mutate(df1, Include = as.logical(Include))
     
     Typing <- cbind(df1, df2)
@@ -238,12 +240,13 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
         meta_info$append_city,
         as.character(meta_info$append_analysisdate),
         length(allele_vector) - sum(sapply(allele_vector, is.na)),
-        sum(sapply(allele_vector, is.na))
+        sum(sapply(allele_vector, is.na)),
+        "No"
       )
     
-    if ((ncol(Database$Typing)-12) != length(allele_vector)) {
+    if ((ncol(Database$Typing)-13) != length(allele_vector)) {
       
-      cust_var <- dplyr::select(Database$Typing, 13:(ncol(Database$Typing) - length(allele_vector)))
+      cust_var <- dplyr::select(Database$Typing, 14:(ncol(Database$Typing) - length(allele_vector)))
       cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
       
       class_df <- data.frame()
@@ -262,7 +265,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
     
     merged <- cbind(metadata, df_profile)
     
-    if ((ncol(Database$Typing)-12) != length(allele_vector)) {
+    if ((ncol(Database$Typing)-13) != length(allele_vector)) {
       names_vec <- character(0)
       # Add new columns to df1
       for (i in 1:nrow(cust_var)) {
@@ -283,7 +286,8 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
             "City",
             "Typing Date",
             "Successes",
-            "Errors"
+            "Errors",
+            "Screened"
           ),
           names_vec,
           gsub(".fasta", "", basename(list.files(allele_folder)))
@@ -303,7 +307,8 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
             "City",
             "Typing Date",
             "Successes",
-            "Errors"
+            "Errors",
+            "Screened"
           ),
           gsub(".fasta", "", basename(list.files(allele_folder)))
         )
@@ -318,6 +323,42 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
   # Save new Entry in Typing Database
   saveRDS(Database, paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Typing.rds"))
   
+  if(dir.exists(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates"))) {
+    
+    # Create folder for new isolate
+    dir.create(paste0(db_path, "/", 
+                      gsub(" ", "_", meta_info$cgmlst_typing), 
+                      "/Isolates/", basename(assembly)))
+    
+    # Copy assembly file in isolate directory
+    file.copy(assembly, paste0(db_path, "/", 
+                               gsub(" ", "_", meta_info$cgmlst_typing), 
+                               "/Isolates/", basename(assembly)))
+    
+    log_print(paste0("Saved assembly of ", basename(assembly)))
+    
+  } else {
+    
+    log_print("No isolate folder present yet. Isolate directory created.")
+    
+    # Create isolate filder for species
+    dir.create(paste0(db_path, "/", 
+                      gsub(" ", "_", meta_info$cgmlst_typing), 
+                      "/Isolates"))
+    
+    # Create folder for new isolate
+    dir.create(paste0(db_path, "/", 
+                      gsub(" ", "_", meta_info$cgmlst_typing), 
+                      "/Isolates/", basename(assembly)))
+    
+    # Copy assembly file in isolate directory
+    file.copy(assembly, paste0(db_path, "/", 
+                               gsub(" ", "_", meta_info$cgmlst_typing), 
+                               "/Isolates/", basename(assembly)))
+    
+    log_print(paste0("Saved assembly of ", basename(assembly)))
+  }
+  
   # Logging successes
   log.message(log_file = paste0(getwd(), "/logs/script_log.txt"), 
               message = paste0("Successful typing of ", sub("\\.(fasta|fna|fa)$", "", basename(assembly))))
diff --git a/execute/screening.sh b/execute/screening.sh
index f0ed3d0..75b0351 100755
--- a/execute/screening.sh
+++ b/execute/screening.sh
@@ -44,11 +44,7 @@ fi
 
 mkdir "$base_path/execute/screening"
 
-# Get cores
-coresall=$(nproc --all)
-cores=$((num_processors - 2))
-
-amrfinder -n "$path_assembly" --threads $cores --plus --organism $species -o "screening/output_file.tsv" > amrfinder_stdout.txt 2> amrfinder_stderr.txt
+amrfinder -n "$path_assembly" --plus --organism $species -o "screening/output_file.tsv" > amrfinder_stdout.txt 2> amrfinder_stderr.txt
 status=$?
 
 # Check if status variable is set and is an integer
diff --git a/execute/single_eval.R b/execute/single_eval.R
index 9b65f81..098a17d 100644
--- a/execute/single_eval.R
+++ b/execute/single_eval.R
@@ -3,7 +3,9 @@ library(logr)
 # Hand over variables
 meta_info <- readRDS("meta_info_single.rds")
 db_path <- readRDS("single_typing_df.rds")[, "db_path"]
-assembly <- paste0(meta_info$db_directory, "/execute/blat_single/assembly.fasta")
+file_list <- list.files(paste0(meta_info$db_directory, "/execute/blat_single"), 
+                        full.names = TRUE)
+assembly <- file_list[which(list.files(paste0(meta_info$db_directory, "/execute/blat_single")) != "results")]
 
 source("variant_validation.R")
 
@@ -147,7 +149,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
     
     Database <- list(Typing = data.frame())
     
-    Typing <- data.frame(matrix(NA, nrow = 0, ncol = 12 + length(psl_files)))
+    Typing <- data.frame(matrix(NA, nrow = 0, ncol = 13 + length(psl_files)))
     
     metadata <- c(
       1,
@@ -161,7 +163,8 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
       meta_info$append_city,
       as.character(meta_info$append_analysisdate),
       length(allele_vector) - sum(sapply(allele_vector, is.na)),
-      sum(sapply(allele_vector, is.na))
+      sum(sapply(allele_vector, is.na)),
+      "No"
     )
     
     new_row <- c(metadata, allele_vector)
@@ -182,16 +185,17 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
           "City",
           "Typing Date",
           "Successes",
-          "Errors"
+          "Errors",
+          "Screened"
         ),
         gsub(".fasta", "", basename(list.files(allele_folder)))
       )
     
     Database[["Typing"]] <- Typing
     
-    df2 <- dplyr::mutate_all(dplyr::select(Database$Typing, 13:(12+length(list.files(allele_folder)))), function(x) as.character(x))
+    df2 <- dplyr::mutate_all(dplyr::select(Database$Typing, 14:(13+length(list.files(allele_folder)))), function(x) as.character(x))
     
-    df1 <- dplyr::select(Database$Typing, 1:12)
+    df1 <- dplyr::select(Database$Typing, 1:13)
     df1 <- dplyr::mutate(df1, Include = as.logical(Include))
     
     Typing <- cbind(df1, df2)
@@ -215,12 +219,13 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
         meta_info$append_city,
         as.character(meta_info$append_analysisdate),
         length(allele_vector) - sum(sapply(allele_vector, is.na)),
-        sum(sapply(allele_vector, is.na))
+        sum(sapply(allele_vector, is.na)),
+        "No"
       )
     
-    if ((ncol(Database$Typing)-12) != length(allele_vector)) {
+    if ((ncol(Database$Typing)-13) != length(allele_vector)) {
       
-      cust_var <- dplyr::select(Database$Typing, 13:(ncol(Database$Typing) - length(allele_vector)))
+      cust_var <- dplyr::select(Database$Typing, 14:(ncol(Database$Typing) - length(allele_vector)))
       cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
       
       class_df <- data.frame()
@@ -239,7 +244,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
     
     merged <- cbind(metadata, df_profile)
     
-    if ((ncol(Database$Typing)-12) != length(allele_vector)) {
+    if ((ncol(Database$Typing)-13) != length(allele_vector)) {
       names_vec <- character(0)
       # Add new columns to df1
       for (i in 1:nrow(cust_var)) {
@@ -260,7 +265,8 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
             "City",
             "Typing Date",
             "Successes",
-            "Errors"
+            "Errors",
+            "Screened"
           ),
           names_vec,
           gsub(".fasta", "", basename(list.files(allele_folder)))
@@ -280,7 +286,8 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
             "City",
             "Typing Date",
             "Successes",
-            "Errors"
+            "Errors",
+            "Screened"
           ),
           gsub(".fasta", "", basename(list.files(allele_folder)))
         )
@@ -300,6 +307,42 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
               message = paste0("Successful typing of ", meta_info$assembly_name))
   log_print(paste0("Successful typing of ", meta_info$assembly_name))
   
+  if(dir.exists(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates"))) {
+    
+    # Create folder for new isolate
+    dir.create(paste0(db_path, "/", 
+                      gsub(" ", "_", meta_info$cgmlst_typing), 
+                      "/Isolates/", meta_info$assembly_id))
+    
+    # Copy assembly file in isolate directory
+    file.copy(assembly, paste0(db_path, "/", 
+                               gsub(" ", "_", meta_info$cgmlst_typing), 
+                               "/Isolates/", meta_info$assembly_id))
+    
+    log_print(paste0("Saved assembly of ", meta_info$assembly_id))
+    
+  } else {
+    
+    log_print("No isolate folder present yet. Isolate directory created.")
+    
+    # Create isolate filder for species
+    dir.create(paste0(db_path, "/", 
+                      gsub(" ", "_", meta_info$cgmlst_typing), 
+                      "/Isolates"))
+    
+    # Create folder for new isolate
+    dir.create(paste0(db_path, "/", 
+                      gsub(" ", "_", meta_info$cgmlst_typing), 
+                      "/Isolates/", meta_info$assembly_id))
+    
+    # Copy assembly file in isolate directory
+    file.copy(assembly, paste0(db_path, "/", 
+                               gsub(" ", "_", meta_info$cgmlst_typing), 
+                               "/Isolates/", meta_info$assembly_id))
+    
+    log_print(paste0("Saved assembly of ", meta_info$assembly_id))
+  }
+  
 } else {
   
   failures <- sum(unname(base::sapply(psl_files, file.size)) <= 100) / length(psl_files) * 100
diff --git a/execute/single_typing.sh b/execute/single_typing.sh
index a41d05a..2b0490f 100755
--- a/execute/single_typing.sh
+++ b/execute/single_typing.sh
@@ -37,7 +37,7 @@ mkdir "$results"
 # Check assembly file and save in the execute folder
 Rscript "$base_path/execute/check_duplicate_single.R"
 wait
-genome="$base_path/execute/blat_single/assembly.fasta"
+genome="$base_path/execute/blat_single/$genome_name"
 
 # Run parallelized BLAT
 find "$alleles" -type f \( -name "*.fasta" -o -name "*.fa" -o -name "*.fna" \) | parallel pblat $genome {} "$results/{/.}.psl" > /dev/null 2>&1
diff --git a/execute/variant_validation.R b/execute/variant_validation.R
index 9c9524e..8144843 100644
--- a/execute/variant_validation.R
+++ b/execute/variant_validation.R
@@ -104,7 +104,7 @@ variant_validation <- function(references, start_codons, stop_codons) {
   for(i in 1:nrow(references)){
     
     # extract new variant sequence from template
-    contig <- template[(which(template == paste0(">", references$V14[i])) + 1)]
+    contig <- template[(which(sub(" .*", "", template) == paste0(">", references$V14[i])) + 1)]
     
     seq <- substring(contig, references$V16[i] + 1, references$V17[i])
     
diff --git a/www/body.css b/www/body.css
index 28d78c4..127cbc5 100644
--- a/www/body.css
+++ b/www/body.css
@@ -724,9 +724,13 @@ background: #20E6E5;
 
 /* Typing */
   
-  .mult_res_sel {
-    margin-bottom: 15px;
-  }
+.mult_res_sel {
+  margin-bottom: 15px;
+}
+
+#multi_typing_results .mult_res_sel .selectize-input.items.full.has-options.has-items {
+  width: auto;
+}
 
 body > div.htDatepickerHolder > div > div > table > tbody > tr > td.is-today.is-selected > button{
   color: white;

From b34f4a30bc218d5c884754ef3b4c3d4a77677f58 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Sun, 4 Aug 2024 19:00:29 +0200
Subject: [PATCH 30/75] UI improvements; User feedback for multi typing;
 Robustified multi typing

---
 App.R                 | 1771 +++++++++++++++++++++++++++--------------
 execute/multi_eval.R  |   72 +-
 execute/single_eval.R |   72 +-
 www/body.css          |  138 +++-
 4 files changed, 1391 insertions(+), 662 deletions(-)

diff --git a/App.R b/App.R
index ecdf699..0107f47 100644
--- a/App.R
+++ b/App.R
@@ -549,11 +549,13 @@ ui <- dashboardPage(
       
       tabItem(
         tabName = "typing",
-        fluidRow(column(
+        fluidRow(
+          column(
           width = 3,
           align = "center",
           h2(p("Generate Allelic Profile"), style = "color:white")
-        )),
+          )
+        ),
         hr(),
         uiOutput("typing_no_db"),
         conditionalPanel(
@@ -563,7 +565,7 @@ ui <- dashboardPage(
             uiOutput("single_typing_progress"),
             column(1),
             uiOutput("metadata_single_box"),
-            column(width = 1),
+            column(1),
             uiOutput("start_typing_ui")
           )
         ),
@@ -5305,14 +5307,14 @@ ui <- dashboardPage(
       tabItem(
         tabName = "gs_screening",
         fluidRow(
-          column(1),
           column(
             width = 3,
-            align = "left",
-            h2(p("Gene Screening"), style = "color:white")
+            align = "center",
+            h2(p("Gene Screening"), style = "color:white; margin-bottom: -20px;")
           ),
           column(
             width = 7,
+            align = "left",
             uiOutput("gene_screening_info")
           )
         ),
@@ -5326,14 +5328,14 @@ ui <- dashboardPage(
       tabItem(
         tabName = "gs_profile",
         fluidRow(
-          column(1),
           column(
             width = 3,
             align = "left",
-            h2(p("Resistance Profiles"), style = "color:white")
+            h2(p("Resistance Profiles"), style = "color:white; margin-bottom: -20px")
           ),
           column(
             width = 7,
+            align = "left",
             uiOutput("gene_resistance_info")
           )
         ),
@@ -5671,6 +5673,29 @@ server <- function(input, output, session) {
     groups
   }
   
+  #Function to check for duplicate isolate IDs for multi typing start
+  dupl_mult_id <- reactive({
+    req(Typing$multi_sel_table, DB$data)
+    if(!is.null(Typing$new_table)) {
+      selection <- Typing$new_table[which(unlist(Typing$new_table$Files) %in% unlist(DB$data["Assembly ID"])),]
+      as.numeric(rownames(selection[selection$Include == TRUE,]))
+    } else {
+      selection <- Typing$multi_sel_table[which(unlist(Typing$multi_sel_table$Files) %in% unlist(DB$data["Assembly ID"])),]
+      as.numeric(rownames(selection[selection$Include == TRUE,]))
+    }
+  })
+  
+  dupl_mult_id_names <- reactive({
+    req(Typing$multi_sel_table, DB$data)
+    if(!is.null(Typing$new_table)) {
+      selection <- Typing$new_table[which(unlist(Typing$new_table$Files) %in% unlist(DB$data["Assembly ID"])),]
+      selection$Files
+    } else {
+      selection <- Typing$multi_sel_table[which(unlist(Typing$multi_sel_table$Files) %in% unlist(DB$data["Assembly ID"])),]
+      selection$Files
+    }
+  })
+  
   # Function to check single typing log file
   check_new_entry <- reactive({
     
@@ -5962,7 +5987,8 @@ server <- function(input, output, session) {
           br(),
           actionButton(
             "load",
-            "Create"
+            "Create",
+            class = "load-start"
           )
         )
       } else if(length(DB$available) > 0 & !(DB$select_new)) {
@@ -5990,7 +6016,8 @@ server <- function(input, output, session) {
             br(),
             actionButton(
               "load",
-              "Load"
+              "Load",
+              class = "load-start"
             )
           )
         } else {
@@ -6008,7 +6035,8 @@ server <- function(input, output, session) {
             br(), br(),
             actionButton(
               "load",
-              "Load"
+              "Load",
+              class = "load-start"
             )
           )
         }
@@ -6039,7 +6067,8 @@ server <- function(input, output, session) {
             br(),
             actionButton(
               "load",
-              "Load"
+              "Load",
+              class = "load-start"
             )
           )
         } else {
@@ -6057,7 +6086,8 @@ server <- function(input, output, session) {
             br(), br(),
             actionButton(
               "load",
-              "Load"
+              "Load",
+              class = "load-start"
             )
           )
         }
@@ -6075,7 +6105,8 @@ server <- function(input, output, session) {
           br(),
           actionButton(
             "load",
-            "Load"
+            "Load",
+            class = "load-start"
           )
         )
       }
@@ -6422,7 +6453,7 @@ server <- function(input, output, session) {
               text = "Gene Screening",
               tabName = "gene_screening",
               icon = icon("dna"),
-              startExpanded = FALSE,
+              startExpanded = TRUE,
               menuSubItem(
                 text = "Screen Assembly",
                 tabName = "gs_screening"
@@ -6589,7 +6620,7 @@ server <- function(input, output, session) {
                   text = "Gene Screening",
                   tabName = "gene_screening",
                   icon = icon("dna"),
-                  startExpanded = FALSE,
+                  startExpanded = TRUE,
                   menuSubItem(
                     text = "Screen Assembly",
                     tabName = "gs_screening"
@@ -6679,7 +6710,7 @@ server <- function(input, output, session) {
                   text = "Gene Screening",
                   tabName = "gene_screening",
                   icon = icon("dna"),
-                  startExpanded = FALSE,
+                  startExpanded = TRUE,
                   menuSubItem(
                     text = "Screen Assembly",
                     tabName = "gs_screening"
@@ -6771,7 +6802,7 @@ server <- function(input, output, session) {
                   text = "Gene Screening",
                   tabName = "gene_screening",
                   icon = icon("dna"),
-                  startExpanded = FALSE,
+                  startExpanded = TRUE,
                   menuSubItem(
                     text = "Screen Assembly",
                     tabName = "gs_screening"
@@ -6892,7 +6923,7 @@ server <- function(input, output, session) {
                     text = "Gene Screening",
                     tabName = "gene_screening",
                     icon = icon("dna"),
-                    startExpanded = FALSE,
+                    startExpanded = TRUE,
                     menuSubItem(
                       text = "Screen Assembly",
                       tabName = "gs_screening"
@@ -7002,34 +7033,41 @@ server <- function(input, output, session) {
                 
                 output$initiate_typing_ui <- renderUI({
                   column(
-                    width = 3,
+                    width = 4,
                     align = "center",
                     br(),
                     br(),
-                    h3(p("Initiate Typing"), style = "color:white"),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
                     br(),
                     br(),
                     p(
                       HTML(
                         paste(
-                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Assembly File')
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
                         )
                       )
                     ),
-                    shinyFilesButton(
-                      "genome_file",
-                      "Browse",
-                      icon = icon("folder-open"),
-                      title = "Please select the genome in .fasta/.fna/.fa format:",
-                      multiple = FALSE,
-                      buttonType = "default",
-                      class = NULL,
-                      filetypes = c('fasta', 'fna', 'fa'),
-                      root = path_home()
-                    ),
-                    br(),
-                    br(),
-                    uiOutput("genome_path")
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyFilesButton(
+                          "genome_file",
+                          "Browse" ,
+                          icon = icon("file"),
+                          title = "Select the assembly in .fasta/.fna/.fa format:",
+                          multiple = FALSE,
+                          buttonType = "default",
+                          class = NULL,
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("genome_path"),
+                        br()
+                      )
+                    )
                   )
                 })
                 
@@ -7077,7 +7115,7 @@ server <- function(input, output, session) {
                         text = "Gene Screening",
                         tabName = "gene_screening",
                         icon = icon("dna"),
-                        startExpanded = FALSE,
+                        startExpanded = TRUE,
                         menuSubItem(
                           text = "Screen Assembly",
                           tabName = "gs_screening"
@@ -8523,7 +8561,7 @@ server <- function(input, output, session) {
                           align = "center",
                           actionButton(
                             "sel_all_entries",
-                            "Select all",
+                            "Select All",
                             icon = icon("check")
                           )
                         ),
@@ -8532,7 +8570,7 @@ server <- function(input, output, session) {
                           align = "left",
                           actionButton(
                             "desel_all_entries",
-                            "Deselect all",
+                            "Deselect All",
                             icon = icon("xmark")
                           )
                         )
@@ -22369,34 +22407,22 @@ server <- function(input, output, session) {
   # Availablity feedback
   output$gene_screening_info <- renderUI({
     if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
-      fluidRow(
-        column(
-          width = 11,
-          align = "left",
-          p(
-            HTML(
-              paste(
-                '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
-                tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                          paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
-              )
-            )
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
           )
         )
       )
     } else {
-      fluidRow(
-        column(
-          width = 11,
-          align = "left",
-          p(
-            HTML(
-              paste(
-                '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
-                tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                          paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
-              )
-            )
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
           )
         )
       )
@@ -22405,34 +22431,22 @@ server <- function(input, output, session) {
   
   output$gene_resistance_info <- renderUI({
     if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
-      fluidRow(
-        column(
-          width = 11,
-          align = "left",
-          p(
-            HTML(
-              paste(
-                '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
-                tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                          paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
-              )
-            )
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
           )
         )
       )
     } else {
-      fluidRow(
-        column(
-          width = 11,
-          align = "left",
-          p(
-            HTML(
-              paste(
-                '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
-                tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                          paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
-              )
-            )
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
           )
         )
       )
@@ -22825,33 +22839,41 @@ server <- function(input, output, session) {
   # Render Initiate Typing UI
   output$initiate_typing_ui <- renderUI({
     column(
-      width = 3,
+      width = 4,
       align = "center",
       br(),
       br(),
-      h3(p("Initiate Typing"), style = "color:white"),
+      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
       br(),
       br(),
       p(
         HTML(
           paste(
-            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Assembly File (FASTA)')
+            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File (FASTA)')
           )
         )
       ),
-      shinyFilesButton(
-        "genome_file",
-        "Browse" ,
-        icon = icon("file"),
-        title = "Select the assembly in .fasta/.fna/.fa format:",
-        multiple = FALSE,
-        buttonType = "default",
-        class = NULL,
-        root = path_home()
-      ),
-      br(),
-      br(),
-      uiOutput("genome_path")
+      fluidRow(
+        column(1),
+        column(
+          width = 11,
+          align = "center",
+          shinyFilesButton(
+            "genome_file",
+            "Browse" ,
+            icon = icon("file"),
+            title = "Select the assembly in .fasta/.fna/.fa format:",
+            multiple = FALSE,
+            buttonType = "default",
+            class = NULL,
+            root = path_home()
+          ),
+          br(),
+          br(),
+          uiOutput("genome_path"),
+          br()
+        )
+      )
     )
   })
   
@@ -22860,7 +22882,7 @@ server <- function(input, output, session) {
   observe({
     if (nrow(Typing$single_path) < 1) {
       output$genome_path <- renderUI(HTML(
-        paste("<span style='color: white;'>", "No file selected.")
+        paste("<span style='color: white; margin-left:-30px'>", "No file selected.")
       ))
       
       # dont show subsequent metadata declaration and typing start UI
@@ -22877,7 +22899,7 @@ server <- function(input, output, session) {
         output$genome_path <- renderUI({
           HTML(
             paste(
-              "<span style='color: white; font-weight: bolder'>",
+              "<span style='color: white; margin-left:-30px; font-weight: bolder'>",
               as.character(Typing$single_path$name)
             )
           )
@@ -22893,157 +22915,158 @@ server <- function(input, output, session) {
           column(
             width = 3,
             align = "center",
-            br(),
-            br(),
-            h3(p("Declare Metadata"), style = "color:white"),
-            br(),
-            br(),
-            box(
-              solidHeader = TRUE,
-              status = "primary",
-              width = "90%",
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
-                ),
-                column(
-                  width = 7,
-                  align = "left",
-                  div(
-                    class = "append_table",
-                    textInput("assembly_id",
-                              value = "",
-                              label = "",
-                              width = "80%")
+            br(), br(),
+            h3(p("Declare Metadata"), style = "color:white; margin-left:-40px"),
+            br(), br(),
+            div(
+              class = "multi_meta_box",
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "90%",
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("assembly_id",
+                                value = "",
+                                label = "",
+                                width = "80%")
+                    )
                   )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  div(
-                    class = "append_table",
-                    textInput("assembly_name",
-                              label = "",
-                              width = "80%")
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("assembly_name",
+                                label = "",
+                                width = "80%")
+                    )
                   )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  div(
-                    class = "append_table",
-                    dateInput("append_isodate",
-                              label = "",
-                              width = "80%",
-                              max = Sys.Date())
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      dateInput("append_isodate",
+                                label = "",
+                                width = "80%",
+                                max = Sys.Date())
+                    )
                   )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  div(
-                    class = "append_table",
-                    textInput("append_host",
-                              label = "",
-                              width = "80%")
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("append_host",
+                                label = "",
+                                width = "80%")
+                    )
                   )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  div(
-                    class = "append_table_country",
-                    pickerInput(
-                      "append_country",
-                      label = "",
-                      choices = list("Common" = sel_countries,
-                                     "All Countries" = country_names),
-                      options = list(
-                        `live-search` = TRUE,
-                        `actions-box` = TRUE,
-                        size = 10,
-                        style = "background-color: white; border-radius: 5px;"
-                      ),
-                      width = "90%"
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table_country",
+                      pickerInput(
+                        "append_country",
+                        label = "",
+                        choices = list("Common" = sel_countries,
+                                       "All Countries" = country_names),
+                        options = list(
+                          `live-search` = TRUE,
+                          `actions-box` = TRUE,
+                          size = 10,
+                          style = "background-color: white; border-radius: 5px;"
+                        ),
+                        width = "90%"
+                      )
                     )
                   )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  div(
-                    class = "append_table",
-                    textInput(
-                      "append_city",
-                      label = "",
-                      width = "80%"
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput(
+                        "append_city",
+                        label = "",
+                        width = "80%"
+                      )
                     )
                   )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 12,
-                  align = "center",
-                  br(), br(),
-                  actionButton(
-                    inputId = "conf_meta_single",
-                    label = "Confirm"
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
                   ),
-                  br()
-                )
-              ),
-              br()
-            )
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 12,
+                    align = "center",
+                    br(), br(),
+                    actionButton(
+                      inputId = "conf_meta_single",
+                      label = "Confirm"
+                    ),
+                    br()
+                  )
+                ),
+                br()
+              )
+            )
           )
         })
       } else {
@@ -23150,6 +23173,7 @@ server <- function(input, output, session) {
         single_typing_df <- data.frame(
           db_path = DB$database,
           wd = getwd(),
+          save = input$save_assembly_st,
           scheme = paste0(gsub(" ", "_", DB$scheme)),
           genome = Typing$single_path$datapath,
           alleles = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", search_string)
@@ -23359,7 +23383,6 @@ server <- function(input, output, session) {
   #### Declare Metadata  ----
   
   observeEvent(input$conf_meta_single, {
-    log_print("Single typing metadata confirmed")
     
     if(nchar(trimws(input$assembly_id)) < 1) {
       ass_id <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
@@ -23373,57 +23396,87 @@ server <- function(input, output, session) {
       ass_name <- trimws(input$assembly_name)
     }
     
-    meta_info <- data.frame(assembly_id = ass_id,
-                            assembly_name = ass_name,
-                            cgmlst_typing = DB$scheme,
-                            append_isodate = input$append_isodate,
-                            append_host = trimws(input$append_host),
-                            append_country = trimws(input$append_country),
-                            append_city = trimws(input$append_city),
-                            append_analysisdate = Sys.Date(),
-                            db_directory = getwd()) 
-    
-    saveRDS(meta_info, paste0(
-      getwd(),
-      "/execute/meta_info_single.rds"
-    ))
-    
-    show_toast(
-      title = "Metadata declared",
-      type = "success",
-      position = "bottom-end",
-      timer = 3000,
-      width = "500px"
-    )
-    
-    # Render Start Typing UI
-    
-    output$start_typing_ui <- renderUI({
-      column(
-        width = 3,
-        align = "center",
-        br(),
-        br(),
-        h3(p("Start Typing"), style = "color:white"),
-        br(),
-        br(),
-        HTML(
-          paste(
-            "<span style='color: white;'>",
-            "Typing by <strong>",
-            DB$scheme,
-            "</strong> scheme."
+    if(ass_id %in% unlist(DB$data["Assembly ID"])) {
+      show_toast(
+        title = "Assembly ID already present",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000,
+        width = "500px"
+      )
+    } else {
+      
+      log_print("Single typing metadata confirmed")
+      
+      meta_info <- data.frame(assembly_id = ass_id,
+                              assembly_name = ass_name,
+                              cgmlst_typing = DB$scheme,
+                              append_isodate = input$append_isodate,
+                              append_host = trimws(input$append_host),
+                              append_country = trimws(input$append_country),
+                              append_city = trimws(input$append_city),
+                              append_analysisdate = Sys.Date(),
+                              db_directory = getwd()) 
+      
+      saveRDS(meta_info, paste0(
+        getwd(),
+        "/execute/meta_info_single.rds"
+      ))
+      
+      show_toast(
+        title = "Metadata declared",
+        type = "success",
+        position = "bottom-end",
+        timer = 3000,
+        width = "500px"
+      )
+      
+      # Render Start Typing UI
+      
+      output$start_typing_ui <- renderUI({
+        div(
+          class = "multi_start_col",
+          column(
+            width = 3,
+            align = "center",
+            br(),
+            br(),
+            h3(p("Start Typing"), style = "color:white"),
+            br(),
+            br(),
+            HTML(
+              paste(
+                "<span style='color: white;'>",
+                "Typing by <strong>",
+                DB$scheme,
+                "</strong> scheme."
+              )
+            ),
+            br(), br(), br(), br(),
+            div(
+              class = "save-assembly",
+              materialSwitch(
+                "save_assembly_st",
+                h5(p("Save Assemblies in Local Database"), style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
+                value = TRUE,
+                right = TRUE)
+            ),
+            HTML(
+              paste(
+                "<span style='color: orange;'>",
+                "Isolates with unsaved assembly files can NOT be applied to screening for resistance genes."
+              )
+            ),
+            br(), br(), br(), br(),
+            actionButton(
+              inputId = "typing_start",
+              label = "Start",
+              icon = icon("circle-play")
+            )
           )
-        ),
-        br(), br(),
-        actionButton(
-          inputId = "typing_start",
-          label = "Start",
-          icon = icon("circle-play")
         )
-      )
-    })
-    
+      })
+    }
   })
   
   ####  Events Single Typing ----
@@ -23460,33 +23513,41 @@ server <- function(input, output, session) {
     
     output$initiate_typing_ui <- renderUI({
       column(
-        width = 3,
+        width = 4,
         align = "center",
         br(),
         br(),
-        h3(p("Initiate Typing"), style = "color:white"),
+        h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
         br(),
         br(),
         p(
           HTML(
             paste(
-              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Assembly File (FASTA)')
+              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File (FASTA)')
             )
           )
         ),
-        shinyFilesButton(
-          "genome_file",
-          "Browse",
-          icon = icon("folder-open"),
-          title = "Please select the genome in .fasta/.fna/.fa format:",
-          multiple = FALSE,
-          buttonType = "default",
-          class = NULL,
-          root = path_home()
-        ),
-        br(),
-        br(),
-        uiOutput("genome_path")
+        fluidRow(
+          column(1),
+          column(
+            width = 11,
+            align = "center",
+            shinyFilesButton(
+              "genome_file",
+              "Browse" ,
+              icon = icon("file"),
+              title = "Select the assembly in .fasta/.fna/.fa format:",
+              multiple = FALSE,
+              buttonType = "default",
+              class = NULL,
+              root = path_home()
+            ),
+            br(),
+            br(),
+            uiOutput("genome_path"),
+            br()
+          )
+        )
       )
     })
   })
@@ -23515,40 +23576,47 @@ server <- function(input, output, session) {
   #### Render Multi Typing UI Elements ----
   output$initiate_multi_typing_ui <- renderUI({
     column(
-      width = 3,
+      width = 4,
       align = "center",
       br(),
       br(),
-      h3(p("Initiate Typing"), style = "color:white"),
-      br(),
-      br(),
+      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+      br(), br(),
       p(
         HTML(
           paste(
-            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Assembly Folder')
+            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
           )
         )
       ),
-      column(
-        width = 12,
-        align = "center",
-        shinyDirButton(
-          "genome_file_multi",
-          "Browse",
-          icon = icon("folder-open"),
-          title = "Select the folder containing the genome assemblies (FASTA)",
-          buttonType = "default",
-          root = path_home()
-        ),
-        br(),
-        br(),
-        uiOutput("multi_select_info"),
-        br()
+      fluidRow(
+        column(1),
+        column(
+          width = 11,
+          align = "center",
+          shinyDirButton(
+            "genome_file_multi",
+            "Browse",
+            icon = icon("folder-open"),
+            title = "Select the folder containing the genome assemblies (FASTA)",
+            buttonType = "default",
+            root = path_home()
+          ),
+          br(),
+          br(),
+          uiOutput("multi_select_info"),
+          br()
+        )
       ),
-      column(
-        width = 12,
-        align = "left",
-        rHandsontableOutput("multi_select_table")
+      uiOutput("multi_select_tab_ctrls"),#
+      br(),
+      fluidRow(
+        column(1),
+        column(
+          width = 11,
+          align = "left",
+          rHandsontableOutput("multi_select_table")
+        )
       )
     )
   })
@@ -23557,29 +23625,91 @@ server <- function(input, output, session) {
   output$multi_select_info <- renderUI({
     if(!is.null(Typing$multi_path)) {
       if(length(Typing$multi_path) < 1) {
-        HTML(paste("<span style='color: white;'>", 
+        HTML(paste("<span style='color: white; margin-left:-30px'>", 
                    "No files selected."))
       } else {
-        if(!is.null(Typing$multi_sel_table)) {
-          if(sum(Typing$multi_sel_table$Include == TRUE) < 1) {
-            HTML(paste("<span style='color: white;'>", 
-                       "No files selected."))
-          } else {
-            req(Typing$genome_selected)
-            HTML(paste("<span style='color: white;'>", 
-                       sum(Typing$genome_selected$Include == TRUE),
-                       " files selected."))
-          }
-        }
+        HTML(paste("<span style='color: white; margin-left:-30px'>",
+                   sum(Typing$genome_selected$Include == TRUE),
+                   " files selected."))
       }
     }
   })
   
+  # Render multi selection table issues
+  output$multi_select_issues <- renderUI({
+    req(Typing$multi_sel_table, Typing$genome_selected, input$multi_select_table)
+    if(any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id_names()) & 
+       any(duplicated(hot_to_r(input$multi_select_table)$Files))){
+      HTML(
+        paste(
+          paste("<span style='color: #e0b300;'>",
+                "Some name(s) are already present in local database.<br/>"),
+          paste("<span style='color: #ff7334;'>",
+                "Duplicated name(s). <br/>")
+        )
+      )
+    } else if (any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id_names()) & 
+               !any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
+      HTML(
+        paste("<span style='color: #e0b300;'>",
+              "Some name(s) are already present in local database.<br/>")
+      )
+    } else if (!any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id_names()) & 
+               any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
+      HTML(
+        paste("<span style='color: #ff7334;'>",
+              "Duplicated name(s). <br/>")
+      )
+    }
+  })
+  
+  output$multi_select_issue_info <- renderUI({
+    req(Typing$multi_sel_table, Typing$genome_selected, input$multi_select_table)
+    if(any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id_names()) | 
+       any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
+      HTML(
+        paste("<span style='color: orange; font-style:italic'>",
+              "Rename highlighted isolates.")
+      )
+    }
+  })
+  
   # Render Metadata Select Box after Folder selection
   observe({
     if(!is.null(Typing$multi_sel_table)) {
       if (nrow(Typing$multi_sel_table) > 0) {
         
+        output$multi_select_tab_ctrls <- renderUI(
+          fluidRow(
+            column(1),
+            column(
+              width = 2,
+              align = "left",
+              actionButton(
+                "sel_all_mt",
+                "All",
+                icon = icon("check")
+              )
+            ),
+            column(
+              width = 2,
+              align = "left",
+              actionButton(
+                "desel_all_mt",
+                "None",
+                icon = icon("xmark")
+              )
+            ),
+            column(2),
+            column(
+              width = 5,
+              align = "right",
+              br(),
+              uiOutput("multi_select_issues")
+            )
+          )
+        )
+        
         Typing$genome_selected <- hot_to_r(input$multi_select_table)
         
         output$metadata_multi_box <- renderUI({
@@ -23588,140 +23718,143 @@ server <- function(input, output, session) {
             align = "center",
             br(),
             br(),
-            h3(p("Declare Metadata"), style = "color:white"),
+            h3(p("Declare Metadata"), style = "color:white;margin-left:-40px"),
             br(), br(),
-            box(
-              solidHeader = TRUE,
-              status = "primary",
-              width = "90%",
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
-                ),
-                column(
-                  width = 7,
-                  align = "left",
-                  h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
+            div(
+              class = "multi_meta_box",
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "90%",
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  div(
-                    class = "append_table",
-                    dateInput("append_isodate_multi",
-                              label = "",
-                              width = "80%",
-                              max = Sys.Date())
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      dateInput("append_isodate_multi",
+                                label = "",
+                                width = "80%",
+                                max = Sys.Date())
+                    )
                   )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  div(
-                    class = "append_table",
-                    textInput("append_host_multi",
-                              label = "",
-                              width = "80%")
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("append_host_multi",
+                                label = "",
+                                width = "80%")
+                    )
                   )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  div(
-                    class = "append_table_country",
-                    pickerInput(
-                      "append_country_multi",
-                      label = "",
-                      choices = list("Common" = sel_countries,
-                                     "All Countries" = country_names),
-                      options = list(
-                        `live-search` = TRUE,
-                        `actions-box` = TRUE,
-                        size = 10,
-                        style = "background-color: white; border-radius: 5px;"
-                      ),
-                      width = "90%"
-                    )
-                  )  
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table_country",
+                      pickerInput(
+                        "append_country_multi",
+                        label = "",
+                        choices = list("Common" = sel_countries,
+                                       "All Countries" = country_names),
+                        options = list(
+                          `live-search` = TRUE,
+                          `actions-box` = TRUE,
+                          size = 10,
+                          style = "background-color: white; border-radius: 5px;"
+                        ),
+                        width = "90%"
+                      )
+                    )  
+                  )
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  div(
-                    class = "append_table",
-                    textInput("append_city_multi",
-                              label = "",
-                              width = "80%")
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("append_city_multi",
+                                label = "",
+                                width = "80%")
+                    )
                   )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 5,
-                  align = "left",
-                  h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
                 ),
-                column(
-                  width = 7,
-                  align = "left",
-                  h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 12,
-                  align = "center",
-                  br(), br(),
-                  actionButton(
-                    inputId = "conf_meta_multi",
-                    label = "Confirm"
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
                   ),
-                  br()
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 12,
+                    align = "center",
+                    br(), br(),
+                    actionButton(
+                      inputId = "conf_meta_multi",
+                      label = "Confirm"
+                    ),
+                    br(), br(),
+                    uiOutput("multi_select_issue_info")
+                  )
                 )
-              ),
-              br()
+              )    
             )
           )
         }) 
@@ -23743,96 +23876,551 @@ server <- function(input, output, session) {
     
     Typing$multi_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)
     
-    multi_sel_table <- data.frame(Include = rep(TRUE, length(list.files(as.character(Typing$multi_path)))),
-                                  Files = list.files(as.character(Typing$multi_path)))
-    
-    Typing$multi_sel_table <- multi_sel_table[which(grepl("\\.fasta|\\.fna|\\.fa", multi_sel_table$Files)),]
-    
-    if (between(nrow(Typing$multi_sel_table), 1, 15)) {
-      output$multi_select_table <- renderRHandsontable({
-        rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
-                      stretchH = "all", contextMenu = FALSE) %>%
-          hot_cols(columnSorting = TRUE) %>%
-          hot_rows(rowHeights = 25) %>%
-          hot_col(2,
-                  readOnly = TRUE,
-                  valign = "htBottom") %>%
-          hot_col(1,
-                  halign = "htCenter",
-                  valign = "htTop", 
-                  colWidths = 60)
-      })
+    selected_files <- list.files(as.character(Typing$multi_path))[which(!endsWith(list.files(as.character(Typing$multi_path)), ".gz"))]
+    
+    Typing$multi_sel_table <- data.frame(
+      Include = rep(TRUE, length(selected_files)),
+      Files = gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", 
+                   selected_files),
+      Type = sub(".*(\\.fasta|\\.fasta\\.gz|\\.fna|\\.fna\\.gz|\\.fa|\\.fa\\.gz)$",
+                 "\\1", selected_files, perl = F))
+    
+    if(nrow(Typing$multi_sel_table) > 0) {
+      output$multi_select_tab_ctrls <- renderUI(
+        fluidRow(
+          column(1),
+          column(
+            width = 2,
+            align = "left",
+            actionButton(
+              "sel_all_mt",
+              "All",
+              icon = icon("check")
+            )
+          ),
+          column(
+            width = 2,
+            align = "left",
+            actionButton(
+              "desel_all_mt",
+              "None",
+              icon = icon("xmark")
+            )
+          ),
+          column(2),
+          column(
+            width = 5,
+            align = "left",
+            uiOutput("multi_select_issues")
+          )
+        )
+      )
+    } else {
+      output$multi_select_tab_ctrls <- NULL
+    }
+    
+     if (between(nrow(Typing$multi_sel_table), 1, 15)) {
+       if(!is.null(Typing$new_table)) {
+         output$multi_select_table <- renderRHandsontable({
+           rht <- rhandsontable(Typing$new_table, rowHeaders = NULL, 
+                         stretchH = "all", contextMenu = FALSE
+           ) %>%
+             hot_cols(columnSorting = TRUE) %>%
+             hot_rows(rowHeights = 25) %>%
+             hot_col(2,
+                     readOnly = FALSE,
+                     valign = "htBottom") %>%
+             hot_col(3, readOnly = TRUE) %>%
+             hot_col(1,
+                     halign = "htCenter",
+                     valign = "htTop", 
+                     colWidths = 60)
+           
+           htmlwidgets::onRender(rht, sprintf(
+             "function(el, x) {
+        var hot = this.hot;
+        
+        var columnData = hot.getDataAtCol(1); // Change column index if needed
+        var duplicates = {};
+          
+        var highlightInvalidAndDuplicates = function(invalidValues) {
+          
+          var columnData = hot.getDataAtCol(1); // Change column index if needed
+          var duplicates = {};
+
+          // Find all duplicate values
+          for (var i = 0; i < columnData.length; i++) {
+            var value = columnData[i];
+            if (value !== null && value !== undefined) {
+              if (duplicates[value]) {
+                duplicates[value].push(i);
+              } else {
+                duplicates[value] = [i];
+              }
+            }
+          }
+
+          // Reset all cell backgrounds in the column
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            if (cell) {
+              cell.style.background = 'white';
+            }
+          }
+
+          // Highlight duplicates and invalid values
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            var value = columnData[i];
+            if (cell) {
+              if (invalidValues.includes(value)) {
+                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
+              } else if (duplicates[value] && duplicates[value].length > 1) {
+                cell.style.background = '#FF7334'; // Highlight color for duplicates
+              }
+            }
+          }
+        };
+
+        var changefn = function(changes, source) {
+          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
+            highlightInvalidAndDuplicates(%s);
+          }
+        };
+
+        hot.addHook('afterChange', changefn);
+        hot.addHook('afterLoadData', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+        hot.addHook('afterRender', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+
+        highlightInvalidAndDuplicates(%s); // Initial highlight on load
+        
+        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
+          var colData = hot.getDataAtCol(0);
+          for (var i = 0; i < colData.length; i++) {
+            hot.setDataAtCell(i, 0, message.value);
+          }
+          hot.render(); // Re-render the table
+        });
+      }", 
+             jsonlite::toJSON(dupl_mult_id_names()), 
+             jsonlite::toJSON(dupl_mult_id_names()), 
+             jsonlite::toJSON(dupl_mult_id_names()), 
+             jsonlite::toJSON(dupl_mult_id_names())))
+         })
+       } else {
+         output$multi_select_table <- renderRHandsontable({
+           rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
+                         stretchH = "all", contextMenu = FALSE
+           ) %>%
+             hot_cols(columnSorting = TRUE) %>%
+             hot_rows(rowHeights = 25) %>%
+             hot_col(2,
+                     readOnly = FALSE,
+                     valign = "htBottom") %>%
+             hot_col(3, readOnly = TRUE) %>%
+             hot_col(1,
+                     halign = "htCenter",
+                     valign = "htTop", 
+                     colWidths = 60)
+           
+           htmlwidgets::onRender(rht, sprintf(
+             "function(el, x) {
+        var hot = this.hot;
+        
+        var columnData = hot.getDataAtCol(1); // Change column index if needed
+        var duplicates = {};
+          
+        var highlightInvalidAndDuplicates = function(invalidValues) {
+          
+          var columnData = hot.getDataAtCol(1); // Change column index if needed
+          var duplicates = {};
+
+          // Find all duplicate values
+          for (var i = 0; i < columnData.length; i++) {
+            var value = columnData[i];
+            if (value !== null && value !== undefined) {
+              if (duplicates[value]) {
+                duplicates[value].push(i);
+              } else {
+                duplicates[value] = [i];
+              }
+            }
+          }
+
+          // Reset all cell backgrounds in the column
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            if (cell) {
+              cell.style.background = 'white';
+            }
+          }
+
+          // Highlight duplicates and invalid values
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            var value = columnData[i];
+            if (cell) {
+              if (invalidValues.includes(value)) {
+                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
+              } else if (duplicates[value] && duplicates[value].length > 1) {
+                cell.style.background = '#FF7334'; // Highlight color for duplicates
+              }
+            }
+          }
+        };
+
+        var changefn = function(changes, source) {
+          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
+            highlightInvalidAndDuplicates(%s);
+          }
+        };
+
+        hot.addHook('afterChange', changefn);
+        hot.addHook('afterLoadData', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+        hot.addHook('afterRender', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+
+        highlightInvalidAndDuplicates(%s); // Initial highlight on load
+        
+        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
+          var colData = hot.getDataAtCol(0);
+          for (var i = 0; i < colData.length; i++) {
+            hot.setDataAtCell(i, 0, message.value);
+          }
+          hot.render(); // Re-render the table
+        });
+      }", 
+             jsonlite::toJSON(dupl_mult_id_names()), 
+             jsonlite::toJSON(dupl_mult_id_names()), 
+             jsonlite::toJSON(dupl_mult_id_names()), 
+             jsonlite::toJSON(dupl_mult_id_names())))
+         })
+       }
     } else if(nrow(Typing$multi_sel_table) > 15) {
-      output$multi_select_table <- renderRHandsontable({
-        rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
-                      stretchH = "all", height = 500,
-                      contextMenu = FALSE) %>%
-          hot_cols(columnSorting = TRUE) %>%
-          hot_rows(rowHeights = 25) %>%
-          hot_col(2,
-                  readOnly = TRUE,
-                  valign = "htBottom") %>%
-          hot_col(1,
-                  halign = "htCenter",
-                  valign = "htTop", 
-                  colWidths = 60)
-      })
+      if(!is.null(Typing$new_table)) {
+        output$multi_select_table <- renderRHandsontable({
+          rht <- rhandsontable(Typing$new_table, rowHeaders = NULL, 
+                        stretchH = "all", height = 500,
+                        contextMenu = FALSE
+          ) %>%
+            hot_cols(columnSorting = TRUE) %>%
+            hot_rows(rowHeights = 25) %>%
+            hot_col(2,
+                    readOnly = FALSE,
+                    valign = "htBottom") %>%
+            hot_col(3, readOnly = TRUE) %>%
+            hot_col(1,
+                    halign = "htCenter",
+                    valign = "htTop", 
+                    colWidths = 60)
+          
+          htmlwidgets::onRender(rht, sprintf(
+            "function(el, x) {
+        var hot = this.hot;
+        
+        var columnData = hot.getDataAtCol(1); // Change column index if needed
+        var duplicates = {};
+          
+        var highlightInvalidAndDuplicates = function(invalidValues) {
+          
+          var columnData = hot.getDataAtCol(1); // Change column index if needed
+          var duplicates = {};
+
+          // Find all duplicate values
+          for (var i = 0; i < columnData.length; i++) {
+            var value = columnData[i];
+            if (value !== null && value !== undefined) {
+              if (duplicates[value]) {
+                duplicates[value].push(i);
+              } else {
+                duplicates[value] = [i];
+              }
+            }
+          }
+
+          // Reset all cell backgrounds in the column
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            if (cell) {
+              cell.style.background = 'white';
+            }
+          }
+
+          // Highlight duplicates and invalid values
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            var value = columnData[i];
+            if (cell) {
+              if (invalidValues.includes(value)) {
+                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
+              } else if (duplicates[value] && duplicates[value].length > 1) {
+                cell.style.background = '#FF7334'; // Highlight color for duplicates
+              }
+            }
+          }
+        };
+
+        var changefn = function(changes, source) {
+          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
+            highlightInvalidAndDuplicates(%s);
+          }
+        };
+
+        hot.addHook('afterChange', changefn);
+        hot.addHook('afterLoadData', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+        hot.addHook('afterRender', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+
+        highlightInvalidAndDuplicates(%s); // Initial highlight on load
+        
+        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
+          var colData = hot.getDataAtCol(0);
+          for (var i = 0; i < colData.length; i++) {
+            hot.setDataAtCell(i, 0, message.value);
+          }
+          hot.render(); // Re-render the table
+        });
+      }", 
+            jsonlite::toJSON(dupl_mult_id_names()), 
+            jsonlite::toJSON(dupl_mult_id_names()), 
+            jsonlite::toJSON(dupl_mult_id_names()), 
+            jsonlite::toJSON(dupl_mult_id_names())))
+        })
+      } else {
+        output$multi_select_table <- renderRHandsontable({
+          rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
+                        stretchH = "all", height = 500,
+                        contextMenu = FALSE
+          ) %>%
+            hot_cols(columnSorting = TRUE) %>%
+            hot_rows(rowHeights = 25) %>%
+            hot_col(2,
+                    readOnly = FALSE,
+                    valign = "htBottom") %>%
+            hot_col(3, readOnly = TRUE) %>%
+            hot_col(1,
+                    halign = "htCenter",
+                    valign = "htTop", 
+                    colWidths = 60)
+          
+          htmlwidgets::onRender(rht, sprintf(
+            "function(el, x) {
+        var hot = this.hot;
+        
+        var columnData = hot.getDataAtCol(1); // Change column index if needed
+        var duplicates = {};
+          
+        var highlightInvalidAndDuplicates = function(invalidValues) {
+          
+          var columnData = hot.getDataAtCol(1); // Change column index if needed
+          var duplicates = {};
+
+          // Find all duplicate values
+          for (var i = 0; i < columnData.length; i++) {
+            var value = columnData[i];
+            if (value !== null && value !== undefined) {
+              if (duplicates[value]) {
+                duplicates[value].push(i);
+              } else {
+                duplicates[value] = [i];
+              }
+            }
+          }
+
+          // Reset all cell backgrounds in the column
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            if (cell) {
+              cell.style.background = 'white';
+            }
+          }
+
+          // Highlight duplicates and invalid values
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            var value = columnData[i];
+            if (cell) {
+              if (invalidValues.includes(value)) {
+                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
+              } else if (duplicates[value] && duplicates[value].length > 1) {
+                cell.style.background = '#FF7334'; // Highlight color for duplicates
+              }
+            }
+          }
+        };
+
+        var changefn = function(changes, source) {
+          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
+            highlightInvalidAndDuplicates(%s);
+          }
+        };
+
+        hot.addHook('afterChange', changefn);
+        hot.addHook('afterLoadData', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+        hot.addHook('afterRender', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+
+        highlightInvalidAndDuplicates(%s); // Initial highlight on load
+        
+        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
+          var colData = hot.getDataAtCol(0);
+          for (var i = 0; i < colData.length; i++) {
+            hot.setDataAtCell(i, 0, message.value);
+          }
+          hot.render(); // Re-render the table
+        });
+      }", 
+            jsonlite::toJSON(dupl_mult_id_names()), 
+            jsonlite::toJSON(dupl_mult_id_names()), 
+            jsonlite::toJSON(dupl_mult_id_names()), 
+            jsonlite::toJSON(dupl_mult_id_names())))
+          
+        })
+      }
     } else {
       output$multi_select_table <- NULL
     }
   })
   
   observeEvent(input$conf_meta_multi, {
-    log_print("Multi typing metadata confirmed")
     
-    meta_info <- data.frame(cgmlst_typing = DB$scheme,
-                            append_isodate = trimws(input$append_isodate_multi),
-                            append_host = trimws(input$append_host_multi),
-                            append_country = trimws(input$append_country_multi),
-                            append_city = trimws(input$append_city_multi),
-                            append_analysisdate = Sys.Date(),
-                            db_directory = getwd())
+    Typing$new_table <- mutate(hot_to_r(input$multi_select_table),
+                               Include = as.logical(Include))
     
-    saveRDS(meta_info, paste0(getwd(), "/execute/meta_info.rds"))
-    
-    show_toast(
-      title = "Metadata declared",
-      type = "success",
-      position = "bottom-end",
-      timer = 3000,
-      width = "500px"
-    )
-    
-    output$start_multi_typing_ui <- renderUI({
-      column(
-        width = 3,
-        align = "center",
-        br(),
-        br(),
-        h3(p("Start Typing"), style = "color:white"),
-        br(),
-        br(),
-        HTML(
-          paste(
-            "<span style='color: white;'>",
-            "Typing by <strong>",
-            DB$scheme,
-            "</strong> scheme."
+    if(any(unlist(gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", Typing$genome_selected[which(Typing$genome_selected$Include == TRUE),]$Files)) %in% unlist(DB$data["Assembly ID"]))) {
+      show_toast(
+        title = "Assembly ID(s) already present",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000,
+        width = "500px"
+      )
+    } else if (any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
+      show_toast(
+        title = "Duplicated file name(s)",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000,
+        width = "500px"
+      )
+    } else if (any(hot_to_r(input$multi_select_table)$Files == "")) {
+      show_toast(
+        title = "Empty file name(s)",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000,
+        width = "500px"
+      )
+    } 
+    else if (any(grepl("[/\\:*?\"<>|]", hot_to_r(input$multi_select_table)$Files))) {
+      show_toast(
+        title = "Invalid file name(s). Not allowed: /\\:*?\"<>|",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000,
+        width = "500px"
+      )
+    }
+    else if (!any(hot_to_r(input$multi_select_table)$Include == TRUE)) {
+      show_toast(
+        title = "No files selected",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000,
+        width = "500px"
+      )
+    }
+    else {
+      
+      log_print("Multi typing metadata confirmed")
+      
+      meta_info <- data.frame(cgmlst_typing = DB$scheme,
+                              append_isodate = trimws(input$append_isodate_multi),
+                              append_host = trimws(input$append_host_multi),
+                              append_country = trimws(input$append_country_multi),
+                              append_city = trimws(input$append_city_multi),
+                              append_analysisdate = Sys.Date(),
+                              db_directory = getwd())
+      
+      saveRDS(meta_info, paste0(getwd(), "/execute/meta_info.rds"))
+      
+      show_toast(
+        title = "Metadata declared",
+        type = "success",
+        position = "bottom-end",
+        timer = 3000,
+        width = "500px"
+      )
+      
+      output$start_multi_typing_ui <- renderUI({
+        div(
+          class = "multi_start_col",
+          column(
+            width = 3,
+            align = "center",
+            br(),
+            br(),
+            h3(p("Start Typing"), style = "color:white"),
+            br(),
+            br(),
+            HTML(
+              paste(
+                "<span style='color: white;'>",
+                "Typing by <strong>",
+                DB$scheme,
+                "</strong> scheme."
+              )
+            ),
+            br(), br(), br(), br(),
+            div(
+              class = "save-assembly",
+              materialSwitch(
+                "save_assembly_mt",
+                h5(p("Save Assemblies in Local Database"), style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
+                value = TRUE,
+                right = TRUE)
+            ),
+            HTML(
+              paste(
+                "<span style='color: orange;font-style:italic'>",
+                "Isolates with unsaved assembly files can NOT be applied to screening for resistance genes."
+              )
+            ),
+            br(), br(), br(), br(),
+            actionButton(
+              "start_typ_multi",
+              "Start",
+              icon = icon("circle-play")
+            )
           )
-        ),
-        br(), br(),
-        actionButton(
-          "start_typ_multi",
-          "Start",
-          icon = icon("circle-play")
         )
-      )
-    })
-    
+      })
+    }
   })
   
   #### Events Multi Typing ----
   
+  observeEvent(input$sel_all_mt, {
+    session$sendCustomMessage(type = "setColumnValue", message = list(value = TRUE))
+  })
+  
+  observeEvent(input$desel_all_mt, {
+    session$sendCustomMessage(type = "setColumnValue", message = list(value = FALSE))
+  })
+  
   # Print Log
   output$print_log <- downloadHandler(
     filename = function() {
@@ -23880,40 +24468,46 @@ server <- function(input, output, session) {
       
       output$initiate_multi_typing_ui <- renderUI({
         column(
-          width = 3,
+          width = 4,
           align = "center",
           br(),
           br(),
-          h3(p("Initiate Typing"), style = "color:white"),
+          h3(p("Initiate Typing"), style = "color:white, margin-left: 15px"),
           br(),
           br(),
           p(
             HTML(
               paste(
-                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Assembly Folder')
+                tags$span(style='color: white; font-size: 15px; margin-left: 15px', 'Select Assembly Folder')
               )
             )
           ),
-          column(
-            width = 12,
-            align = "center",
-            shinyDirButton(
-              "genome_file_multi",
-              "Browse",
-              icon = icon("folder-open"),
-              title = "Select the folder containing the genome assemblies (FASTA)",
-              buttonType = "default",
-              root = path_home()
-            ),
-            br(),
-            br(),
-            uiOutput("multi_select_info"),
-            br()
+          fluidRow(
+            column(1),
+            column(
+              width = 11,
+              align = "center",
+              shinyDirButton(
+                "genome_file_multi",
+                "Browse",
+                icon = icon("folder-open"),
+                title = "Select the folder containing the genome assemblies (FASTA)",
+                buttonType = "default",
+                root = path_home()
+              ),
+              br(),
+              br(),
+              uiOutput("multi_select_info"),
+              br()
+            )
           ),
-          column(
-            width = 12,
-            align = "left",
-            rHandsontableOutput("multi_select_table")
+          fluidRow(
+            column(1),
+            column(
+              width = 11,
+              align = "left",
+              rHandsontableOutput("multi_select_table")
+            )
           )
         )
       })
@@ -23961,40 +24555,46 @@ server <- function(input, output, session) {
     
     output$initiate_multi_typing_ui <- renderUI({
       column(
-        width = 3,
+        width = 4,
         align = "center",
         br(),
         br(),
-        h3(p("Initiate Typing"), style = "color:white"),
+        h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
         br(),
         br(),
         p(
           HTML(
             paste(
-              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Assembly Folder')
+              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
             )
           )
         ),
-        column(
-          width = 12,
-          align = "center",
-          shinyDirButton(
-            "genome_file_multi",
-            "Browse",
-            icon = icon("folder-open"),
-            title = "Please select the folder containing the genome assemblies (FASTA)",
-            buttonType = "default",
-            root = path_home()
-          ),
-          br(),
-          br(),
-          uiOutput("multi_select_info"),
-          br()
+        fluidRow(
+          column(1),
+          column(
+            width = 11,
+            align = "center",
+            shinyDirButton(
+              "genome_file_multi",
+              "Browse",
+              icon = icon("folder-open"),
+              title = "Select the folder containing the genome assemblies (FASTA)",
+              buttonType = "default",
+              root = path_home()
+            ),
+            br(),
+            br(),
+            uiOutput("multi_select_info"),
+            br()
+          )
         ),
-        column(
-          width = 12,
-          align = "left",
-          rHandsontableOutput("multi_select_table")
+        fluidRow(
+          column(1),
+          column(
+            width = 11,
+            align = "left",
+            rHandsontableOutput("multi_select_table")
+          )
         )
       )
     })
@@ -24044,6 +24644,8 @@ server <- function(input, output, session) {
           width = "500px"
         )
         
+        Typing$new_table <- NULL
+        
         # Remove Allelic Typing Controls
         output$initiate_multi_typing_ui <- NULL
         output$metadata_multi_box <- NULL
@@ -24062,6 +24664,7 @@ server <- function(input, output, session) {
         multi_typing_df <- data.frame(
           db_path = DB$database,
           wd = getwd(),
+          save = input$save_assembly_mt,
           scheme = paste0(gsub(" ", "_", DB$scheme)),
           genome_folder = as.character(parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)),
           genome_names = paste(Typing$genome_selected$Files[which(Typing$genome_selected$Include == TRUE)], collapse= " "),
diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index 6a12612..97c2a0d 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -2,6 +2,7 @@ library(logr)
 
 meta_info <- readRDS("meta_info.rds")
 db_path <- readRDS("multi_typing_df.rds")[, "db_path"]
+save_assembly <- readRDS("multi_typing_df.rds")[, "save"]
 assembly_folder <- dir(paste0(getwd(), "/selected_genomes"), full.names = TRUE)
 assembly <- assembly_folder[which(commandArgs(trailingOnly = TRUE)[1] == basename(assembly_folder))]
 results_folder <- dir(paste0(meta_info$db_directory, "/execute/blat_multi/results"), full.names = TRUE)
@@ -323,40 +324,43 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
   # Save new Entry in Typing Database
   saveRDS(Database, paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Typing.rds"))
   
-  if(dir.exists(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates"))) {
-    
-    # Create folder for new isolate
-    dir.create(paste0(db_path, "/", 
-                      gsub(" ", "_", meta_info$cgmlst_typing), 
-                      "/Isolates/", basename(assembly)))
-    
-    # Copy assembly file in isolate directory
-    file.copy(assembly, paste0(db_path, "/", 
-                               gsub(" ", "_", meta_info$cgmlst_typing), 
-                               "/Isolates/", basename(assembly)))
-    
-    log_print(paste0("Saved assembly of ", basename(assembly)))
-    
-  } else {
-    
-    log_print("No isolate folder present yet. Isolate directory created.")
-    
-    # Create isolate filder for species
-    dir.create(paste0(db_path, "/", 
-                      gsub(" ", "_", meta_info$cgmlst_typing), 
-                      "/Isolates"))
-    
-    # Create folder for new isolate
-    dir.create(paste0(db_path, "/", 
-                      gsub(" ", "_", meta_info$cgmlst_typing), 
-                      "/Isolates/", basename(assembly)))
-    
-    # Copy assembly file in isolate directory
-    file.copy(assembly, paste0(db_path, "/", 
-                               gsub(" ", "_", meta_info$cgmlst_typing), 
-                               "/Isolates/", basename(assembly)))
-    
-    log_print(paste0("Saved assembly of ", basename(assembly)))
+  # Save assembly file if TRUE
+  if(save_assembly) {
+    if(dir.exists(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates"))) {
+      
+      # Create folder for new isolate
+      dir.create(paste0(db_path, "/", 
+                        gsub(" ", "_", meta_info$cgmlst_typing), 
+                        "/Isolates/", basename(assembly)))
+      
+      # Copy assembly file in isolate directory
+      file.copy(assembly, paste0(db_path, "/", 
+                                 gsub(" ", "_", meta_info$cgmlst_typing), 
+                                 "/Isolates/", basename(assembly)))
+      
+      log_print(paste0("Saved assembly of ", basename(assembly)))
+      
+    } else {
+      
+      log_print("No isolate folder present yet. Isolate directory created.")
+      
+      # Create isolate filder for species
+      dir.create(paste0(db_path, "/", 
+                        gsub(" ", "_", meta_info$cgmlst_typing), 
+                        "/Isolates"))
+      
+      # Create folder for new isolate
+      dir.create(paste0(db_path, "/", 
+                        gsub(" ", "_", meta_info$cgmlst_typing), 
+                        "/Isolates/", basename(assembly)))
+      
+      # Copy assembly file in isolate directory
+      file.copy(assembly, paste0(db_path, "/", 
+                                 gsub(" ", "_", meta_info$cgmlst_typing), 
+                                 "/Isolates/", basename(assembly)))
+      
+      log_print(paste0("Saved assembly of ", basename(assembly)))
+    }
   }
   
   # Logging successes
diff --git a/execute/single_eval.R b/execute/single_eval.R
index 098a17d..abbe0fb 100644
--- a/execute/single_eval.R
+++ b/execute/single_eval.R
@@ -3,6 +3,7 @@ library(logr)
 # Hand over variables
 meta_info <- readRDS("meta_info_single.rds")
 db_path <- readRDS("single_typing_df.rds")[, "db_path"]
+save_assembly <- readRDS("multi_typing_df.rds")[, "save"]
 file_list <- list.files(paste0(meta_info$db_directory, "/execute/blat_single"), 
                         full.names = TRUE)
 assembly <- file_list[which(list.files(paste0(meta_info$db_directory, "/execute/blat_single")) != "results")]
@@ -307,40 +308,43 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
               message = paste0("Successful typing of ", meta_info$assembly_name))
   log_print(paste0("Successful typing of ", meta_info$assembly_name))
   
-  if(dir.exists(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates"))) {
-    
-    # Create folder for new isolate
-    dir.create(paste0(db_path, "/", 
-                      gsub(" ", "_", meta_info$cgmlst_typing), 
-                      "/Isolates/", meta_info$assembly_id))
-    
-    # Copy assembly file in isolate directory
-    file.copy(assembly, paste0(db_path, "/", 
-                               gsub(" ", "_", meta_info$cgmlst_typing), 
-                               "/Isolates/", meta_info$assembly_id))
-    
-    log_print(paste0("Saved assembly of ", meta_info$assembly_id))
-    
-  } else {
-    
-    log_print("No isolate folder present yet. Isolate directory created.")
-    
-    # Create isolate filder for species
-    dir.create(paste0(db_path, "/", 
-                      gsub(" ", "_", meta_info$cgmlst_typing), 
-                      "/Isolates"))
-    
-    # Create folder for new isolate
-    dir.create(paste0(db_path, "/", 
-                      gsub(" ", "_", meta_info$cgmlst_typing), 
-                      "/Isolates/", meta_info$assembly_id))
-    
-    # Copy assembly file in isolate directory
-    file.copy(assembly, paste0(db_path, "/", 
-                               gsub(" ", "_", meta_info$cgmlst_typing), 
-                               "/Isolates/", meta_info$assembly_id))
-    
-    log_print(paste0("Saved assembly of ", meta_info$assembly_id))
+  # Save assembly file if TRUE
+  if(save_assembly) {
+    if(dir.exists(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates"))) {
+      
+      # Create folder for new isolate
+      dir.create(paste0(db_path, "/", 
+                        gsub(" ", "_", meta_info$cgmlst_typing), 
+                        "/Isolates/", meta_info$assembly_id))
+      
+      # Copy assembly file in isolate directory
+      file.copy(assembly, paste0(db_path, "/", 
+                                 gsub(" ", "_", meta_info$cgmlst_typing), 
+                                 "/Isolates/", meta_info$assembly_id))
+      
+      log_print(paste0("Saved assembly of ", meta_info$assembly_id))
+      
+    } else {
+      
+      log_print("No isolate folder present yet. Isolate directory created.")
+      
+      # Create isolate filder for species
+      dir.create(paste0(db_path, "/", 
+                        gsub(" ", "_", meta_info$cgmlst_typing), 
+                        "/Isolates"))
+      
+      # Create folder for new isolate
+      dir.create(paste0(db_path, "/", 
+                        gsub(" ", "_", meta_info$cgmlst_typing), 
+                        "/Isolates/", meta_info$assembly_id))
+      
+      # Copy assembly file in isolate directory
+      file.copy(assembly, paste0(db_path, "/", 
+                                 gsub(" ", "_", meta_info$cgmlst_typing), 
+                                 "/Isolates/", meta_info$assembly_id))
+      
+      log_print(paste0("Saved assembly of ", meta_info$assembly_id))
+    }
   }
   
 } else {
diff --git a/www/body.css b/www/body.css
index 127cbc5..696f955 100644
--- a/www/body.css
+++ b/www/body.css
@@ -85,6 +85,22 @@ label {
   font-size: 16px;
 }
 
+.pretty input:checked~.state.p-primary label:after, .pretty.p-toggle .state.p-primary label:after {
+  background-color: #20E6E5 !important;
+}
+
+.irs--shiny .irs-bar {
+  border-color: #20E6E5;
+  background: #20E6E5;
+}
+
+.irs--shiny .irs-to,
+.irs--shiny .irs-from,
+.irs--shiny .irs-single{
+  background-color: #20E6E5;
+  color: black;
+}
+
 .main-sidebar .sidebar .sidebar-menu .treeview-menu a {
   color: #ffffff !important; 
     margin-left: 25px; 
@@ -224,6 +240,10 @@ left: -20px;
 border: 1px solid white;
 }
 
+#db_location {
+  width: 121px
+}
+
 .irs.irs--shiny.js-irs-0 {
   margin-right: -15px;
 }
@@ -276,7 +296,7 @@ margin-top: -15px;
 }
 
 button#load.pulsating-button.btn.btn-default.action-button.shiny-bound-input {
-background: #20E6E5; 
+  background: #20E6E5; 
   color: #000000; 
   width: 40px;
 }
@@ -286,13 +306,31 @@ background: #20E6E5;
 }
 
 #load .fas.fa-rotate {
-position: relative; 
-left: 0px !important;
+  position: relative; 
+  left: 0px !important;
 }
 
+.load-start {
+  width: 150px;
+  font-size: 17px;
+  overflow: hidden;
+  box-shadow: 0px 0px 20px 10px rgba(255, 255, 255, 0.23);
+  transition: box-shadow 0.5s ease;
+  border: none;
+  height: 45px;
+  z-index: 0;
+}
+
+.load-start:hover {
+  background: #3c8c56 !important; 
+  border: none;
+  color: white !important;
+  box-shadow: 0px 0px 20px 15px rgba(40, 47, 56, 1);
+}
+
+
 .shiny-input-container input[type="text"] {
   border-radius: 5px;
-  
 }
 
 .box.box-solid.box-primary>.box-header {
@@ -459,10 +497,18 @@ left: -6px;
 }
 
 /* Icons */
-  
-  i.fas {
-    margin-right: 5px;
-  }
+
+i.fa-solid .fa-arrow-right-long {
+  font-size: 30px;
+  color: white;
+  position: relative;
+  top: -38px;
+  left: 300px;
+}
+
+i.fas {
+  margin-right: 5px;
+}
 
 i.greenstatus.fa-solid.fa-circle-dot. {
   lightgreen
@@ -539,6 +585,11 @@ top: 1px !important;
 border-color: white;
 }
 
+#genome_file_multi,
+#genome_file {
+  margin-left: -30px;
+}
+
 .btn-default:hover {
   border-color: transparent !important;
 }
@@ -723,11 +774,34 @@ background: #20E6E5;
   }
 
 /* Typing */
+
+#sel_all_mt {
+  margin-left: 10px;
+}
+
+#sel_all_mt,
+#desel_all_mt{
+  margin-top: 27px;
+  margin-bottom: 25px;
+}
+
+#multi_select_issues {
+  margin-top: 5px;
+}
   
 .mult_res_sel {
   margin-bottom: 15px;
 }
 
+.multi_meta_box {
+  margin-left: -40px;
+}
+
+.multi_start_col {
+  position: relative;
+  left: -40px;
+}
+
 #multi_typing_results .mult_res_sel .selectize-input.items.full.has-options.has-items {
   width: auto;
 }
@@ -1166,7 +1240,7 @@ top: -10px;
 
 .material-switch>label.switch:before {
   background: #20e6e559 !important;
-    border-radius: 8px;
+  border-radius: 8px;
   content: "";
   height: 13px;
   margin-top: -10px;
@@ -1177,15 +1251,43 @@ top: -10px;
   border: 1px solid transparent;
 }
 
+.save-assembly .material-switch>label.switch:before {
+  background: #20e6e559 !important;
+  border-radius: 8px;
+  content: "";
+  height: 13px;
+  left: -10px;
+  margin-top: -10px;
+  opacity: 1;
+  position: absolute;
+  width: 40px;
+  transition: all 0.3s ease-in-out;
+  border: 1px solid transparent;
+}
+
 .material-switch>label.switch:hover:before {
   border: 1px solid #20e6e5;
 }
 
 .material-switch>input[type=checkbox]:checked+label.switch:before {
   background: #20e6e5 !important;
-    border-radius: 8px;
+  border-radius: 8px;
+  content: "";
+  height: 13px;
+  margin-top: -10px;
+  opacity: 1;
+  position: absolute;
+  width: 40px;
+  transition: all 0.3s ease-in-out;
+  border: 1px solid #20e6e559;
+}
+
+.save-assembly .material-switch>input[type=checkbox]:checked+label.switch:before {
+  background: #20e6e5 !important;
+  border-radius: 8px;
   content: "";
   height: 13px;
+  left: -10px;
   margin-top: -10px;
   opacity: 1;
   position: absolute;
@@ -1214,6 +1316,22 @@ top: -10px;
   border: 1px solid transparent;
 }
 
+.save-assembly .material-switch>label.switch:after {
+  background: #E6E6E6 !important;
+    border-radius: 1pc;
+  box-shadow: 0 0 5px rgba(0,0,0,.3);
+  content: "";
+  height: 20px;
+  opacity: 1;
+  left: -20px;
+  margin-top: -10px;
+  position: absolute;
+  top: -4px;
+  transition: all 0.3s ease-in-out;
+  width: 20px;
+  border: 1px solid transparent;
+}
+
 .material-switch>label.switch:hover:after {
   border: 1px solid #20e6e5 !important;
 }

From e841ac723f4e82ba74b68973b037f328e870ca6b Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Sun, 4 Aug 2024 19:15:46 +0200
Subject: [PATCH 31/75] Fix in multi metadata confirmation

---
 App.R | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/App.R b/App.R
index 0107f47..d6280c7 100644
--- a/App.R
+++ b/App.R
@@ -23642,7 +23642,7 @@ server <- function(input, output, session) {
        any(duplicated(hot_to_r(input$multi_select_table)$Files))){
       HTML(
         paste(
-          paste("<span style='color: #e0b300;'>",
+          paste("<span style='color: orange;'>",
                 "Some name(s) are already present in local database.<br/>"),
           paste("<span style='color: #ff7334;'>",
                 "Duplicated name(s). <br/>")
@@ -24300,6 +24300,10 @@ server <- function(input, output, session) {
     Typing$new_table <- mutate(hot_to_r(input$multi_select_table),
                                Include = as.logical(Include))
     
+    ahaaa <<- hot_to_r(input$multi_select_table)
+    
+    multi_select_table <<- hot_to_r(input$multi_select_table)[hot_to_r(input$multi_select_table)$Include == TRUE,]
+    
     if(any(unlist(gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", Typing$genome_selected[which(Typing$genome_selected$Include == TRUE),]$Files)) %in% unlist(DB$data["Assembly ID"]))) {
       show_toast(
         title = "Assembly ID(s) already present",
@@ -24308,7 +24312,7 @@ server <- function(input, output, session) {
         timer = 3000,
         width = "500px"
       )
-    } else if (any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
+    } else if (any(duplicated(multi_select_table$Files))) {
       show_toast(
         title = "Duplicated file name(s)",
         type = "error",
@@ -24316,7 +24320,7 @@ server <- function(input, output, session) {
         timer = 3000,
         width = "500px"
       )
-    } else if (any(hot_to_r(input$multi_select_table)$Files == "")) {
+    } else if (any(multi_select_table$Files == "")) {
       show_toast(
         title = "Empty file name(s)",
         type = "error",
@@ -24325,7 +24329,7 @@ server <- function(input, output, session) {
         width = "500px"
       )
     } 
-    else if (any(grepl("[/\\:*?\"<>|]", hot_to_r(input$multi_select_table)$Files))) {
+    else if (any(grepl("[/\\:*?\"<>|]", multi_select_table$Files))) {
       show_toast(
         title = "Invalid file name(s). Not allowed: /\\:*?\"<>|",
         type = "error",
@@ -24334,7 +24338,7 @@ server <- function(input, output, session) {
         width = "500px"
       )
     }
-    else if (!any(hot_to_r(input$multi_select_table)$Include == TRUE)) {
+    else if (!any(multi_select_table$Include == TRUE)) {
       show_toast(
         title = "No files selected",
         type = "error",

From ba03ee7f36879d6b31954f46d8897fc650626966 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Sun, 4 Aug 2024 19:20:39 +0200
Subject: [PATCH 32/75] Disallow editing of entry table Assembly ID

---
 App.R | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/App.R b/App.R
index d6280c7..7e5763f 100644
--- a/App.R
+++ b/App.R
@@ -7788,6 +7788,7 @@ server <- function(input, output, session) {
                               hot_col(1, 
                                       valign = "htMiddle",
                                       halign = "htCenter") %>%
+                              hot_col(3, readOnly = TRUE) %>%
                               hot_col(c(1, 5, 10, 11, 12),
                                       readOnly = TRUE) %>%
                               hot_col(3:(12 + nrow(DB$cust_var)), 
@@ -7890,6 +7891,7 @@ server <- function(input, output, session) {
                                 hot_col(1, 
                                         valign = "htMiddle",
                                         halign = "htCenter") %>%
+                                hot_col(3, readOnly = TRUE) %>%
                                 hot_col(c(1, 5, 10, 11, 12),
                                         readOnly = TRUE) %>%
                                 hot_col(3, validator = "
@@ -8046,6 +8048,7 @@ server <- function(input, output, session) {
                                 hot_col(1, 
                                         valign = "htMiddle",
                                         halign = "htCenter") %>%
+                                hot_col(3, readOnly = TRUE) %>%
                                 hot_col(c(1, 5, 10, 11, 12),
                                         readOnly = TRUE) %>%
                                 hot_col(3:(12 + nrow(DB$cust_var)), 
@@ -8190,6 +8193,7 @@ server <- function(input, output, session) {
                                 hot_col(3:(12 + nrow(DB$cust_var)), 
                                         valign = "htMiddle",
                                         halign = "htLeft") %>%
+                                hot_col(3, readOnly = TRUE) %>%
                                 hot_col(3, validator = "
                                   function(value, callback) {
                                     try {
@@ -8341,6 +8345,7 @@ server <- function(input, output, session) {
                                 hot_col(1, 
                                         valign = "htMiddle",
                                         halign = "htCenter") %>%
+                                hot_col(3, readOnly = TRUE) %>%
                                 hot_col(c(1, 5, 10, 11, 12),
                                         readOnly = TRUE) %>%
                                 hot_col(3, validator = "
@@ -9819,6 +9824,7 @@ server <- function(input, output, session) {
                 hot_col(1, 
                         valign = "htMiddle",
                         halign = "htCenter") %>%
+                hot_col(3, readOnly = TRUE) %>%
                 hot_col(c(1, 5, 10, 11, 12),
                         readOnly = TRUE) %>%
                 hot_col(3:(12 + nrow(DB$cust_var)), 
@@ -9921,6 +9927,7 @@ server <- function(input, output, session) {
                   hot_col(1, 
                           valign = "htMiddle",
                           halign = "htCenter") %>%
+                  hot_col(3, readOnly = TRUE) %>%
                   hot_col(c(1, 5, 10, 11, 12),
                           readOnly = TRUE) %>%
                   hot_col(3:(12 + nrow(DB$cust_var)), 
@@ -10077,6 +10084,7 @@ server <- function(input, output, session) {
                   hot_col(1, 
                           valign = "htMiddle",
                           halign = "htCenter") %>%
+                  hot_col(3, readOnly = TRUE) %>%
                   hot_col(c(1, 5, 10, 11, 12),
                           readOnly = TRUE) %>%
                   hot_col(3:(12 + nrow(DB$cust_var)), 
@@ -10221,6 +10229,7 @@ server <- function(input, output, session) {
                   hot_col(3:(12 + nrow(DB$cust_var)), 
                           valign = "htMiddle",
                           halign = "htLeft") %>%
+                  hot_col(3, readOnly = TRUE) %>%
                   hot_col(3, validator = "
                                   function(value, callback) {
                                     try {
@@ -10374,6 +10383,7 @@ server <- function(input, output, session) {
                           halign = "htCenter") %>%
                   hot_col(c(1, 5, 10, 11, 12),
                           readOnly = TRUE) %>%
+                  hot_col(3, readOnly = TRUE) %>%
                   hot_col(3, validator = "
                                   function(value, callback) {
                                     try {
@@ -24300,9 +24310,7 @@ server <- function(input, output, session) {
     Typing$new_table <- mutate(hot_to_r(input$multi_select_table),
                                Include = as.logical(Include))
     
-    ahaaa <<- hot_to_r(input$multi_select_table)
-    
-    multi_select_table <<- hot_to_r(input$multi_select_table)[hot_to_r(input$multi_select_table)$Include == TRUE,]
+    multi_select_table <- hot_to_r(input$multi_select_table)[hot_to_r(input$multi_select_table)$Include == TRUE,]
     
     if(any(unlist(gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", Typing$genome_selected[which(Typing$genome_selected$Include == TRUE),]$Files)) %in% unlist(DB$data["Assembly ID"]))) {
       show_toast(

From 675b68b1c4975300a57ab612a04a41a435b662d8 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Mon, 5 Aug 2024 12:43:37 +0200
Subject: [PATCH 33/75] Fixes in multi typing file selection & UI

---
 App.R           | 164 +++++++++++++++++++++++++++++++++++-------------
 www/resources.R |   2 +
 2 files changed, 124 insertions(+), 42 deletions(-)

diff --git a/App.R b/App.R
index 7e5763f..79a0d05 100644
--- a/App.R
+++ b/App.R
@@ -5330,7 +5330,7 @@ ui <- dashboardPage(
         fluidRow(
           column(
             width = 3,
-            align = "left",
+            align = "center",
             h2(p("Resistance Profiles"), style = "color:white; margin-bottom: -20px")
           ),
           column(
@@ -6128,8 +6128,11 @@ server <- function(input, output, session) {
     
     log_print("Input load")
     
+    # reset typing status on start(
     if(Typing$status == "Finalized") {Typing$status <- "Inactive"}
-    
+    if(!is.null(Typing$single_path)) {Typing$single_path <- data.frame()}
+    if(!is.null(Screening$single_path)) {Screening$single_path <- data.frame()}
+   
     #### Render status bar ----
     observe({
       req(DB$scheme)
@@ -6495,6 +6498,14 @@ server <- function(input, output, session) {
         output$download_scheme_info <- NULL
         output$download_loci <- NULL
         output$entry_table_controls <- NULL
+        output$multi_stop <- NULL
+        output$metadata_multi_box <- NULL
+        output$start_multi_typing_ui <- NULL
+        output$test_yes_pending <- NULL
+        output$multi_typing_results <- NULL
+        output$single_typing_progress <- NULL
+        output$metadata_single_box <- NULL
+        output$start_typing_ui <- NULL
       }
     } else {
       log_print(paste0("Loading existing ", input$scheme_db, " database from ", DB$database))
@@ -6530,6 +6541,16 @@ server <- function(input, output, session) {
         output$tree_nj <- NULL
         output$tree_upgma <- NULL
         
+        # null typing initiation UI
+        output$multi_stop <- NULL
+        output$metadata_multi_box <- NULL
+        output$start_multi_typing_ui <- NULL
+        output$test_yes_pending <- NULL
+        output$multi_typing_results <- NULL
+        output$single_typing_progress <- NULL
+        output$metadata_single_box <- NULL
+        output$start_typing_ui <- NULL
+        
         # null report values
         Report$report_list_mst <- list()
         Report$report_list_nj <- list()
@@ -7071,6 +7092,53 @@ server <- function(input, output, session) {
                   )
                 })
                 
+                output$initiate_multi_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(), br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyDirButton(
+                          "genome_file_multi",
+                          "Browse",
+                          icon = icon("folder-open"),
+                          title = "Select the folder containing the genome assemblies (FASTA)",
+                          buttonType = "default",
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("multi_select_info"),
+                        br()
+                      )
+                    ),
+                    uiOutput("multi_select_tab_ctrls"),#
+                    br(),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "left",
+                        rHandsontableOutput("multi_select_table")
+                      )
+                    )
+                  )
+                })
+                
                 if(!anyNA(DB$allelic_profile)) {
                   
                   # no NA's -> dont render missing values sidebar elements
@@ -9284,6 +9352,14 @@ server <- function(input, output, session) {
                 output$missing_values <- NULL
                 output$delete_box <- NULL
                 output$entry_table_controls <- NULL
+                output$multi_stop <- NULL
+                output$metadata_multi_box <- NULL
+                output$start_multi_typing_ui <- NULL
+                output$test_yes_pending <- NULL
+                output$multi_typing_results <- NULL
+                output$single_typing_progress <- NULL
+                output$metadata_single_box <- NULL
+                output$start_typing_ui <- NULL
                 
               }
             }
@@ -11667,34 +11743,33 @@ server <- function(input, output, session) {
     )
   })
   
-  # Download Target Info (CSV Table)#
-  #TODO
-  # observe({
-  #   input$download_cgMLST
-  #   
-  #   scheme_overview <- read_html(Scheme$link_scheme) %>%
-  #     html_table(header = FALSE) %>%
-  #     as.data.frame(stringsAsFactors = FALSE)
-  #   
-  #   last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"], 
-  #                                  format = "%B %d, %Y, %H:%M %p")
-  #   names(scheme_overview) <- NULL
-  #   
-  #   last_file_change <- format(
-  #     file.info(file.path(DB$database,
-  #                         ".downloaded_schemes",
-  #                         paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
-  #   
-  #   output$cgmlst_scheme <- renderTable({scheme_overview})
-  #   output$scheme_update_info <- renderText({
-  #     req(last_file_change)
-  #     if (last_file_change < last_scheme_change) {
-  #       "(Newer scheme available \u274c)"
-  #     } else {
-  #       "(Scheme is up-to-date \u2705)"
-  #     }
-  #   })
-  # })
+  # Download Target Info (CSV Table)
+  observe({
+    input$download_cgMLST
+
+    scheme_overview <- read_html(Scheme$link_scheme) %>%
+      html_table(header = FALSE) %>%
+      as.data.frame(stringsAsFactors = FALSE)
+
+    last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"],
+                                   format = "%B %d, %Y, %H:%M %p")
+    names(scheme_overview) <- NULL
+
+    last_file_change <- format(
+      file.info(file.path(DB$database,
+                          ".downloaded_schemes",
+                          paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
+
+    output$cgmlst_scheme <- renderTable({scheme_overview})
+    output$scheme_update_info <- renderText({
+      req(last_file_change)
+      if (last_file_change < last_scheme_change) {
+        "(Newer scheme available \u274c)"
+      } else {
+        "(Scheme is up-to-date \u2705)"
+      }
+    })
+  })
   
   # _______________________ ####
   
@@ -23886,14 +23961,16 @@ server <- function(input, output, session) {
     
     Typing$multi_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)
     
-    selected_files <- list.files(as.character(Typing$multi_path))[which(!endsWith(list.files(as.character(Typing$multi_path)), ".gz"))]
+    files_selected <- list.files(as.character(Typing$multi_path))
+    files_filtered <- files_selected[which(!endsWith(files_selected, ".gz") &
+                                             grepl("\\.fasta|\\.fna|\\.fa", files_selected))]
     
     Typing$multi_sel_table <- data.frame(
-      Include = rep(TRUE, length(selected_files)),
+      Include = rep(TRUE, length(files_filtered)),
       Files = gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", 
-                   selected_files),
+                   files_filtered),
       Type = sub(".*(\\.fasta|\\.fasta\\.gz|\\.fna|\\.fna\\.gz|\\.fa|\\.fa\\.gz)$",
-                 "\\1", selected_files, perl = F))
+                 "\\1", files_filtered, perl = F))
     
     if(nrow(Typing$multi_sel_table) > 0) {
       output$multi_select_tab_ctrls <- renderUI(
@@ -23920,7 +23997,8 @@ server <- function(input, output, session) {
           column(2),
           column(
             width = 5,
-            align = "left",
+            align = "right",
+            br(),
             uiOutput("multi_select_issues")
           )
         )
@@ -24312,7 +24390,7 @@ server <- function(input, output, session) {
     
     multi_select_table <- hot_to_r(input$multi_select_table)[hot_to_r(input$multi_select_table)$Include == TRUE,]
     
-    if(any(unlist(gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", Typing$genome_selected[which(Typing$genome_selected$Include == TRUE),]$Files)) %in% unlist(DB$data["Assembly ID"]))) {
+    if(any(unlist(gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", multi_select_table$Files)) %in% unlist(DB$data["Assembly ID"]))) {
       show_toast(
         title = "Assembly ID(s) already present",
         type = "error",
@@ -24484,13 +24562,12 @@ server <- function(input, output, session) {
           align = "center",
           br(),
           br(),
-          h3(p("Initiate Typing"), style = "color:white, margin-left: 15px"),
-          br(),
-          br(),
+          h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+          br(), br(),
           p(
             HTML(
               paste(
-                tags$span(style='color: white; font-size: 15px; margin-left: 15px', 'Select Assembly Folder')
+                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
               )
             )
           ),
@@ -24513,6 +24590,8 @@ server <- function(input, output, session) {
               br()
             )
           ),
+          uiOutput("multi_select_tab_ctrls"),#
+          br(),
           fluidRow(
             column(1),
             column(
@@ -24572,8 +24651,7 @@ server <- function(input, output, session) {
         br(),
         br(),
         h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-        br(),
-        br(),
+        br(), br(),
         p(
           HTML(
             paste(
@@ -24600,6 +24678,8 @@ server <- function(input, output, session) {
             br()
           )
         ),
+        uiOutput("multi_select_tab_ctrls"),#
+        br(),
         fluidRow(
           column(1),
           column(
diff --git a/www/resources.R b/www/resources.R
index fc46c7f..812f092 100644
--- a/www/resources.R
+++ b/www/resources.R
@@ -1,7 +1,9 @@
 # Resources
 
+#TODO remove B pertussis from list
 amrfinder_species <- c(
   "Acinetobacter_baumannii", "Burkholderia_cepacia", "Burkholderia_mallei_FLI", 
+  "Bordetella_pertussis",
   "Burkholderia_mallei_RKI", "Burkholderia_pseudomallei", "Campylobacter_jejuni_coli",
   "Citrobacter_freundii", "Clostridioides_difficile", "Corynebacterium_diphtheriae", 
   "Enterobacter_asburiae", "Enterobacter_cloacae", "Enterococcus_faecalis", 

From d3db7c29533cd05fb7ed2d4133c90feaaaa26c0a Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Mon, 5 Aug 2024 17:53:16 +0200
Subject: [PATCH 34/75] Short hash formating in Loci Info tab

---
 App.R | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/App.R b/App.R
index 07d717b..eb1ac4c 100644
--- a/App.R
+++ b/App.R
@@ -11080,7 +11080,7 @@ server <- function(input, output, session) {
     
     fasta <- format_fasta(DB$loci[input$db_loci_rows_selected])
     
-    seq <- fasta[[which(fasta == paste0(">", gsub("Variant ", "", sub(" -.*", "", input$seq_sel)))) + 1]]
+    seq <- fasta[[which(fasta == paste0(">", gsub("Allele ", "", sub(" -.*", "", input$seq_sel)))) + 1]]
     
     DB$seq <- seq
     
@@ -11131,12 +11131,18 @@ server <- function(input, output, session) {
       present <- which(choices %in% names(vec))
       absent <- which(!(choices %in% names(vec)))
       
-      choices[present] <- paste0("Variant ", choices[present], " - ", unname(var_count), " times in DB (", unname(perc), ")")
+      choices[present] <- paste0("Allele ", choices[present], " - ", unname(var_count), " times in DB (", unname(perc), ")")
       
-      choices[absent] <- paste0("Variant ", choices[absent], " - not present")
+      choices[absent] <- paste0("Allele ", choices[absent], " - not present")
       
       choices <- c(choices[present], choices[absent])
       
+      names(choices) <- sapply(choices, function(x) {
+        x <- strsplit(x, " ")[[1]]
+        x[2] <- paste0(substr(x[2], 1, 4), "...", substr(x[2], nchar(x[2])-3, nchar(x[2])))
+        paste(x, collapse = " ")
+      })
+      
       column(
         width = 3,
         selectInput(

From a510d298cb59284cf163aee9b11200b6c7991923 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Mon, 5 Aug 2024 19:08:17 +0200
Subject: [PATCH 35/75] Fixed minor hashing errors

---
 execute/multi_eval.R  | 4 ++--
 execute/single_eval.R | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index d2c19f3..3e99c4c 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -123,7 +123,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
           
         } else if(variant_valid != FALSE) {
           
-          hashed_variant <- openssl::sha256(variant_valid)
+          hashed_variant <- as.character(openssl::sha256(variant_valid))
           
           # Append new variant number to allele fasta file
           cat(paste0("\n>", hashed_variant), file = locus_file, append = TRUE)
@@ -132,7 +132,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
           cat(paste0("\n", variant_valid, "\n"), file = locus_file, append = TRUE)
           
           # Entry in results data frame
-          event_list[[basename(assembly)]] <- rbind(event_list[[basename(assembly)]], data.frame(Locus = allele_index, Event = "New Variant", Value = as.character(hashed_variant)))
+          event_list[[basename(assembly)]] <- rbind(event_list[[basename(assembly)]], data.frame(Locus = allele_index, Event = "New Variant", Value = hashed_variant))
           
           allele_vector[[i]] <- hashed_variant
           
diff --git a/execute/single_eval.R b/execute/single_eval.R
index 9b65f81..26681ff 100644
--- a/execute/single_eval.R
+++ b/execute/single_eval.R
@@ -111,7 +111,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
           
         } else if(variant_valid != FALSE) {
           
-          hashed_variant <- openssl::sha256(variant_valid)
+          hashed_variant <- as.character(openssl::sha256(variant_valid))
           
           # Append new variant number to allele fasta file
           cat(paste0("\n>", hashed_variant), file = locus_file, append = TRUE)

From 7ddb27ec968a311312a4c7c071c6066231196157 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Mon, 5 Aug 2024 19:08:48 +0200
Subject: [PATCH 36/75] Added short hash formatting in Browse Local Database

---
 App.R | 53 ++++++++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 48 insertions(+), 5 deletions(-)

diff --git a/App.R b/App.R
index eb1ac4c..128daa5 100644
--- a/App.R
+++ b/App.R
@@ -7744,8 +7744,10 @@ server <- function(input, output, session) {
                   observe({
                     
                     if (!is.null(DB$data)) {
+                      save(DB, file="database.Rdata")
                       if (nrow(DB$data) == 1) {
                         if(!is.null(DB$data) & !is.null(DB$cust_var)) {
+                          write.csv(DB$data, "dataframe.csv")
                           output$db_entries <- renderRHandsontable({
                             rhandsontable(
                               select(DB$data, 1:(12 + nrow(DB$cust_var))),
@@ -7838,7 +7840,7 @@ server <- function(input, output, session) {
                                                        }") 
                           })
                         }
-                      } else if (between(nrow(DB$data), 1, 40)) {
+                      } else if (between(nrow(DB$data), 2, 40)) {
                         if (length(input$compare_select) > 0) {
                           if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
                             output$db_entries <- renderRHandsontable({
@@ -7856,7 +7858,18 @@ server <- function(input, output, session) {
                               )  %>%
                                 hot_col((13 + nrow(DB$cust_var)):((12 + nrow(DB$cust_var)) + length(input$compare_select)), 
                                         valign = "htMiddle",
-                                        halign = "htCenter") %>%
+                                        halign = "htCenter",
+                                        renderer = htmlwidgets::JS(
+                                          "function(instance, td, row, col, prop, value, cellProperties) {
+                                            if (value.length > 8) {
+                                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                                            }
+                                            td.innerHTML = value;
+                                            td.style.textAlign = 'center';
+                                            return td;
+                                           }"
+                                          )
+                                        ) %>%
                                 hot_col(1, 
                                         valign = "htMiddle",
                                         halign = "htCenter") %>%
@@ -8156,7 +8169,17 @@ server <- function(input, output, session) {
                                 hot_col((13 + nrow(DB$cust_var)):((12 + nrow(DB$cust_var)) + length(input$compare_select)),
                                         readOnly = TRUE, 
                                         valign = "htMiddle",
-                                        halign = "htCenter") %>%
+                                        halign = "htCenter",
+                                        renderer = htmlwidgets::JS(
+                                          "function(instance, td, row, col, prop, value, cellProperties) {
+                                            if (value.length > 8) {
+                                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                                            }
+                                            td.innerHTML = value;
+                                            td.style.textAlign = 'center';
+                                            return td;
+                                           }")
+                                        ) %>%
                                 hot_col(3:(12 + nrow(DB$cust_var)), 
                                         valign = "htMiddle",
                                         halign = "htLeft") %>%
@@ -9861,7 +9884,17 @@ server <- function(input, output, session) {
                 )  %>%
                   hot_col((13 + nrow(DB$cust_var)):((12 + nrow(DB$cust_var)) + length(input$compare_select)), 
                           valign = "htMiddle",
-                          halign = "htCenter") %>%
+                          halign = "htCenter",
+                          renderer = htmlwidgets::JS(
+                            "function(instance, td, row, col, prop, value, cellProperties) {
+                                            if (value.length > 8) {
+                                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                                            }
+                                            td.innerHTML = value;
+                                            td.style.textAlign = 'center';
+                                            return td;
+                                           }")
+                          ) %>%
                   hot_col(1, 
                           valign = "htMiddle",
                           halign = "htCenter") %>%
@@ -10161,7 +10194,17 @@ server <- function(input, output, session) {
                   hot_col((13 + nrow(DB$cust_var)):((12 + nrow(DB$cust_var)) + length(input$compare_select)),
                           readOnly = TRUE, 
                           valign = "htMiddle",
-                          halign = "htCenter") %>%
+                          halign = "htCenter",
+                          renderer = htmlwidgets::JS(
+                            "function(instance, td, row, col, prop, value, cellProperties) {
+                                            if (value.length > 8) {
+                                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                                            }
+                                            td.innerHTML = value;
+                                            td.style.textAlign = 'center';
+                                            return td;
+                                           }")
+                          ) %>%
                   hot_col(3:(12 + nrow(DB$cust_var)), 
                           valign = "htMiddle",
                           halign = "htLeft") %>%

From 49576b218708d603ac8ba03aebaa6f85c694cc47 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Mon, 5 Aug 2024 19:12:37 +0200
Subject: [PATCH 37/75] Removed debug lines

---
 App.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/App.R b/App.R
index 128daa5..67289fa 100644
--- a/App.R
+++ b/App.R
@@ -7744,10 +7744,8 @@ server <- function(input, output, session) {
                   observe({
                     
                     if (!is.null(DB$data)) {
-                      save(DB, file="database.Rdata")
                       if (nrow(DB$data) == 1) {
                         if(!is.null(DB$data) & !is.null(DB$cust_var)) {
-                          write.csv(DB$data, "dataframe.csv")
                           output$db_entries <- renderRHandsontable({
                             rhandsontable(
                               select(DB$data, 1:(12 + nrow(DB$cust_var))),

From 8b6ec3d593461e0075a1c117bc0304dc94e015c2 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Tue, 6 Aug 2024 00:11:35 +0200
Subject: [PATCH 38/75] Adaptions of assembly file naming and saving for multi
 typing

---
 App.R                   | 732 ++++++++++++++++++----------------------
 execute/multi_eval.R    |  13 +
 execute/multi_typing.sh |  12 +-
 3 files changed, 347 insertions(+), 410 deletions(-)

diff --git a/App.R b/App.R
index 79a0d05..6a1bbba 100644
--- a/App.R
+++ b/App.R
@@ -551,9 +551,9 @@ ui <- dashboardPage(
         tabName = "typing",
         fluidRow(
           column(
-          width = 3,
-          align = "center",
-          h2(p("Generate Allelic Profile"), style = "color:white")
+            width = 3,
+            align = "center",
+            h2(p("Generate Allelic Profile"), style = "color:white")
           )
         ),
         hr(),
@@ -5368,7 +5368,7 @@ server <- function(input, output, session) {
   session$onSessionEnded( function() {
     stopApp()
   })
-   
+  
   # Disable various user inputs (visualization control)
   shinyjs::disable('mst_edge_label') 
   
@@ -5675,25 +5675,11 @@ server <- function(input, output, session) {
   
   #Function to check for duplicate isolate IDs for multi typing start
   dupl_mult_id <- reactive({
-    req(Typing$multi_sel_table, DB$data)
-    if(!is.null(Typing$new_table)) {
-      selection <- Typing$new_table[which(unlist(Typing$new_table$Files) %in% unlist(DB$data["Assembly ID"])),]
-      as.numeric(rownames(selection[selection$Include == TRUE,]))
-    } else {
-      selection <- Typing$multi_sel_table[which(unlist(Typing$multi_sel_table$Files) %in% unlist(DB$data["Assembly ID"])),]
-      as.numeric(rownames(selection[selection$Include == TRUE,]))
-    }
-  })
-  
-  dupl_mult_id_names <- reactive({
-    req(Typing$multi_sel_table, DB$data)
-    if(!is.null(Typing$new_table)) {
-      selection <- Typing$new_table[which(unlist(Typing$new_table$Files) %in% unlist(DB$data["Assembly ID"])),]
-      selection$Files
-    } else {
+    req(Typing$multi_sel_table)
+    if(!is.null(DB$data)) {
       selection <- Typing$multi_sel_table[which(unlist(Typing$multi_sel_table$Files) %in% unlist(DB$data["Assembly ID"])),]
       selection$Files
-    }
+    } else {""}
   })
   
   # Function to check single typing log file
@@ -6132,7 +6118,7 @@ server <- function(input, output, session) {
     if(Typing$status == "Finalized") {Typing$status <- "Inactive"}
     if(!is.null(Typing$single_path)) {Typing$single_path <- data.frame()}
     if(!is.null(Screening$single_path)) {Screening$single_path <- data.frame()}
-   
+    
     #### Render status bar ----
     observe({
       req(DB$scheme)
@@ -6314,8 +6300,6 @@ server <- function(input, output, session) {
       
       Typing$single_path <- data.frame()
       
-      Typing$multi_path <- data.frame()
-      
       # reset results file 
       if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
         unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
@@ -6519,19 +6503,12 @@ server <- function(input, output, session) {
         saveRDS(DB$database, paste0(getwd(), "/execute/last_db.rds"))
         
         DB$check_new_entries <- TRUE
-        
         DB$data <- NULL
-        
         DB$meta_gs <- NULL
-        
         DB$meta <- NULL
-        
         DB$meta_true <- NULL
-        
         DB$allelic_profile <- NULL
-        
         DB$allelic_profile_true <- NULL
-        
         DB$scheme <- input$scheme_db
         
         # null Distance matrix, entry table and plots
@@ -7036,8 +7013,6 @@ server <- function(input, output, session) {
                 
                 Typing$single_path <- data.frame()
                 
-                Typing$multi_path <- data.frame()
-                
                 # Null multi typing feedback variable
                 Typing$reset <- TRUE
                 
@@ -7126,7 +7101,7 @@ server <- function(input, output, session) {
                         br()
                       )
                     ),
-                    uiOutput("multi_select_tab_ctrls"),#
+                    uiOutput("multi_select_tab_ctrls"),
                     br(),
                     fluidRow(
                       column(1),
@@ -9361,6 +9336,132 @@ server <- function(input, output, session) {
                 output$metadata_single_box <- NULL
                 output$start_typing_ui <- NULL
                 
+                output$initiate_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(),
+                    br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyFilesButton(
+                          "genome_file",
+                          "Browse" ,
+                          icon = icon("file"),
+                          title = "Select the assembly in .fasta/.fna/.fa format:",
+                          multiple = FALSE,
+                          buttonType = "default",
+                          class = NULL,
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("genome_path"),
+                        br()
+                      )
+                    )
+                  )
+                })
+                
+                output$initiate_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(),
+                    br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyFilesButton(
+                          "genome_file",
+                          "Browse" ,
+                          icon = icon("file"),
+                          title = "Select the assembly in .fasta/.fna/.fa format:",
+                          multiple = FALSE,
+                          buttonType = "default",
+                          class = NULL,
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("genome_path"),
+                        br()
+                      )
+                    )
+                  )
+                })
+                
+                output$initiate_multi_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(), br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyDirButton(
+                          "genome_file_multi",
+                          "Browse",
+                          icon = icon("folder-open"),
+                          title = "Select the folder containing the genome assemblies (FASTA)",
+                          buttonType = "default",
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("multi_select_info"),
+                        br()
+                      )
+                    ),
+                    uiOutput("multi_select_tab_ctrls"),
+                    br(),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "left",
+                        rHandsontableOutput("multi_select_table")
+                      )
+                    )
+                  )
+                })
               }
             }
           }
@@ -11746,20 +11847,20 @@ server <- function(input, output, session) {
   # Download Target Info (CSV Table)
   observe({
     input$download_cgMLST
-
+    
     scheme_overview <- read_html(Scheme$link_scheme) %>%
       html_table(header = FALSE) %>%
       as.data.frame(stringsAsFactors = FALSE)
-
+    
     last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"],
                                    format = "%B %d, %Y, %H:%M %p")
     names(scheme_overview) <- NULL
-
+    
     last_file_change <- format(
       file.info(file.path(DB$database,
                           ".downloaded_schemes",
                           paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
-
+    
     output$cgmlst_scheme <- renderTable({scheme_overview})
     output$scheme_update_info <- renderText({
       req(last_file_change)
@@ -17741,9 +17842,9 @@ server <- function(input, output, session) {
   mst_tree <- reactive({
     Typing$data <- toVisNetworkData(Vis$ggraph_1)
     Typing$data$nodes <- mutate(Typing$data$nodes, 
-                         label = label_mst(),
-                         value = mst_node_scaling(),
-                         opacity = node_opacity())
+                                label = label_mst(),
+                                value = mst_node_scaling(),
+                                opacity = node_opacity())
     
     ctxRendererJS <- htmlwidgets::JS("({ctx, id, x, y, state: { selected, hover }, style, font, label, metadata}) => {
                             var pieData = JSON.parse(metadata);
@@ -17866,13 +17967,13 @@ server <- function(input, output, session) {
     }
     
     Typing$data$edges <- mutate(Typing$data$edges,
-                         length = if(input$mst_scale_edges == FALSE) {
-                           input$mst_edge_length
-                         } else {
-                           Typing$data$edges$weight * input$mst_edge_length_scale
-                         },
-                         label = as.character(Typing$data$edges$weight),
-                         opacity = input$mst_edge_opacity)
+                                length = if(input$mst_scale_edges == FALSE) {
+                                  input$mst_edge_length
+                                } else {
+                                  Typing$data$edges$weight * input$mst_edge_length_scale
+                                },
+                                label = as.character(Typing$data$edges$weight),
+                                opacity = input$mst_edge_opacity)
     
     if (input$mst_show_clusters) {
       Typing$data$nodes$group <- compute_clusters(Typing$data$nodes, Typing$data$edges, input$mst_cluster_threshold)
@@ -17884,36 +17985,36 @@ server <- function(input, output, session) {
                                    main = mst_title(),
                                    background = mst_background_color(),
                                    submain = mst_subtitle()) %>%
-                          visNodes(size = mst_node_size(),
-                                   shape = input$mst_node_shape,
-                                   shadow = input$mst_shadow,
-                                   color = mst_color_node(),
-                                   ctxRenderer = ctxRendererJS,
-                                   scaling = list(min = mst_node_size_min(),
-                                                  max = mst_node_size_max()),
-                                   font = list(color = node_font_color(),
-                                               size = input$node_label_fontsize)) %>%
-                          visEdges(color = mst_color_edge(),
-                                   font = list(color = mst_edge_font_color(),
-                                               size = mst_edge_font_size(),
-                                               strokeWidth = 4)) %>%
-                          visOptions(collapse = TRUE) %>%
-                          visInteraction(hover = TRUE) %>%
-                          visLayout(randomSeed = 1) %>%
-                          visLegend(useGroups = FALSE,
-                                    zoom = TRUE,
-                                    width = legend_width(),
-                                    position = input$mst_legend_ori,
-                                    ncol = legend_col(),
-                                    addNodes = mst_legend())
-
+      visNodes(size = mst_node_size(),
+               shape = input$mst_node_shape,
+               shadow = input$mst_shadow,
+               color = mst_color_node(),
+               ctxRenderer = ctxRendererJS,
+               scaling = list(min = mst_node_size_min(),
+                              max = mst_node_size_max()),
+               font = list(color = node_font_color(),
+                           size = input$node_label_fontsize)) %>%
+      visEdges(color = mst_color_edge(),
+               font = list(color = mst_edge_font_color(),
+                           size = mst_edge_font_size(),
+                           strokeWidth = 4)) %>%
+      visOptions(collapse = TRUE) %>%
+      visInteraction(hover = TRUE) %>%
+      visLayout(randomSeed = 1) %>%
+      visLegend(useGroups = FALSE,
+                zoom = TRUE,
+                width = legend_width(),
+                position = input$mst_legend_ori,
+                ncol = legend_col(),
+                addNodes = mst_legend())
+    
     if (input$mst_show_clusters) {
       if (input$mst_cluster_col_scale == "Viridis") {
         color_palette <- viridis(length(data$nodes$group))
       } else {
         color_palette <- rainbow(length(data$nodes$group))
       }
-
+      
       for (i in 1:length(unique(data$nodes$group))) {
         visNetwork_graph <- visNetwork_graph %>% 
           visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
@@ -22768,7 +22869,7 @@ server <- function(input, output, session) {
     }
   })
   
-
+  
   # _______________________ ####
   
   ## Typing  ----
@@ -23693,7 +23794,7 @@ server <- function(input, output, session) {
           br()
         )
       ),
-      uiOutput("multi_select_tab_ctrls"),#
+      uiOutput("multi_select_tab_ctrls"),
       br(),
       fluidRow(
         column(1),
@@ -23708,13 +23809,14 @@ server <- function(input, output, session) {
   
   # Render selection info
   output$multi_select_info <- renderUI({
+    
     if(!is.null(Typing$multi_path)) {
       if(length(Typing$multi_path) < 1) {
         HTML(paste("<span style='color: white; margin-left:-30px'>", 
                    "No files selected."))
       } else {
         HTML(paste("<span style='color: white; margin-left:-30px'>",
-                   sum(Typing$genome_selected$Include == TRUE),
+                   sum(hot_to_r(input$multi_select_table)$Include == TRUE),
                    " files selected."))
       }
     }
@@ -23722,8 +23824,8 @@ server <- function(input, output, session) {
   
   # Render multi selection table issues
   output$multi_select_issues <- renderUI({
-    req(Typing$multi_sel_table, Typing$genome_selected, input$multi_select_table)
-    if(any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id_names()) & 
+    req(Typing$multi_sel_table, input$multi_select_table)
+    if(any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
        any(duplicated(hot_to_r(input$multi_select_table)$Files))){
       HTML(
         paste(
@@ -23733,13 +23835,13 @@ server <- function(input, output, session) {
                 "Duplicated name(s). <br/>")
         )
       )
-    } else if (any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id_names()) & 
+    } else if (any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
                !any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
       HTML(
         paste("<span style='color: #e0b300;'>",
               "Some name(s) are already present in local database.<br/>")
       )
-    } else if (!any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id_names()) & 
+    } else if (!any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
                any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
       HTML(
         paste("<span style='color: #ff7334;'>",
@@ -23749,13 +23851,32 @@ server <- function(input, output, session) {
   })
   
   output$multi_select_issue_info <- renderUI({
-    req(Typing$multi_sel_table, Typing$genome_selected, input$multi_select_table)
-    if(any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id_names()) | 
-       any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
-      HTML(
-        paste("<span style='color: orange; font-style:italic'>",
-              "Rename highlighted isolates.")
-      )
+    req(Typing$multi_sel_table, input$multi_select_table)
+    
+    multi_select_table <- hot_to_r(input$multi_select_table)
+    
+    if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
+       any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)])) |
+       any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
+      
+      if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)])))  {
+        
+        if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
+           any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
+          HTML(paste(
+            paste("<span style='color: orange; font-style:italic'>",
+                  "Rename highlighted isolates or deselect them.</br>"),
+            paste("<span style='color: orange; font-style:italic'>",
+                  "Filename(s) contain(s) empty spaces.")
+          ))
+        } else {
+          HTML(paste("<span style='color: orange; font-style:italic'>",
+                     "Filename(s) contain(s) empty spaces."))
+        }
+      } else {
+        HTML(paste("<span style='color: orange; font-style:italic'>", 
+                   "Rename highlighted isolates or deselect them."))
+      }
     }
   })
   
@@ -23795,8 +23916,6 @@ server <- function(input, output, session) {
           )
         )
         
-        Typing$genome_selected <- hot_to_r(input$multi_select_table)
-        
         output$metadata_multi_box <- renderUI({
           column(
             width = 3,
@@ -23962,15 +24081,15 @@ server <- function(input, output, session) {
     Typing$multi_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)
     
     files_selected <- list.files(as.character(Typing$multi_path))
-    files_filtered <- files_selected[which(!endsWith(files_selected, ".gz") &
-                                             grepl("\\.fasta|\\.fna|\\.fa", files_selected))]
+    Typing$files_filtered <- files_selected[which(!endsWith(files_selected, ".gz") &
+                                                    grepl("\\.fasta|\\.fna|\\.fa", files_selected))]
     
     Typing$multi_sel_table <- data.frame(
-      Include = rep(TRUE, length(files_filtered)),
+      Include = rep(TRUE, length(Typing$files_filtered)),
       Files = gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", 
-                   files_filtered),
+                   Typing$files_filtered),
       Type = sub(".*(\\.fasta|\\.fasta\\.gz|\\.fna|\\.fna\\.gz|\\.fa|\\.fa\\.gz)$",
-                 "\\1", files_filtered, perl = F))
+                 "\\1", Typing$files_filtered, perl = F))
     
     if(nrow(Typing$multi_sel_table) > 0) {
       output$multi_select_tab_ctrls <- renderUI(
@@ -24007,116 +24126,23 @@ server <- function(input, output, session) {
       output$multi_select_tab_ctrls <- NULL
     }
     
-     if (between(nrow(Typing$multi_sel_table), 1, 15)) {
-       if(!is.null(Typing$new_table)) {
-         output$multi_select_table <- renderRHandsontable({
-           rht <- rhandsontable(Typing$new_table, rowHeaders = NULL, 
-                         stretchH = "all", contextMenu = FALSE
-           ) %>%
-             hot_cols(columnSorting = TRUE) %>%
-             hot_rows(rowHeights = 25) %>%
-             hot_col(2,
-                     readOnly = FALSE,
-                     valign = "htBottom") %>%
-             hot_col(3, readOnly = TRUE) %>%
-             hot_col(1,
-                     halign = "htCenter",
-                     valign = "htTop", 
-                     colWidths = 60)
-           
-           htmlwidgets::onRender(rht, sprintf(
-             "function(el, x) {
-        var hot = this.hot;
-        
-        var columnData = hot.getDataAtCol(1); // Change column index if needed
-        var duplicates = {};
-          
-        var highlightInvalidAndDuplicates = function(invalidValues) {
-          
-          var columnData = hot.getDataAtCol(1); // Change column index if needed
-          var duplicates = {};
-
-          // Find all duplicate values
-          for (var i = 0; i < columnData.length; i++) {
-            var value = columnData[i];
-            if (value !== null && value !== undefined) {
-              if (duplicates[value]) {
-                duplicates[value].push(i);
-              } else {
-                duplicates[value] = [i];
-              }
-            }
-          }
-
-          // Reset all cell backgrounds in the column
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            if (cell) {
-              cell.style.background = 'white';
-            }
-          }
-
-          // Highlight duplicates and invalid values
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            var value = columnData[i];
-            if (cell) {
-              if (invalidValues.includes(value)) {
-                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
-              } else if (duplicates[value] && duplicates[value].length > 1) {
-                cell.style.background = '#FF7334'; // Highlight color for duplicates
-              }
-            }
-          }
-        };
-
-        var changefn = function(changes, source) {
-          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
-            highlightInvalidAndDuplicates(%s);
-          }
-        };
-
-        hot.addHook('afterChange', changefn);
-        hot.addHook('afterLoadData', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-        hot.addHook('afterRender', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-
-        highlightInvalidAndDuplicates(%s); // Initial highlight on load
+    if(between(nrow(Typing$multi_sel_table), 1, 15)) {
+      output$multi_select_table <- renderRHandsontable({
+        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
+                             stretchH = "all", contextMenu = FALSE
+        ) %>%
+          hot_cols(columnSorting = TRUE) %>%
+          hot_rows(rowHeights = 25) %>%
+          hot_col(2, readOnly = FALSE,
+                  valign = "htBottom") %>%
+          hot_col(3, readOnly = TRUE) %>%
+          hot_col(1,
+                  halign = "htCenter",
+                  valign = "htTop", 
+                  colWidths = 60)
         
-        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
-          var colData = hot.getDataAtCol(0);
-          for (var i = 0; i < colData.length; i++) {
-            hot.setDataAtCell(i, 0, message.value);
-          }
-          hot.render(); // Re-render the table
-        });
-      }", 
-             jsonlite::toJSON(dupl_mult_id_names()), 
-             jsonlite::toJSON(dupl_mult_id_names()), 
-             jsonlite::toJSON(dupl_mult_id_names()), 
-             jsonlite::toJSON(dupl_mult_id_names())))
-         })
-       } else {
-         output$multi_select_table <- renderRHandsontable({
-           rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
-                         stretchH = "all", contextMenu = FALSE
-           ) %>%
-             hot_cols(columnSorting = TRUE) %>%
-             hot_rows(rowHeights = 25) %>%
-             hot_col(2,
-                     readOnly = FALSE,
-                     valign = "htBottom") %>%
-             hot_col(3, readOnly = TRUE) %>%
-             hot_col(1,
-                     halign = "htCenter",
-                     valign = "htTop", 
-                     colWidths = 60)
-           
-           htmlwidgets::onRender(rht, sprintf(
-             "function(el, x) {
+        htmlwidgets::onRender(rht, sprintf(
+          "function(el, x) {
         var hot = this.hot;
         
         var columnData = hot.getDataAtCol(1); // Change column index if needed
@@ -24185,124 +24211,31 @@ server <- function(input, output, session) {
           hot.render(); // Re-render the table
         });
       }", 
-             jsonlite::toJSON(dupl_mult_id_names()), 
-             jsonlite::toJSON(dupl_mult_id_names()), 
-             jsonlite::toJSON(dupl_mult_id_names()), 
-             jsonlite::toJSON(dupl_mult_id_names())))
-         })
-       }
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id())))
+      })
+      
     } else if(nrow(Typing$multi_sel_table) > 15) {
-      if(!is.null(Typing$new_table)) {
-        output$multi_select_table <- renderRHandsontable({
-          rht <- rhandsontable(Typing$new_table, rowHeaders = NULL, 
-                        stretchH = "all", height = 500,
-                        contextMenu = FALSE
-          ) %>%
-            hot_cols(columnSorting = TRUE) %>%
-            hot_rows(rowHeights = 25) %>%
-            hot_col(2,
-                    readOnly = FALSE,
-                    valign = "htBottom") %>%
-            hot_col(3, readOnly = TRUE) %>%
-            hot_col(1,
-                    halign = "htCenter",
-                    valign = "htTop", 
-                    colWidths = 60)
-          
-          htmlwidgets::onRender(rht, sprintf(
-            "function(el, x) {
-        var hot = this.hot;
+      output$multi_select_table <- renderRHandsontable({
+        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
+                             stretchH = "all", height = 500,
+                             contextMenu = FALSE
+        ) %>%
+          hot_cols(columnSorting = TRUE) %>%
+          hot_rows(rowHeights = 25) %>%
+          hot_col(2,
+                  readOnly = FALSE,
+                  valign = "htBottom") %>%
+          hot_col(3, readOnly = TRUE) %>%
+          hot_col(1,
+                  halign = "htCenter",
+                  valign = "htTop", 
+                  colWidths = 60)
         
-        var columnData = hot.getDataAtCol(1); // Change column index if needed
-        var duplicates = {};
-          
-        var highlightInvalidAndDuplicates = function(invalidValues) {
-          
-          var columnData = hot.getDataAtCol(1); // Change column index if needed
-          var duplicates = {};
-
-          // Find all duplicate values
-          for (var i = 0; i < columnData.length; i++) {
-            var value = columnData[i];
-            if (value !== null && value !== undefined) {
-              if (duplicates[value]) {
-                duplicates[value].push(i);
-              } else {
-                duplicates[value] = [i];
-              }
-            }
-          }
-
-          // Reset all cell backgrounds in the column
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            if (cell) {
-              cell.style.background = 'white';
-            }
-          }
-
-          // Highlight duplicates and invalid values
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            var value = columnData[i];
-            if (cell) {
-              if (invalidValues.includes(value)) {
-                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
-              } else if (duplicates[value] && duplicates[value].length > 1) {
-                cell.style.background = '#FF7334'; // Highlight color for duplicates
-              }
-            }
-          }
-        };
-
-        var changefn = function(changes, source) {
-          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
-            highlightInvalidAndDuplicates(%s);
-          }
-        };
-
-        hot.addHook('afterChange', changefn);
-        hot.addHook('afterLoadData', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-        hot.addHook('afterRender', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-
-        highlightInvalidAndDuplicates(%s); // Initial highlight on load
-        
-        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
-          var colData = hot.getDataAtCol(0);
-          for (var i = 0; i < colData.length; i++) {
-            hot.setDataAtCell(i, 0, message.value);
-          }
-          hot.render(); // Re-render the table
-        });
-      }", 
-            jsonlite::toJSON(dupl_mult_id_names()), 
-            jsonlite::toJSON(dupl_mult_id_names()), 
-            jsonlite::toJSON(dupl_mult_id_names()), 
-            jsonlite::toJSON(dupl_mult_id_names())))
-        })
-      } else {
-        output$multi_select_table <- renderRHandsontable({
-          rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
-                        stretchH = "all", height = 500,
-                        contextMenu = FALSE
-          ) %>%
-            hot_cols(columnSorting = TRUE) %>%
-            hot_rows(rowHeights = 25) %>%
-            hot_col(2,
-                    readOnly = FALSE,
-                    valign = "htBottom") %>%
-            hot_col(3, readOnly = TRUE) %>%
-            hot_col(1,
-                    halign = "htCenter",
-                    valign = "htTop", 
-                    colWidths = 60)
-          
-          htmlwidgets::onRender(rht, sprintf(
-            "function(el, x) {
+        htmlwidgets::onRender(rht, sprintf(
+          "function(el, x) {
         var hot = this.hot;
         
         var columnData = hot.getDataAtCol(1); // Change column index if needed
@@ -24371,23 +24304,20 @@ server <- function(input, output, session) {
           hot.render(); // Re-render the table
         });
       }", 
-            jsonlite::toJSON(dupl_mult_id_names()), 
-            jsonlite::toJSON(dupl_mult_id_names()), 
-            jsonlite::toJSON(dupl_mult_id_names()), 
-            jsonlite::toJSON(dupl_mult_id_names())))
-          
-        })
-      }
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id())))
+        
+      })
+      
     } else {
       output$multi_select_table <- NULL
-    }
+    } 
   })
   
   observeEvent(input$conf_meta_multi, {
     
-    Typing$new_table <- mutate(hot_to_r(input$multi_select_table),
-                               Include = as.logical(Include))
-    
     multi_select_table <- hot_to_r(input$multi_select_table)[hot_to_r(input$multi_select_table)$Include == TRUE,]
     
     if(any(unlist(gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", multi_select_table$Files)) %in% unlist(DB$data["Assembly ID"]))) {
@@ -24400,7 +24330,7 @@ server <- function(input, output, session) {
       )
     } else if (any(duplicated(multi_select_table$Files))) {
       show_toast(
-        title = "Duplicated file name(s)",
+        title = "Duplicated filename(s)",
         type = "error",
         position = "bottom-end",
         timer = 3000,
@@ -24408,23 +24338,21 @@ server <- function(input, output, session) {
       )
     } else if (any(multi_select_table$Files == "")) {
       show_toast(
-        title = "Empty file name(s)",
+        title = "Empty filename(s)",
         type = "error",
         position = "bottom-end",
         timer = 3000,
         width = "500px"
       )
-    } 
-    else if (any(grepl("[/\\:*?\"<>|]", multi_select_table$Files))) {
+    } else if (any(grepl("[/\\:*?\"<>|]", multi_select_table$Files))) {
       show_toast(
-        title = "Invalid file name(s). Not allowed: /\\:*?\"<>|",
+        title = "Invalid filename(s). Not allowed: /\\:*?\"<>|",
         type = "error",
         position = "bottom-end",
         timer = 3000,
         width = "500px"
       )
-    }
-    else if (!any(multi_select_table$Include == TRUE)) {
+    } else if (!any(multi_select_table$Include == TRUE)) {
       show_toast(
         title = "No files selected",
         type = "error",
@@ -24432,8 +24360,15 @@ server <- function(input, output, session) {
         timer = 3000,
         width = "500px"
       )
-    }
-    else {
+    } else if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
+      show_toast(
+        title = "Empty spaces in filename(s) not allowed",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000,
+        width = "500px"
+      )
+    } else {
       
       log_print("Multi typing metadata confirmed")
       
@@ -24554,7 +24489,6 @@ server <- function(input, output, session) {
       # Reset User Feedback variable
       Typing$pending_format <- 0
       Typing$multi_started <- FALSE
-      Typing$multi_path <- data.frame()
       
       output$initiate_multi_typing_ui <- renderUI({
         column(
@@ -24590,7 +24524,7 @@ server <- function(input, output, session) {
               br()
             )
           ),
-          uiOutput("multi_select_tab_ctrls"),#
+          uiOutput("multi_select_tab_ctrls"),
           br(),
           fluidRow(
             column(1),
@@ -24603,8 +24537,6 @@ server <- function(input, output, session) {
         )
       })
       
-      Typing$multi_sel_table <- data.frame()
-      
       output$test_yes_pending <- NULL
       output$multi_typing_results <- NULL
     }
@@ -24678,7 +24610,7 @@ server <- function(input, output, session) {
             br()
           )
         ),
-        uiOutput("multi_select_tab_ctrls"),#
+        uiOutput("multi_select_tab_ctrls"),
         br(),
         fluidRow(
           column(1),
@@ -24713,68 +24645,58 @@ server <- function(input, output, session) {
         width = "500px"
       )
     } else {
-      if (any(!grepl("\\.fasta|\\.fna|\\.fa", str_sub(Typing$genome_selected$Files[which(Typing$genome_selected$Include == TRUE)], start = -6)))) {
-        
-        log_print("Wrong file type (include only fasta/fna/fa)")
-        
-        show_toast(
-          title = "Wrong file type (include only fasta/fna/fa)",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000,
-          width = "500px"
-        )
-      } else {
-        
-        removeModal()
-        
-        show_toast(
-          title = "Multi Typing started",
-          type = "success",
-          position = "bottom-end",
-          timer = 10000,
-          width = "500px"
-        )
-        
-        Typing$new_table <- NULL
-        
-        # Remove Allelic Typing Controls
-        output$initiate_multi_typing_ui <- NULL
-        output$metadata_multi_box <- NULL
-        output$start_multi_typing_ui <- NULL
-        
-        # Activate entry detection
-        DB$check_new_entries <- TRUE
-        
-        # Initiate Feedback variables
-        Typing$multi_started <- TRUE
-        Typing$pending <- TRUE
-        Typing$failures <- 0
-        Typing$successes <- 0
-        
-        # Start Multi Typing Script
-        multi_typing_df <- data.frame(
-          db_path = DB$database,
-          wd = getwd(),
-          save = input$save_assembly_mt,
-          scheme = paste0(gsub(" ", "_", DB$scheme)),
-          genome_folder = as.character(parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)),
-          genome_names = paste(Typing$genome_selected$Files[which(Typing$genome_selected$Include == TRUE)], collapse= " "),
-          alleles = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")
-        )
-        
-        saveRDS(multi_typing_df, "execute/multi_typing_df.rds")
-        
-        # Reset selected
-        Typing$genome_selected <- NULL
-        
-        # Execute multi blat script  
-        system(paste("bash", paste0(getwd(), "/execute/multi_typing.sh")), 
-               wait = FALSE)
-        
-      }
+      removeModal()
+      
+      show_toast(
+        title = "Multi Typing started",
+        type = "success",
+        position = "bottom-end",
+        timer = 10000,
+        width = "500px"
+      )
+      
+      Typing$new_table <- NULL
+      
+      # Remove Allelic Typing Controls
+      output$initiate_multi_typing_ui <- NULL
+      output$metadata_multi_box <- NULL
+      output$start_multi_typing_ui <- NULL
+      
+      # Activate entry detection
+      DB$check_new_entries <- TRUE
+      
+      # Initiate Feedback variables
+      Typing$multi_started <- TRUE
+      Typing$pending <- TRUE
+      Typing$failures <- 0
+      Typing$successes <- 0
+      
+      # get selected file table
+      multi_select_table <- hot_to_r(input$multi_select_table)
+      
+      filenames <- paste(multi_select_table$Files[which(multi_select_table$Include == TRUE)], collapse = " ")
+      
+      files <- Typing$multi_sel_table$Files[which(multi_select_table$Include == TRUE)]
+      type <- Typing$multi_sel_table$Type[which(multi_select_table$Include == TRUE)]
+      genome_names <- paste(paste0(gsub(" ", "~", files), type), collapse = " ")
+      
+      # Start Multi Typing Script
+      multi_typing_df <- data.frame(
+        db_path = DB$database,
+        wd = getwd(),
+        save = input$save_assembly_mt,
+        scheme = paste0(gsub(" ", "_", DB$scheme)),
+        genome_folder = as.character(parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)),
+        filenames = paste0(filenames, collapse= " "),
+        genome_names = genome_names,
+        alleles = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")
+      )
+      
+      saveRDS(multi_typing_df, "execute/multi_typing_df.rds")
+      
+      # Execute multi blat script  
+      system(paste("bash", paste0(getwd(), "/execute/multi_typing.sh")), wait = FALSE)
     }
-    
   })
   
   
@@ -25119,8 +25041,6 @@ server <- function(input, output, session) {
     )
   })
   
-  
-  
 } # end server
 
 # _______________________ ####
diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index 97c2a0d..e0935ae 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -3,6 +3,7 @@ library(logr)
 meta_info <- readRDS("meta_info.rds")
 db_path <- readRDS("multi_typing_df.rds")[, "db_path"]
 save_assembly <- readRDS("multi_typing_df.rds")[, "save"]
+filename <- stringr::str_split(readRDS("multi_typing_df.rds")[, "filenames"], " ")[which(commandArgs(trailingOnly = TRUE)[1] == basename(assembly_folder))]
 assembly_folder <- dir(paste0(getwd(), "/selected_genomes"), full.names = TRUE)
 assembly <- assembly_folder[which(commandArgs(trailingOnly = TRUE)[1] == basename(assembly_folder))]
 results_folder <- dir(paste0(meta_info$db_directory, "/execute/blat_multi/results"), full.names = TRUE)
@@ -338,6 +339,13 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
                                  gsub(" ", "_", meta_info$cgmlst_typing), 
                                  "/Isolates/", basename(assembly)))
       
+      file.rename(paste0(db_path, "/", 
+                         gsub(" ", "_", meta_info$cgmlst_typing), 
+                         "/Isolates/", basename(assembly)),
+                  filename)
+      
+      save_assembly <- readRDS("multi_typing_df.rds")[, "save"]
+      
       log_print(paste0("Saved assembly of ", basename(assembly)))
       
     } else {
@@ -359,6 +367,11 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
                                  gsub(" ", "_", meta_info$cgmlst_typing), 
                                  "/Isolates/", basename(assembly)))
       
+      file.rename(paste0(db_path, "/", 
+                         gsub(" ", "_", meta_info$cgmlst_typing), 
+                         "/Isolates/", basename(assembly)),
+                  filename)
+      
       log_print(paste0("Saved assembly of ", basename(assembly)))
     }
   }
diff --git a/execute/multi_typing.sh b/execute/multi_typing.sh
index 0bb43b7..26274ab 100755
--- a/execute/multi_typing.sh
+++ b/execute/multi_typing.sh
@@ -41,14 +41,18 @@ file_names=($genome_names)
 
 # Loop through the list of file names and copy them to the new folder
 for file in "${file_names[@]}"; do
-    if [ -f "$genome_folder/$file" ]; then
-        cp "$genome_folder/$file" "$selected_genomes/"
-        echo "$(date +"%Y-%m-%d %H:%M:%S") - Initiated $file" >> "$log_file"
+    # Replace tilde with space in the filename
+    new_file="${file//\~/ }"
+    
+    if [ -f "$genome_folder/$new_file" ]; then
+        cp "$genome_folder/$new_file" "$selected_genomes/"
+        echo "$(date +"%Y-%m-%d %H:%M:%S") - Initiated $new_file" >> "$log_file"
     else
-        echo "$(date +"%Y-%m-%d %H:%M:%S") - $file not found in $genome_folder" >> "$log_file"
+        echo "$(date +"%Y-%m-%d %H:%M:%S") - $new_file not found in $genome_folder" >> "$log_file"
     fi
 done
 
+
 #INDEXING GENOME AS DATABASE
 blat_database="$base_path/execute/blat_multi/$scheme"
 

From 0df998d9d5eaeab4ff02eea61752475035d5fc24 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Wed, 7 Aug 2024 15:40:00 +0200
Subject: [PATCH 39/75] Fixes in multi typing analysis chain; slight UI
 adaptions

---
 App.R                   | 46 +++++++++++++++++++++++++++--------------
 execute/multi_eval.R    | 38 +++++++++++-----------------------
 execute/multi_typing.sh | 37 +++++++++++++++++++++++++--------
 www/body.css            | 29 +++++++++++++++++++++-----
 www/head.css            |  6 ++++--
 5 files changed, 98 insertions(+), 58 deletions(-)

diff --git a/App.R b/App.R
index 6a1bbba..61c0c33 100644
--- a/App.R
+++ b/App.R
@@ -23864,19 +23864,32 @@ server <- function(input, output, session) {
         if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
            any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
           HTML(paste(
-            paste("<span style='color: orange; font-style:italic'>",
-                  "Rename highlighted isolates or deselect them.</br>"),
-            paste("<span style='color: orange; font-style:italic'>",
-                  "Filename(s) contain(s) empty spaces.")
+            paste(
+              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+              paste("<span style='color: white; font-style:italic'>",
+                  "&nbspRename highlighted isolates or deselect them.</br>")),
+            paste(
+              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+              paste("<span style='color: white; font-style:italic'>",
+                  "&nbspFilename(s) contain(s) empty spaces."))
           ))
         } else {
-          HTML(paste("<span style='color: orange; font-style:italic'>",
-                     "Filename(s) contain(s) empty spaces."))
+          HTML(paste(
+            '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+            paste("<span style='color: white; font-style:italic'>",
+                     "&nbspFilename(s) contain(s) empty spaces.")))
         }
       } else {
-        HTML(paste("<span style='color: orange; font-style:italic'>", 
-                   "Rename highlighted isolates or deselect them."))
+        HTML(paste(
+          '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+          paste("<span style='color: white; font-style:italic'>", 
+                   "&nbspRename highlighted isolates or deselect them.")))
       }
+    } else {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
+        paste("<span style='color: white; font-style:italic'>",
+              "&nbspFiles ready for allelic typing.")))
     }
   })
   
@@ -24131,7 +24144,7 @@ server <- function(input, output, session) {
         rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
                              stretchH = "all", contextMenu = FALSE
         ) %>%
-          hot_cols(columnSorting = TRUE) %>%
+          hot_cols(columnSorting = FALSE) %>%
           hot_rows(rowHeights = 25) %>%
           hot_col(2, readOnly = FALSE,
                   valign = "htBottom") %>%
@@ -24223,7 +24236,7 @@ server <- function(input, output, session) {
                              stretchH = "all", height = 500,
                              contextMenu = FALSE
         ) %>%
-          hot_cols(columnSorting = TRUE) %>%
+          hot_cols(columnSorting = FALSE) %>%
           hot_rows(rowHeights = 25) %>%
           hot_col(2,
                   readOnly = FALSE,
@@ -24344,9 +24357,9 @@ server <- function(input, output, session) {
         timer = 3000,
         width = "500px"
       )
-    } else if (any(grepl("[/\\:*?\"<>|]", multi_select_table$Files))) {
+    } else if (any(grepl("[()/\\:*?\"<>|]", multi_select_table$Files))) {
       show_toast(
-        title = "Invalid filename(s). Not allowed: /\\:*?\"<>|",
+        title = "Invalid filename(s). No special characters allowed: ()/\\:*?\"<>|",
         type = "error",
         position = "bottom-end",
         timer = 3000,
@@ -24741,9 +24754,9 @@ server <- function(input, output, session) {
     } else if(str_detect(tail(log, 1), "failed")) {
       Typing$status <- "Failed"
       show_toast(
-        title = paste0("Failed typing of ", sub(".*failed for ", "", tail(log, 1))),
+        title = sub(".* - ", "", tail(log, 1)),
         type = "error",
-        width = "500px",
+        width = "700px",
         position = "bottom-end",
         timer = 8000
       )
@@ -24764,11 +24777,12 @@ server <- function(input, output, session) {
           
           Typing$last_success <- tail(log, 2)[1]
         }
-      } else if(any(str_detect(tail(log, 2), "failed for"))) {
+      } else if(any(str_detect(tail(log, 2), "failed"))) {
         
         if(!identical(Typing$last_failure, tail(log, 2)[1])) {
+          
           show_toast(
-            title = paste0("Failed typing of ", sub(".*failed for ", "", tail(log, 2)[1])),
+            title = sub(".* - ", "", tail(log, 2)[1]),
             type = "error",
             width = "500px",
             position = "bottom-end",
diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index e0935ae..d045bc5 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -3,10 +3,13 @@ library(logr)
 meta_info <- readRDS("meta_info.rds")
 db_path <- readRDS("multi_typing_df.rds")[, "db_path"]
 save_assembly <- readRDS("multi_typing_df.rds")[, "save"]
-filename <- stringr::str_split(readRDS("multi_typing_df.rds")[, "filenames"], " ")[which(commandArgs(trailingOnly = TRUE)[1] == basename(assembly_folder))]
-assembly_folder <- dir(paste0(getwd(), "/selected_genomes"), full.names = TRUE)
+assembly_folder <- paste0(paste0(getwd(), "/selected_genomes/"), 
+                          paste0(stringr::str_split_1(readRDS("multi_typing_df.rds")[, "filenames"], " "), 
+                                 ".fasta"))
 assembly <- assembly_folder[which(commandArgs(trailingOnly = TRUE)[1] == basename(assembly_folder))]
-results_folder <- dir(paste0(meta_info$db_directory, "/execute/blat_multi/results"), full.names = TRUE)
+filename <- stringr::str_split_1(readRDS("multi_typing_df.rds")[, "filenames"], " ")[which(commandArgs(trailingOnly = TRUE)[1] == basename(assembly_folder))]
+results_folder <- paste0(paste0(meta_info$db_directory, "/execute/blat_multi/results/"),
+                         stringr::str_split_1(readRDS("multi_typing_df.rds")[, "filenames"], " "))
 
 source("variant_validation.R")
 
@@ -157,9 +160,6 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
   
   saveRDS(event_list, "execute/event_list.rds")
   
-  # Find Alleles folder in directory
-  allele_folder <- list.files(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing)), full.names = TRUE)[grep("_alleles", list.files(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing))))]
-  
   # Create Results Data Frame 
   if(!any(grepl("Typing", list.files(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing)))))) {
     
@@ -332,19 +332,11 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
       # Create folder for new isolate
       dir.create(paste0(db_path, "/", 
                         gsub(" ", "_", meta_info$cgmlst_typing), 
-                        "/Isolates/", basename(assembly)))
+                        "/Isolates/", filename))
       
       # Copy assembly file in isolate directory
-      file.copy(assembly, paste0(db_path, "/", 
-                                 gsub(" ", "_", meta_info$cgmlst_typing), 
-                                 "/Isolates/", basename(assembly)))
-      
-      file.rename(paste0(db_path, "/", 
-                         gsub(" ", "_", meta_info$cgmlst_typing), 
-                         "/Isolates/", basename(assembly)),
-                  filename)
-      
-      save_assembly <- readRDS("multi_typing_df.rds")[, "save"]
+      file.copy(paste0(getwd(), "/execute/selected_genomes/", filename, ".fasta"), 
+                paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates/", filename))
       
       log_print(paste0("Saved assembly of ", basename(assembly)))
       
@@ -360,17 +352,11 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
       # Create folder for new isolate
       dir.create(paste0(db_path, "/", 
                         gsub(" ", "_", meta_info$cgmlst_typing), 
-                        "/Isolates/", basename(assembly)))
+                        "/Isolates/", filename))
       
       # Copy assembly file in isolate directory
-      file.copy(assembly, paste0(db_path, "/", 
-                                 gsub(" ", "_", meta_info$cgmlst_typing), 
-                                 "/Isolates/", basename(assembly)))
-      
-      file.rename(paste0(db_path, "/", 
-                         gsub(" ", "_", meta_info$cgmlst_typing), 
-                         "/Isolates/", basename(assembly)),
-                  filename)
+      file.copy(paste0(getwd(), "/execute/selected_genomes/", filename, ".fasta"), 
+                paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates/", filename))
       
       log_print(paste0("Saved assembly of ", basename(assembly)))
     }
diff --git a/execute/multi_typing.sh b/execute/multi_typing.sh
index 26274ab..1aa57ab 100755
--- a/execute/multi_typing.sh
+++ b/execute/multi_typing.sh
@@ -11,6 +11,7 @@ scheme=$(Rscript -e "cat(readRDS('multi_typing_df.rds')[,'scheme'])")
 genome_folder=$(Rscript -e "cat(readRDS('multi_typing_df.rds')[,'genome_folder'])")
 genome_names=$(Rscript -e "cat(readRDS('multi_typing_df.rds')[,'genome_names'])")
 alleles=$(Rscript -e "cat(readRDS('multi_typing_df.rds')[,'alleles'])")
+rename_file=$(Rscript -e "cat(stringr::str_split_1(readRDS('multi_typing_df.rds')[, 'filenames'], ' '))")
 
 # Remove the existing multi directory
 if [ -d "$base_path/execute/blat_multi" ]; then
@@ -38,21 +39,27 @@ fi
 mkdir $selected_genomes
 
 file_names=($genome_names)
+new_names=($rename_file)
 
+index=0
 # Loop through the list of file names and copy them to the new folder
 for file in "${file_names[@]}"; do
-    # Replace tilde with space in the filename
-    new_file="${file//\~/ }"
+
+    # Replace tilde with space in the filename #TODO
+    new_file=$(echo "$file" | sed 's/~/ /g')
     
     if [ -f "$genome_folder/$new_file" ]; then
         cp "$genome_folder/$new_file" "$selected_genomes/"
+        
+        mv "$selected_genomes/$new_file" "$selected_genomes/${new_names[$index]}.fasta"
+        
         echo "$(date +"%Y-%m-%d %H:%M:%S") - Initiated $new_file" >> "$log_file"
     else
         echo "$(date +"%Y-%m-%d %H:%M:%S") - $new_file not found in $genome_folder" >> "$log_file"
     fi
+    index=$((index + 1))
 done
 
-
 #INDEXING GENOME AS DATABASE
 blat_database="$base_path/execute/blat_multi/$scheme"
 
@@ -60,10 +67,13 @@ blat_database="$base_path/execute/blat_multi/$scheme"
 genome_filename_noext=""
 
 #Indexing Loop
-for genome in "$selected_genomes"/*; do
-    
-    # Check read names of assembly file
-    Rscript "$base_path/execute/check_duplicate_multi.R" "$base_path"
+for genome in "$selected_genomes"/*; do   
+
+    # Check fasta and formatting
+    if ! Rscript "$base_path/execute/check_duplicate_multi.R" "$base_path"; then
+        echo "$(date +"%Y-%m-%d %H:%M:%S") - FASTA check failed. Typing of $(basename "$genome") aborted." >> "$log_file"
+        continue
+    fi
     
     if [ -f "$genome" ]; then
     genome_filename=$(basename "$genome")
@@ -75,9 +85,18 @@ for genome in "$selected_genomes"/*; do
     result_folder="$results/$genome_filename_noext"
     
     # Run parallelized BLAT
-    find "$alleles" -type f \( -name "*.fasta" -o -name "*.fa" -o -name "*.fna" \) | parallel pblat $genome {} "$result_folder/{/.}.psl"  > /dev/null 2>&1
+    if ! find "$alleles" -type f \( -name "*.fasta" -o -name "*.fa" -o -name "*.fna" \) | parallel pblat "$genome" {} "$result_folder/{/.}.psl" > /dev/null 2>&1; then
+        echo "$(date +"%Y-%m-%d %H:%M:%S") - Allele calling failed. Typing of $genome_filename aborted." >> "$log_file"
+        continue
+    fi
     
     echo "$(date +"%Y-%m-%d %H:%M:%S") - Attaching $genome_filename" >> "$log_file"
-    Rscript "$base_path/execute/multi_eval.R" "$genome_filename"
+    
+    # Check fasta and formatting
+    if ! Rscript "$base_path/execute/multi_eval.R" "$genome_filename"; then
+        echo "$(date +"%Y-%m-%d %H:%M:%S") - Results evaluation failed. Typing of $genome_filename aborted." >> "$log_file"
+        continue
+    fi
 done
+
 echo "$(date +"%Y-%m-%d %H:%M:%S") - Multi Typing finalized." >> "$log_file"
diff --git a/www/body.css b/www/body.css
index 696f955..63216a2 100644
--- a/www/body.css
+++ b/www/body.css
@@ -10,10 +10,29 @@ label {
   color: white;
 }
 
+input[type="checkbox"] {
+  accent-color: #20E6E5;
+  height: 15px;
+  width: 15px;
+}
+
+.sF-fileList>div.selected .sF-file-name div, .sF-dirList div.selected>.sF-file-name>div {
+  background: #20E6E5;
+  color: black;
+}
+
+.handsontableInput {
+  box-shadow: inset 0 0 0 2px #20e6e5;
+}
+
+.handsontable .wtBorder.current {
+  background-color: #282F38 !important;
+}
+
 .tooltip-inner {
-      white-space: normal;
-      max-width: 800px; /* Adjust the width as needed */
-    }
+  white-space: normal;
+  max-width: 800px; /* Adjust the width as needed */
+}
 
 .btn-default:active:hover.
 .btn-primary:active:hover{
@@ -23,8 +42,8 @@ label {
 
 .btn-primary.focus, .btn-primary:focus {
   color: #000000;
-    background-color: #20E6E5;  
-    border-color: #20E6E5;  
+  background-color: #20E6E5;  
+  border-color: #20E6E5;  
 }
 
 .btn-primary.focus, .btn-primary:active:focus {
diff --git a/www/head.css b/www/head.css
index 2aa66d2..962b17d 100644
--- a/www/head.css
+++ b/www/head.css
@@ -91,7 +91,8 @@ div#bs-select-12::-webkit-scrollbar-track,
 #logTextFull::-webkit-scrollbar-track,
 #screening_fail::-webkit-scrollbar-track,
 .selectize-dropdown-content::-webkit-scrollbar-track,
-#mst_comm_general_select::-webkit-scrollbar-track {
+#mst_comm_general_select::-webkit-scrollbar-track,
+.sF-dirInfo>div::-webkit-scrollbar-track{
 background: #F0F0F0;
   }
 
@@ -112,7 +113,8 @@ div#bs-select-12::-webkit-scrollbar-thumb,
 #logTextFull::-webkit-scrollbar-thumb,
 #screening_fail::-webkit-scrollbar-thumb,
 .selectize-dropdown-content::-webkit-scrollbar-thumb,
-#mst_comm_general_select::-webkit-scrollbar-thumb {
+#mst_comm_general_select::-webkit-scrollbar-thumb,
+.sF-dirInfo>div::-webkit-scrollbar-thumb {
   background: #bcbcbc;
   border: 2px solid #F0F0F0;
   min-width: 100px;

From 8d6179810caaaa999d85c0fd019332b93b5a52b6 Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Wed, 7 Aug 2024 21:51:05 +0200
Subject: [PATCH 40/75] Adapted single typing to new assembly saving feature;
 several fixes and UI changes

---
 App.R                    | 228 +++++++++++++++++++++------------------
 execute/multi_eval.R     |  44 +++++---
 execute/single_eval.R    |  43 +++++---
 execute/single_typing.sh |   7 +-
 www/body.css             |  10 ++
 5 files changed, 195 insertions(+), 137 deletions(-)

diff --git a/App.R b/App.R
index 61c0c33..8e8276a 100644
--- a/App.R
+++ b/App.R
@@ -6114,6 +6114,9 @@ server <- function(input, output, session) {
     
     log_print("Input load")
     
+    # set typing start control variable
+    Typing$reload <- TRUE
+    
     # reset typing status on start(
     if(Typing$status == "Finalized") {Typing$status <- "Inactive"}
     if(!is.null(Typing$single_path)) {Typing$single_path <- data.frame()}
@@ -6336,7 +6339,6 @@ server <- function(input, output, session) {
         show_toast(
           title = "Directory already contains a database",
           type = "error",
-          width = "500px",
           position = "bottom-end",
           timer = 6000
         )
@@ -8513,6 +8515,7 @@ server <- function(input, output, session) {
                     # Dynamic save button when rhandsontable changes or new entries
                     output$edit_entry_table <- renderUI({
                       if(check_new_entry() & DB$check_new_entries) {
+                        Typing$reload <- FALSE
                         fluidRow(
                           column(
                             width = 8,
@@ -9473,7 +9476,6 @@ server <- function(input, output, session) {
           title = "Invalid scheme folder",
           type = "warning",
           position = "bottom-end",
-          width = "500px",
           timer = 4000
         )
       }
@@ -9861,8 +9863,7 @@ server <- function(input, output, session) {
         title = "Invalid date",
         type = "warning",
         position = "bottom-end",
-        timer = 6000,
-        width = "300px"
+        timer = 6000
       )
       DB$inhibit_change <- TRUE
     } else if (isTRUE(input$empty_name)) {
@@ -9870,8 +9871,7 @@ server <- function(input, output, session) {
         title = "Empty name",
         type = "warning",
         position = "bottom-end",
-        timer = 6000,
-        width = "300px"
+        timer = 6000
       )
       DB$inhibit_change <- TRUE
     } else if (isTRUE(input$empty_id)) {
@@ -9879,8 +9879,7 @@ server <- function(input, output, session) {
         title = "Empty ID",
         type = "warning",
         position = "bottom-end",
-        timer = 6000,
-        width = "300px"
+        timer = 6000
       )
       DB$inhibit_change <- TRUE
     } else {
@@ -9898,16 +9897,14 @@ server <- function(input, output, session) {
         title = "Pending Multi Typing",
         type = "warning",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     } else if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
       show_toast(
         title = "Pending Single Typing",
         type = "warning",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     } else {
       showModal(
@@ -10705,7 +10702,6 @@ server <- function(input, output, session) {
         title = "Max. 10 characters",
         type = "warning",
         position = "bottom-end",
-        width = "500px",
         timer = 6000
       )
     } else {
@@ -10715,7 +10711,6 @@ server <- function(input, output, session) {
           title = "Min. 1 character",
           type = "error",
           position = "bottom-end",
-          width = "500px",
           timer = 6000
         )
       } else {
@@ -10725,7 +10720,6 @@ server <- function(input, output, session) {
             title = "Variable name already existing",
             type = "warning",
             position = "bottom-end",
-            width = "500px",
             timer = 6000
           )
         } else {
@@ -10789,7 +10783,6 @@ server <- function(input, output, session) {
       title = paste0("Variable ", trimws(input$new_var_name), " added"),
       type = "success",
       position = "bottom-end",
-      width = "500px",
       timer = 6000
     )
     
@@ -10804,7 +10797,6 @@ server <- function(input, output, session) {
         title = "No custom variables",
         type = "error",
         position = "bottom-end",
-        width = "500px",
         timer = 6000
       )
     } else {
@@ -10842,7 +10834,6 @@ server <- function(input, output, session) {
       title = paste0("Variable ", input$del_which_var, " removed"),
       type = "warning",
       position = "bottom-end",
-      width = "500px",
       timer = 6000
     )
     
@@ -10969,8 +10960,7 @@ server <- function(input, output, session) {
         title = "Invalid rows entered. Saving not possible.",
         type = "error",
         position = "bottom-end",
-        timer = 6000,
-        width = "600px"
+        timer = 6000
       )
     } else {
       if(!isTRUE(DB$inhibit_change)) {
@@ -11006,8 +10996,7 @@ server <- function(input, output, session) {
           title = "Invalid values entered. Saving not possible.",
           type = "error",
           position = "bottom-end",
-          timer = 6000,
-          width = "600px"
+          timer = 6000
         )
       }
     }
@@ -11101,8 +11090,7 @@ server <- function(input, output, session) {
       title = "Database successfully saved",
       type = "success",
       position = "bottom-end",
-      timer = 4000,
-      width = "500px"
+      timer = 4000
     )
   })
   
@@ -11115,8 +11103,7 @@ server <- function(input, output, session) {
         title = "No entry selected",
         type = "warning",
         position = "bottom-end",
-        timer = 4000,
-        width = "500px"
+        timer = 4000
       )
     } else if((readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") |
               (tail(readLogFile(), 1) != "0")) {
@@ -11126,8 +11113,7 @@ server <- function(input, output, session) {
         title = "Pending Typing",
         type = "warning",
         position = "bottom-end",
-        timer = 4000,
-        width = "500px"
+        timer = 4000
       )
     } else {
       if( (length(input$select_delete) - nrow(DB$data) ) == 0) {
@@ -11222,16 +11208,14 @@ server <- function(input, output, session) {
         title = "Entries deleted",
         type = "success",
         position = "bottom-end",
-        timer = 4000,
-        width = "500px"
+        timer = 4000
       )
     } else {
       show_toast(
         title = "Entry deleted",
         type = "success",
         position = "bottom-end",
-        timer = 4000,
-        width = "500px"
+        timer = 4000
       )
     }
   })
@@ -11438,8 +11422,7 @@ server <- function(input, output, session) {
       title = "Copied sequence",
       type = "success",
       position = "bottom-end",
-      timer = 3000,
-      width = "400px"
+      timer = 3000
     )
   })
   
@@ -11656,8 +11639,7 @@ server <- function(input, output, session) {
       title = "Download started",
       type = "success",
       position = "bottom-end",
-      timer = 5000,
-      width = "400px"
+      timer = 5000
     )
     
     if(length(DB$available) == 0) {
@@ -11818,8 +11800,7 @@ server <- function(input, output, session) {
       title = "Download successful",
       type = "success",
       position = "bottom-end",
-      timer = 5000,
-      width = "400px"
+      timer = 5000
     )
     
     # TODO Add log message regarding the update of the scheme
@@ -12030,8 +12011,7 @@ server <- function(input, output, session) {
           title = "Label already exists",
           type = "error",
           position = "bottom-end",
-          timer = 6000,
-          width = "500px"
+          timer = 6000
         )
       }
     } else {
@@ -12039,8 +12019,7 @@ server <- function(input, output, session) {
         title = "Min. 1 character",
         type = "error",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     }
   })
@@ -12058,8 +12037,7 @@ server <- function(input, output, session) {
           title = "Label already exists",
           type = "error",
           position = "bottom-end",
-          timer = 6000,
-          width = "500px"
+          timer = 6000
         )
       }
     } else {
@@ -12067,8 +12045,7 @@ server <- function(input, output, session) {
         title = "Min. 1 character",
         type = "error",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     }
   })
@@ -21465,8 +21442,7 @@ server <- function(input, output, session) {
         title = "Missing data",
         type = "error",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     } else if(nrow(DB$allelic_profile_true) < 3) {
       log_print("Min. of 3 entries required for visualization")
@@ -21475,8 +21451,7 @@ server <- function(input, output, session) {
         title = "Min. of 3 entries required for visualization",
         type = "error",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     } else {
       
@@ -21543,7 +21518,6 @@ server <- function(input, output, session) {
               title = "Conflicting Custom Variable Names",
               type = "warning",
               position = "bottom-end",
-              width = "500px",
               timer = 6000
             )
           } else {
@@ -21699,7 +21673,6 @@ server <- function(input, output, session) {
               title = "Conflicting Custom Variable Names",
               type = "warning",
               position = "bottom-end",
-              width = "500px",
               timer = 6000
             )
           } else {
@@ -21860,7 +21833,6 @@ server <- function(input, output, session) {
               title = "Computation might take a while",
               type = "warning",
               position = "bottom-end",
-              width = "500px",
               timer = 10000
             )
           }
@@ -22295,7 +22267,6 @@ server <- function(input, output, session) {
         title = "No tree created",
         type = "error",
         position = "bottom-end",
-        width = "500px",
         timer = 6000
       )
     }
@@ -22773,7 +22744,6 @@ server <- function(input, output, session) {
           title = "Wrong file type (only fasta/fna/fa)",
           type = "error",
           position = "bottom-end",
-          width = "500px",
           timer = 6000
         )
         
@@ -22790,16 +22760,14 @@ server <- function(input, output, session) {
         title = "Pending Multi Typing",
         type = "warning",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     } else if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
       show_toast(
         title = "Pending Single Typing",
         type = "warning",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     } else {
       
@@ -22811,7 +22779,6 @@ server <- function(input, output, session) {
         title = "Gene screening started",
         type = "success",
         position = "bottom-end",
-        width = "500px",
         timer = 6000
       )
       
@@ -22851,7 +22818,6 @@ server <- function(input, output, session) {
           title = "Successful gene screening",
           type = "success",
           position = "bottom-end",
-          width = "500px",
           timer = 6000
         )
       } else if(file.exists(paste0(getwd(), "/execute/screening/error.txt"))) {
@@ -22862,7 +22828,6 @@ server <- function(input, output, session) {
           title = "Failed gene screening",
           type = "error",
           position = "bottom-end",
-          width = "500px",
           timer = 6000
         )
       }
@@ -22943,6 +22908,42 @@ server <- function(input, output, session) {
   
   #### Render UI Elements ----
   
+  # Render single typing naming issues
+  output$single_select_issues <- renderUI({
+    req(input$assembly_id)
+    
+    if(nchar(trimws(input$assembly_id)) < 1) {
+      ass_id <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
+    } else {
+      ass_id <- trimws(input$assembly_id)
+    }
+    
+    if(ass_id %in% unlist(DB$data["Assembly ID"])) {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Assembly ID already present in database.")))
+    } else if (ass_id == "") {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Empty Assembly ID.")))
+    } else if (grepl("[()/\\:*?\"<>|]", ass_id)) {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Invalid Assembly ID. Avoid special characters.")))
+    } else if(grepl(" ", ass_id)) {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Invalid Assembly ID. Avoid empty spaces.")))
+    } else {HTML(paste(
+      '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
+      paste("<span style='color: white; font-style:italic'>",
+            "&nbsp Assembly ID compatible with local database.")))}
+  })
+  
   # Render Typing Results if finished
   observe({
     if(Typing$progress_format_end == 999999) {
@@ -23095,8 +23096,8 @@ server <- function(input, output, session) {
         output$metadata_single_box <- renderUI({
           
           # Render placeholder 
-          updateTextInput(session, "assembly_id", placeholder = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
-          updateTextInput(session, "assembly_name", placeholder = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
+          updateTextInput(session, "assembly_id", value = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
+          updateTextInput(session, "assembly_name", value = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
           
           column(
             width = 3,
@@ -23128,6 +23129,12 @@ server <- function(input, output, session) {
                     )
                   )
                 ),
+                fluidRow(
+                  column(
+                    width = 12,
+                    uiOutput("single_select_issues")
+                  )
+                ),
                 fluidRow(
                   column(
                     width = 5,
@@ -23260,7 +23267,6 @@ server <- function(input, output, session) {
           title = "Wrong file type (only fasta/fna/fa)",
           type = "error",
           position = "bottom-end",
-          width = "500px",
           timer = 6000
         )
       }
@@ -23292,16 +23298,14 @@ server <- function(input, output, session) {
         title = "Pending Multi Typing",
         type = "warning",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     } else if (Screening$status == "started") {
       show_toast(
         title = "Pending Gene Screening",
         type = "warning",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     } else {
       
@@ -23348,8 +23352,7 @@ server <- function(input, output, session) {
           title = "Typing Initiated",
           type = "success",
           position = "bottom-end",
-          timer = 6000,
-          width = "400px"
+          timer = 6000
         )
         
         log_print("Initiated single typing")
@@ -23587,8 +23590,35 @@ server <- function(input, output, session) {
         title = "Assembly ID already present",
         type = "error",
         position = "bottom-end",
-        timer = 3000,
-        width = "500px"
+        timer = 3000
+      )
+    } else if (isFALSE(Typing$reload)) {
+      show_toast(
+        title = "Reload Database first",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    }  else if (ass_id == "") {
+    show_toast(
+      title = "Empty Assembly ID",
+      type = "error",
+      position = "bottom-end",
+      timer = 3000
+      )
+    } else if (grepl("[()/\\:*?\"<>|]", ass_id)) {
+      show_toast(
+        title = "Invalid Assembly ID. No special characters allowed: ()/\\:*?\"<>|",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if(grepl(" ", ass_id)) {
+      show_toast(
+        title = "Empty spaces in Assembly ID not allowed",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
       )
     } else {
       
@@ -23613,12 +23643,10 @@ server <- function(input, output, session) {
         title = "Metadata declared",
         type = "success",
         position = "bottom-end",
-        timer = 3000,
-        width = "500px"
+        timer = 3000
       )
       
       # Render Start Typing UI
-      
       output$start_typing_ui <- renderUI({
         div(
           class = "multi_start_col",
@@ -23749,8 +23777,7 @@ server <- function(input, output, session) {
           title = "Single Typing finalized",
           type = "success",
           position = "bottom-end",
-          timer = 8000,
-          width = "500px"
+          timer = 8000
         )
         Typing$single_end <- TRUE
       }
@@ -24338,48 +24365,49 @@ server <- function(input, output, session) {
         title = "Assembly ID(s) already present",
         type = "error",
         position = "bottom-end",
-        timer = 3000,
-        width = "500px"
+        timer = 3000
       )
     } else if (any(duplicated(multi_select_table$Files))) {
       show_toast(
         title = "Duplicated filename(s)",
         type = "error",
         position = "bottom-end",
-        timer = 3000,
-        width = "500px"
+        timer = 3000
       )
     } else if (any(multi_select_table$Files == "")) {
       show_toast(
         title = "Empty filename(s)",
         type = "error",
         position = "bottom-end",
-        timer = 3000,
-        width = "500px"
+        timer = 3000
       )
     } else if (any(grepl("[()/\\:*?\"<>|]", multi_select_table$Files))) {
       show_toast(
         title = "Invalid filename(s). No special characters allowed: ()/\\:*?\"<>|",
         type = "error",
         position = "bottom-end",
-        timer = 3000,
-        width = "500px"
+        timer = 3000
       )
     } else if (!any(multi_select_table$Include == TRUE)) {
       show_toast(
         title = "No files selected",
         type = "error",
         position = "bottom-end",
-        timer = 3000,
-        width = "500px"
+        timer = 3000
       )
     } else if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
       show_toast(
         title = "Empty spaces in filename(s) not allowed",
         type = "error",
         position = "bottom-end",
-        timer = 3000,
-        width = "500px"
+        timer = 3000
+      )
+    } else if (isFALSE(Typing$reload)) {
+      show_toast(
+        title = "Reload Database first",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
       )
     } else {
       
@@ -24399,8 +24427,7 @@ server <- function(input, output, session) {
         title = "Metadata declared",
         type = "success",
         position = "bottom-end",
-        timer = 3000,
-        width = "500px"
+        timer = 3000
       )
       
       output$start_multi_typing_ui <- renderUI({
@@ -24569,8 +24596,7 @@ server <- function(input, output, session) {
       title = "Execution cancelled",
       type = "warning",
       position = "bottom-end",
-      timer = 6000,
-      width = "500px"
+      timer = 6000
     )
     
     # Kill multi typing and reset logfile  
@@ -24646,16 +24672,14 @@ server <- function(input, output, session) {
         title = "Pending Single Typing",
         type = "warning",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     } else if (Screening$status == "started") {
       show_toast(
         title = "Pending Gene Screening",
         type = "warning",
         position = "bottom-end",
-        timer = 6000,
-        width = "500px"
+        timer = 6000
       )
     } else {
       removeModal()
@@ -24664,8 +24688,7 @@ server <- function(input, output, session) {
         title = "Multi Typing started",
         type = "success",
         position = "bottom-end",
-        timer = 10000,
-        width = "500px"
+        timer = 10000
       )
       
       Typing$new_table <- NULL
@@ -24747,7 +24770,6 @@ server <- function(input, output, session) {
       show_toast(
         title = paste0("Successful", sub(".*Successful", "", tail(log, 1))),
         type = "success",
-        width = "500px",
         position = "bottom-end",
         timer = 8000
       )
@@ -24756,7 +24778,6 @@ server <- function(input, output, session) {
       show_toast(
         title = sub(".* - ", "", tail(log, 1)),
         type = "error",
-        width = "700px",
         position = "bottom-end",
         timer = 8000
       )
@@ -24770,7 +24791,6 @@ server <- function(input, output, session) {
           show_toast(
             title = paste0("Successful", sub(".*Successful", "", tail(log, 2)[1])),
             type = "success",
-            width = "500px",
             position = "bottom-end",
             timer = 8000
           )
@@ -24784,7 +24804,6 @@ server <- function(input, output, session) {
           show_toast(
             title = sub(".* - ", "", tail(log, 2)[1]),
             type = "error",
-            width = "500px",
             position = "bottom-end",
             timer = 8000
           )
@@ -24800,7 +24819,6 @@ server <- function(input, output, session) {
         show_toast(
           title = "Typing finalized",
           type = "success",
-          width = "500px",
           position = "bottom-end",
           timer = 8000
         )
diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index d045bc5..eba5b90 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -325,18 +325,26 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
   # Save new Entry in Typing Database
   saveRDS(Database, paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Typing.rds"))
   
+  isolate_dir <- file.path(db_path, gsub(" ", "_", meta_info$cgmlst_typing), "Isolates")
+  
   # Save assembly file if TRUE
   if(save_assembly) {
-    if(dir.exists(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates"))) {
+    if(dir.exists(isolate_dir)) {
       
       # Create folder for new isolate
-      dir.create(paste0(db_path, "/", 
-                        gsub(" ", "_", meta_info$cgmlst_typing), 
-                        "/Isolates/", filename))
+      dir.create(file.path(isolate_dir, filename))
       
       # Copy assembly file in isolate directory
-      file.copy(paste0(getwd(), "/execute/selected_genomes/", filename, ".fasta"), 
-                paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates/", filename))
+      file.copy(file.path(getwd(), "execute/selected_genomes", paste0(filename, ".fasta")), 
+                file.path(isolate_dir, filename))
+      
+      setwd(file.path(isolate_dir, filename))
+      
+      zip(zipfile = paste0(filename, ".zip"),
+          files = paste0(filename, ".fasta"),
+          zip = "zip") 
+      
+      file.remove(paste0(filename, ".fasta"))
       
       log_print(paste0("Saved assembly of ", basename(assembly)))
       
@@ -345,23 +353,29 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
       log_print("No isolate folder present yet. Isolate directory created.")
       
       # Create isolate filder for species
-      dir.create(paste0(db_path, "/", 
-                        gsub(" ", "_", meta_info$cgmlst_typing), 
-                        "/Isolates"))
+      dir.create(isolate_dir)
       
       # Create folder for new isolate
-      dir.create(paste0(db_path, "/", 
-                        gsub(" ", "_", meta_info$cgmlst_typing), 
-                        "/Isolates/", filename))
+      dir.create(file.path(isolate_dir, filename))
       
       # Copy assembly file in isolate directory
-      file.copy(paste0(getwd(), "/execute/selected_genomes/", filename, ".fasta"), 
-                paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates/", filename))
+      file.copy(paste0(getwd(), "/execute/selected_genomes/", filename, ".fasta") , 
+                file.path(isolate_dir, filename))
+      
+      setwd(file.path(isolate_dir, filename))
+      
+      zip(zipfile = paste0(filename, ".zip"),
+          files = paste0(filename, ".fasta"),
+          zip = "zip") 
+      
+      file.remove(paste0(filename, ".fasta"))
       
       log_print(paste0("Saved assembly of ", basename(assembly)))
     }
   }
   
+  setwd(meta_info$db_directory)
+  
   # Logging successes
   log.message(log_file = paste0(getwd(), "/logs/script_log.txt"), 
               message = paste0("Successful typing of ", sub("\\.(fasta|fna|fa)$", "", basename(assembly))))
@@ -369,6 +383,8 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
   
 } else {
   
+  setwd(meta_info$db_directory)
+  
   # Logging failures
   log.message(log_file = paste0(getwd(), "/logs/script_log.txt"), 
               message = paste0("Assembly typing failed for ", 
diff --git a/execute/single_eval.R b/execute/single_eval.R
index abbe0fb..1fb70a3 100644
--- a/execute/single_eval.R
+++ b/execute/single_eval.R
@@ -3,7 +3,7 @@ library(logr)
 # Hand over variables
 meta_info <- readRDS("meta_info_single.rds")
 db_path <- readRDS("single_typing_df.rds")[, "db_path"]
-save_assembly <- readRDS("multi_typing_df.rds")[, "save"]
+save_assembly <- readRDS("single_typing_df.rds")[, "save"]
 file_list <- list.files(paste0(meta_info$db_directory, "/execute/blat_single"), 
                         full.names = TRUE)
 assembly <- file_list[which(list.files(paste0(meta_info$db_directory, "/execute/blat_single")) != "results")]
@@ -310,17 +310,24 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
   
   # Save assembly file if TRUE
   if(save_assembly) {
-    if(dir.exists(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Isolates"))) {
+    
+    isolate_dir <- file.path(db_path, gsub(" ", "_", meta_info$cgmlst_typing), "Isolates")
+    
+    if(dir.exists(isolate_dir)) {
       
       # Create folder for new isolate
-      dir.create(paste0(db_path, "/", 
-                        gsub(" ", "_", meta_info$cgmlst_typing), 
-                        "/Isolates/", meta_info$assembly_id))
+      dir.create(file.path(isolate_dir, meta_info$assembly_id))
       
       # Copy assembly file in isolate directory
-      file.copy(assembly, paste0(db_path, "/", 
-                                 gsub(" ", "_", meta_info$cgmlst_typing), 
-                                 "/Isolates/", meta_info$assembly_id))
+      file.copy(assembly, file.path(isolate_dir, meta_info$assembly_id))
+      
+      setwd(file.path(isolate_dir, meta_info$assembly_id))
+      
+      zip(zipfile = paste0(meta_info$assembly_id, ".zip"),
+          files = basename(assembly),
+          zip = "zip") 
+      
+      file.remove(basename(assembly))
       
       log_print(paste0("Saved assembly of ", meta_info$assembly_id))
       
@@ -329,20 +336,22 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
       log_print("No isolate folder present yet. Isolate directory created.")
       
       # Create isolate filder for species
-      dir.create(paste0(db_path, "/", 
-                        gsub(" ", "_", meta_info$cgmlst_typing), 
-                        "/Isolates"))
+      dir.create(isolate_dir)
       
       # Create folder for new isolate
-      dir.create(paste0(db_path, "/", 
-                        gsub(" ", "_", meta_info$cgmlst_typing), 
-                        "/Isolates/", meta_info$assembly_id))
+      dir.create(file.path(isolate_dir, meta_info$assembly_id))
       
       # Copy assembly file in isolate directory
-      file.copy(assembly, paste0(db_path, "/", 
-                                 gsub(" ", "_", meta_info$cgmlst_typing), 
-                                 "/Isolates/", meta_info$assembly_id))
+      file.copy(assembly, file.path(isolate_dir, meta_info$assembly_id))
+      
+      setwd(file.path(isolate_dir, meta_info$assembly_id))
+      
+      zip(zipfile = paste0(meta_info$assembly_id, ".zip"),
+          files = basename(assembly),
+          zip = "zip") 
       
+      file.remove(basename(assembly))
+       
       log_print(paste0("Saved assembly of ", meta_info$assembly_id))
     }
   }
diff --git a/execute/single_typing.sh b/execute/single_typing.sh
index 2b0490f..92d05ed 100755
--- a/execute/single_typing.sh
+++ b/execute/single_typing.sh
@@ -15,6 +15,8 @@ echo 0 > "$base_path/logs/progress.txt"
 scheme=$(Rscript -e "cat(readRDS('single_typing_df.rds')[,'scheme'])")
 alleles=$(Rscript -e "cat(readRDS('single_typing_df.rds')[,'alleles'])")
 genome_name=$(Rscript -e "cat(basename(readRDS('single_typing_df.rds')[,'genome']))")
+genome_name=$(echo "$genome_name" | sed 's/~/ /g')
+rename_file=$(Rscript -e "cat(readRDS('meta_info_single.rds')[, 'assembly_id'])")
 
 # Remove the existing directory (if it exists)
 if [ -d "$base_path/execute/blat_single" ]; then
@@ -39,8 +41,11 @@ Rscript "$base_path/execute/check_duplicate_single.R"
 wait
 genome="$base_path/execute/blat_single/$genome_name"
 
+# Rename file
+mv "$genome" "$base_path/execute/blat_single/$rename_file.fasta"
+
 # Run parallelized BLAT
-find "$alleles" -type f \( -name "*.fasta" -o -name "*.fa" -o -name "*.fna" \) | parallel pblat $genome {} "$results/{/.}.psl" > /dev/null 2>&1
+find "$alleles" -type f \( -name "*.fasta" -o -name "*.fa" -o -name "*.fna" \) | parallel pblat "$base_path/execute/blat_single/$rename_file.fasta" {} "$results/{/.}.psl" > /dev/null 2>&1
 
 # Start appending results
 echo 888888 >> "$base_path/logs/progress.txt"
diff --git a/www/body.css b/www/body.css
index 63216a2..a4eb6e7 100644
--- a/www/body.css
+++ b/www/body.css
@@ -16,6 +16,11 @@ input[type="checkbox"] {
   width: 15px;
 }
 
+.swal2-container .swal2-bottom-end .swal2-backdrop-show,
+body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
+  width: auto;
+}
+
 .sF-fileList>div.selected .sF-file-name div, .sF-dirList div.selected>.sF-file-name>div {
   background: #20E6E5;
   color: black;
@@ -794,6 +799,11 @@ background: #20E6E5;
 
 /* Typing */
 
+#single_select_issues {
+  margin-top: 15px;
+  margin-bottom: 10px;
+}
+
 #sel_all_mt {
   margin-left: 10px;
 }

From 80276adfc75041f43d7bb6c0171a0d0a69d796bc Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Thu, 8 Aug 2024 12:05:19 +0200
Subject: [PATCH 41/75] Implemented compressing and deletion of saved assembly
 files

---
 App.R        | 31 +++++++++++++++++++++----------
 www/body.css |  4 ++++
 2 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/App.R b/App.R
index 8e8276a..70a1de8 100644
--- a/App.R
+++ b/App.R
@@ -11010,6 +11010,14 @@ server <- function(input, output, session) {
   observeEvent(input$conf_db_save, {
     log_print("Input conf_db_save")
     
+    # Remove isolate assembly file if present
+    if(!is.null(DB$remove_iso)) {
+      if(length(DB$remove_iso) > 0) {
+        lapply(DB$remove_iso, unlink, recursive = TRUE, force = FALSE, expand = TRUE)
+      }
+    }
+    DB$remove_iso <- NULL
+    
     Data <- readRDS(paste0(
       DB$database, "/",
       gsub(" ", "_", DB$scheme),
@@ -11119,7 +11127,7 @@ server <- function(input, output, session) {
       if( (length(input$select_delete) - nrow(DB$data) ) == 0) {
         showModal(
           modalDialog(
-            paste0("Deleting will lead to removal of all entries from local ", DB$scheme, " database. The data can not be recovered afterwards. Continue?"),
+            paste0("Deleting will lead to removal of all entries and assemblies from local ", DB$scheme, " database. The data can not be recovered afterwards. Continue?"),
             easyClose = TRUE,
             title = "Deleting Entries",
             footer = tagList(
@@ -11132,7 +11140,7 @@ server <- function(input, output, session) {
         showModal(
           modalDialog(
             paste0(
-              "Confirmation will lead to irreversible removal of selected entries. Continue?"
+              "Confirmation will lead to irreversible removal of selected entries and the respectively saved assembly. Continue?"
             ),
             title = "Deleting Entries",
             fade = TRUE,
@@ -11154,7 +11162,8 @@ server <- function(input, output, session) {
     log_print("Input conf_delete_all")
     
     # remove file with typing data
-    file.remove(paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/Typing.rds"))
+    file.remove(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+    unlink(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates"), recursive = TRUE, force = FALSE, expand =TRUE)
     
     showModal(
       modalDialog(
@@ -11182,27 +11191,29 @@ server <- function(input, output, session) {
     
     log_print("Input conf_delete")
     
+    # Get isolates selected for deletion
     DB$deleted_entries <- append(DB$deleted_entries, DB$data$Index[as.numeric(input$select_delete)])
     
+    # Set reactive status variables
     DB$no_na_switch <- TRUE
-    
     DB$change <- TRUE
-    
     DB$check_new_entries <- FALSE
     
-    DB$data <- DB$data[!(DB$data$Index %in% as.numeric(input$select_delete)),]
+    # Set isolate directory deletion variables
+    isopath <- dir_ls(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates"))
+    DB$remove_iso <- isopath[which(basename(isopath) == DB$data$`Assembly ID`[as.numeric(input$select_delete)])]
     
+    # Reload updated database reactive variables
+    DB$data <- DB$data[!(DB$data$Index %in% as.numeric(input$select_delete)),]
     DB$meta_gs <- select(DB$data, c(1, 3:13))
-    
     DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
-    
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    
     DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
     
+    # User feedback
     removeModal()
+    
     if(length(input$select_delete) > 1) {
       show_toast(
         title = "Entries deleted",
diff --git a/www/body.css b/www/body.css
index a4eb6e7..ff1d0d9 100644
--- a/www/body.css
+++ b/www/body.css
@@ -57,6 +57,10 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
     border-color: white;  
 }
 
+#conf_delete .btn-default:hover {
+  background-color: #FF5964 !important;
+}
+
 .datepicker table tr td.active:active, .datepicker table tr td.active.active, .datepicker table tr td.active.highlighted:active, .datepicker table tr td.active.highlighted.active {
   color: #000000;
     background-color: #20E6E5;  

From 414fe8a606c4886cc6c7813314a5c21276b96d4a Mon Sep 17 00:00:00 2001
From: infinity-a11y <marian@phylotrace.com>
Date: Fri, 9 Aug 2024 11:18:03 +0200
Subject: [PATCH 42/75] Small fixes

---
 App.R        | 83 +++++++++++++++++++++++++++++-----------------------
 www/body.css |  4 +++
 2 files changed, 50 insertions(+), 37 deletions(-)

diff --git a/App.R b/App.R
index 70a1de8..1c4e894 100644
--- a/App.R
+++ b/App.R
@@ -5522,7 +5522,7 @@ server <- function(input, output, session) {
   get.entry.table.meta <- reactive({
     if(!is.null(hot_to_r(input$db_entries))){
       table <- hot_to_r(input$db_entries)
-      select(table, 1:(12 + nrow(DB$cust_var)))
+      select(table, 1:(13 + nrow(DB$cust_var)))
     }
   })
   
@@ -6976,7 +6976,7 @@ server <- function(input, output, session) {
                 
                 DB$meta_gs <- select(DB$data, c(1, 3:13))
                 
-                DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
+                DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
                 
                 DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
                 
@@ -7823,7 +7823,7 @@ server <- function(input, output, session) {
                         if(!is.null(DB$data) & !is.null(DB$cust_var)) {
                           output$db_entries <- renderRHandsontable({
                             rhandsontable(
-                              select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
+                              select(DB$data, 1:(13 + nrow(DB$cust_var))),
                               error_highlight = err_thresh() - 1,                              
                               rowHeaders = NULL,
                               contextMenu = FALSE,
@@ -7919,7 +7919,7 @@ server <- function(input, output, session) {
                           if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
                             output$db_entries <- renderRHandsontable({
                               rhandsontable(
-                                select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)), input$compare_select),
+                                select(DB$data, 1:(13 + nrow(DB$cust_var)), input$compare_select),
                                 col_highlight = diff_allele() - 1,
                                 dup_names_high = duplicated_names() - 1,
                                 dup_ids_high = duplicated_ids() - 1,
@@ -8079,7 +8079,7 @@ server <- function(input, output, session) {
                           if(!is.null(DB$data) & !is.null(DB$cust_var)) {
                             output$db_entries <- renderRHandsontable({
                               rhandsontable(
-                                select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
+                                select(DB$data, 1:(13 + nrow(DB$cust_var))),
                                 rowHeaders = NULL,
                                 row_highlight = true_rows() - 1,
                                 dup_names_high = duplicated_names()- 1,
@@ -8219,7 +8219,7 @@ server <- function(input, output, session) {
                           if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
                             output$db_entries <- renderRHandsontable({
                               rhandsontable(
-                                select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)), input$compare_select),
+                                select(DB$data, 1:(13 + nrow(DB$cust_var)), input$compare_select),
                                 col_highlight = diff_allele() - 1,
                                 rowHeaders = NULL,
                                 height = table_height(),
@@ -8375,7 +8375,7 @@ server <- function(input, output, session) {
                           if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
                             output$db_entries <- renderRHandsontable({
                               rhandsontable(
-                                select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
+                                select(DB$data, 1:(13 + nrow(DB$cust_var))),
                                 rowHeaders = NULL,
                                 height = table_height(),
                                 dup_names_high = duplicated_names() - 1,
@@ -9889,9 +9889,14 @@ server <- function(input, output, session) {
   
   # Change scheme
   observeEvent(input$reload_db, {
-    
     log_print("Input reload_db")
     
+    cust_var2 <<- DB$cust_var
+    dataa2 <<- DB$data
+    meta_gs2 <<- DB$meta_gs
+    meta2 <<- DB$meta
+    allelic_profile2 <<- DB$allelic_profile
+    
     if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
       show_toast(
         title = "Pending Multi Typing",
@@ -9972,7 +9977,7 @@ server <- function(input, output, session) {
     
     DB$meta_gs <- select(DB$data, c(1, 3:13))
     
-    DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
     
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     
@@ -9988,7 +9993,7 @@ server <- function(input, output, session) {
           if(!is.null(DB$data) & !is.null(DB$cust_var)) {
             output$db_entries <- renderRHandsontable({
               rhandsontable(
-                select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
+                select(DB$data, 1:(13 + nrow(DB$cust_var))),
                 error_highlight = err_thresh() - 1,                              
                 rowHeaders = NULL,
                 contextMenu = FALSE,
@@ -10084,7 +10089,7 @@ server <- function(input, output, session) {
             if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
               output$db_entries <- renderRHandsontable({
                 rhandsontable(
-                  select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)), input$compare_select),
+                  select(DB$data, 1:(13 + nrow(DB$cust_var)), input$compare_select),
                   col_highlight = diff_allele() - 1,
                   dup_names_high = duplicated_names() - 1,
                   dup_ids_high = duplicated_ids() - 1,
@@ -10244,7 +10249,7 @@ server <- function(input, output, session) {
             if(!is.null(DB$data) & !is.null(DB$cust_var)) {
               output$db_entries <- renderRHandsontable({
                 rhandsontable(
-                  select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
+                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
                   rowHeaders = NULL,
                   row_highlight = true_rows() - 1,
                   dup_names_high = duplicated_names()- 1,
@@ -10384,7 +10389,7 @@ server <- function(input, output, session) {
             if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
               output$db_entries <- renderRHandsontable({
                 rhandsontable(
-                  select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)), input$compare_select),
+                  select(DB$data, 1:(13 + nrow(DB$cust_var)), input$compare_select),
                   col_highlight = diff_allele() - 1,
                   rowHeaders = NULL,
                   height = table_height(),
@@ -10540,7 +10545,7 @@ server <- function(input, output, session) {
             if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
               output$db_entries <- renderRHandsontable({
                 rhandsontable(
-                  select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var))),
+                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
                   rowHeaders = NULL,
                   height = table_height(),
                   dup_names_high = duplicated_names() - 1,
@@ -10746,12 +10751,12 @@ server <- function(input, output, session) {
   observeEvent(input$conf_new_var, {
     log_print("Input conf_new_var")
     
+    # User feedback variables
     removeModal()
-    
     DB$count <- DB$count + 1
-    
     DB$change <- TRUE
     
+    # Format variable name
     name <- trimws(input$new_var_name)
     
     if(input$new_var_type == "Categorical (character)") {
@@ -10765,16 +10770,20 @@ server <- function(input, output, session) {
       
       DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "cont"))
     }
-    
+    dataa <<- DB$data
+    cust_var <<- DB$cust_var
     
     DB$meta_gs <- select(DB$data, c(1, 3:13))
     
-    DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
+    meta_gs <<- DB$meta_gs
+    
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+    meta <<- DB$meta
     
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     
     DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    
+    allelic_profile <<- DB$allelic_profile
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
     
     log_print(paste0("New custom variable added: ", input$new_var_name))
@@ -10845,7 +10854,7 @@ server <- function(input, output, session) {
     
     DB$meta_gs <- select(DB$data, c(1, 3:13))
     
-    DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
     
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     
@@ -11018,37 +11027,35 @@ server <- function(input, output, session) {
     }
     DB$remove_iso <- NULL
     
-    Data <- readRDS(paste0(
-      DB$database, "/",
-      gsub(" ", "_", DB$scheme),
-      "/Typing.rds"
-    ))
+    Data <<- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
     
-    if ((ncol(Data[["Typing"]])-12) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-      cust_vars_pre <- select(Data[["Typing"]], 13:(ncol(Data[["Typing"]]) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-      cust_vars_pre <- names(cust_vars_pre)
+    if ((ncol(Data[["Typing"]]) - 13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+      cust_vars_pre <- select(Data[["Typing"]], 
+                              14:(ncol(Data[["Typing"]]) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+      cust_vars_pre <<- names(cust_vars_pre)
     } else {
-      cust_vars_pre <- character()
+      cust_vars_pre <<- character()
     }
     
-    Data[["Typing"]] <- select(Data[["Typing"]], -(1:(12 + length(cust_vars_pre))))
+    checkpoint <<- select(Data[["Typing"]], -(1:(13 + length(cust_vars_pre))))
+    Data[["Typing"]] <- select(Data[["Typing"]], -(1:(13 + length(cust_vars_pre))))
     
-    meta_hot <- hot_to_r(input$db_entries)
+    meta_hot <<- hot_to_r(input$db_entries)
     
-    if(length(DB$deleted_entries > 0)){
+    if(length(DB$deleted_entries > 0)) {
       
       meta_hot <- mutate(meta_hot, Index = as.character(1:nrow(DB$data)))
       
-      Data[["Typing"]] <- mutate(Data[["Typing"]][-as.numeric(DB$deleted_entries),], meta_hot, .before = 1)
+      Data[["Typing"]] <- mutate(Data[["Typing"]][-as.numeric(DB$deleted_entries),  ], 
+                                 meta_hot, .before = 1)
       rownames(Data[["Typing"]]) <- Data[["Typing"]]$Index
     } else {
       Data[["Typing"]] <- mutate(Data[["Typing"]], meta_hot, .before = 1)
-      
     }
     
     # Ensure correct logical data type
     Data[["Typing"]][["Include"]] <- as.logical(Data[["Typing"]][["Include"]])
-    
+    testdata <<- Data
     saveRDS(Data, paste0(
       DB$database, "/",
       gsub(" ", "_", DB$scheme),
@@ -11065,6 +11072,8 @@ server <- function(input, output, session) {
     
     DB$data <- Database[["Typing"]]
     
+    dataa <- DB$data
+    
     if(!is.null(DB$data)){
       if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
         cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
@@ -11082,7 +11091,7 @@ server <- function(input, output, session) {
     
     DB$meta_gs <- select(DB$data, c(1, 3:13))
     
-    DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
     
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     
@@ -11206,7 +11215,7 @@ server <- function(input, output, session) {
     # Reload updated database reactive variables
     DB$data <- DB$data[!(DB$data$Index %in% as.numeric(input$select_delete)),]
     DB$meta_gs <- select(DB$data, c(1, 3:13))
-    DB$meta <- select(select(DB$data, -13), 1:(12 + nrow(DB$cust_var)))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
diff --git a/www/body.css b/www/body.css
index ff1d0d9..a472966 100644
--- a/www/body.css
+++ b/www/body.css
@@ -34,6 +34,10 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
   background-color: #282F38 !important;
 }
 
+.handsontable .wtBorder .area .corner {
+  background-color: #20e6e5 !important;
+}
+
 .tooltip-inner {
   white-space: normal;
   max-width: 800px; /* Adjust the width as needed */

From 9b72a1b26637a1fd5f23f945c38b9d2132f574e9 Mon Sep 17 00:00:00 2001
From: marian <marian@fedora.fritz.box>
Date: Mon, 12 Aug 2024 14:59:13 +0200
Subject: [PATCH 43/75] Gene Screening User Feedback Progression

---
 App.R                | 540 ++++++++++++++++++++++++++-----------------
 execute/screening.sh |  47 ++--
 2 files changed, 350 insertions(+), 237 deletions(-)

diff --git a/App.R b/App.R
index 1c4e894..df76356 100644
--- a/App.R
+++ b/App.R
@@ -5302,7 +5302,7 @@ ui <- dashboardPage(
       ),
       
       
-      ## Tab Gene Screening -------------------------------------------------------
+      ## Tab Screening -------------------------------------------------------
       
       tabItem(
         tabName = "gs_screening",
@@ -5310,7 +5310,7 @@ ui <- dashboardPage(
           column(
             width = 3,
             align = "center",
-            h2(p("Gene Screening"), style = "color:white; margin-bottom: -20px;")
+            h2(p("Screening"), style = "color:white; margin-bottom: -20px;")
           ),
           column(
             width = 7,
@@ -5331,7 +5331,7 @@ ui <- dashboardPage(
           column(
             width = 3,
             align = "center",
-            h2(p("Resistance Profiles"), style = "color:white; margin-bottom: -20px")
+            h2(p("Browse Entries"), style = "color:white; margin-bottom: -20px")
           ),
           column(
             width = 7,
@@ -5673,7 +5673,33 @@ server <- function(input, output, session) {
     groups
   }
   
-  #Function to check for duplicate isolate IDs for multi typing start
+  # Check gene screening status
+  check_status <- function(isolate) {
+    iso_name <- gsub(".zip", "", basename(isolate))
+    if(file.exists(file.path(DB$database, gsub(" ", "_", DB$scheme),
+                             "Isolates", iso_name, "status.txt"))) {
+      if(str_detect(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
+                                        "Isolates", iso_name, "status.txt"))[1], 
+                    "successfully")) {
+        return("success")
+      } else {
+        return("fail")
+      }
+    } else {return("unfinished")}
+  }
+  
+  # Reset gene screening status
+  remove.screening.status <- function(isolate) {
+    file.remove(
+      file.path(DB$database, 
+                gsub(" ", "_", DB$scheme),
+                "Isolates",
+                Screening$status_df$isolate,
+                "status.txt")
+    )
+  }
+  
+  # Function to check for duplicate isolate IDs for multi typing start
   dupl_mult_id <- reactive({
     req(Typing$multi_sel_table)
     if(!is.null(DB$data)) {
@@ -6120,7 +6146,6 @@ server <- function(input, output, session) {
     # reset typing status on start(
     if(Typing$status == "Finalized") {Typing$status <- "Inactive"}
     if(!is.null(Typing$single_path)) {Typing$single_path <- data.frame()}
-    if(!is.null(Screening$single_path)) {Screening$single_path <- data.frame()}
     
     #### Render status bar ----
     observe({
@@ -6439,17 +6464,17 @@ server <- function(input, output, session) {
               icon = icon("gears")
             ),
             menuItem(
-              text = "Gene Screening",
+              text = "Resistance Profile",
               tabName = "gene_screening",
               icon = icon("dna"),
               startExpanded = TRUE,
               menuSubItem(
-                text = "Screen Assembly",
-                tabName = "gs_screening"
+                text = "Browse entries",
+                tabName = "gs_profile"
               ),
               menuSubItem(
-                text = "Resistance Profile",
-                tabName = "gs_profile"
+                text = "Screening",
+                tabName = "gs_screening"
               )
             ),
             menuItem(
@@ -6617,17 +6642,17 @@ server <- function(input, output, session) {
                   icon = icon("gears")
                 ),
                 menuItem(
-                  text = "Gene Screening",
+                  text = "Resistance Profile",
                   tabName = "gene_screening",
                   icon = icon("dna"),
                   startExpanded = TRUE,
                   menuSubItem(
-                    text = "Screen Assembly",
-                    tabName = "gs_screening"
+                    text = "Browse entries",
+                    tabName = "gs_profile"
                   ),
                   menuSubItem(
-                    text = "Resistance Profile",
-                    tabName = "gs_profile"
+                    text = "Screening",
+                    tabName = "gs_screening"
                   )
                 ),
                 menuItem(
@@ -6707,17 +6732,17 @@ server <- function(input, output, session) {
                   icon = icon("gears")
                 ),
                 menuItem(
-                  text = "Gene Screening",
+                  text = "Resistance Profile",
                   tabName = "gene_screening",
                   icon = icon("dna"),
                   startExpanded = TRUE,
                   menuSubItem(
-                    text = "Screen Assembly",
-                    tabName = "gs_screening"
+                    text = "Browse entries",
+                    tabName = "gs_profile"
                   ),
                   menuSubItem(
-                    text = "Resistance Profile",
-                    tabName = "gs_profile"
+                    text = "Screening",
+                    tabName = "gs_screening"
                   )
                 ),
                 menuItem(
@@ -6799,17 +6824,17 @@ server <- function(input, output, session) {
                   icon = icon("gears")
                 ),
                 menuItem(
-                  text = "Gene Screening",
+                  text = "Resistance Profile",
                   tabName = "gene_screening",
                   icon = icon("dna"),
                   startExpanded = TRUE,
                   menuSubItem(
-                    text = "Screen Assembly",
-                    tabName = "gs_screening"
+                    text = "Browse entries",
+                    tabName = "gs_profile"
                   ),
                   menuSubItem(
-                    text = "Resistance Profile",
-                    tabName = "gs_profile"
+                    text = "Screening",
+                    tabName = "gs_screening"
                   )
                 ),
                 menuItem(
@@ -6920,17 +6945,17 @@ server <- function(input, output, session) {
                     icon = icon("gears")
                   ),
                   menuItem(
-                    text = "Gene Screening",
+                    text = "Resistance Profile",
                     tabName = "gene_screening",
                     icon = icon("dna"),
                     startExpanded = TRUE,
                     menuSubItem(
-                      text = "Screen Assembly",
-                      tabName = "gs_screening"
+                      text = "Browse entries",
+                      tabName = "gs_profile"
                     ),
                     menuSubItem(
-                      text = "Resistance Profile",
-                      tabName = "gs_profile"
+                      text = "Screening",
+                      tabName = "gs_screening"
                     )
                   ),
                   menuItem(
@@ -7157,17 +7182,17 @@ server <- function(input, output, session) {
                         icon = icon("gears")
                       ),
                       menuItem(
-                        text = "Gene Screening",
+                        text = "Resistance Profile",
                         tabName = "gene_screening",
                         icon = icon("dna"),
                         startExpanded = TRUE,
                         menuSubItem(
-                          text = "Screen Assembly",
-                          tabName = "gs_screening"
+                          text = "Browse entries",
+                          tabName = "gs_profile"
                         ),
                         menuSubItem(
-                          text = "Resistance Profile",
-                          tabName = "gs_profile"
+                          text = "Screening",
+                          tabName = "gs_screening"
                         )
                       ),
                       menuItem(
@@ -7224,17 +7249,17 @@ server <- function(input, output, session) {
                         icon = icon("gears")
                       ),
                       menuItem(
-                        text = "Gene Screening",
+                        text = "Resistance Profile",
                         tabName = "gene_screening",
                         icon = icon("dna"),
                         startExpanded = TRUE,
                         menuSubItem(
-                          text = "Screen Assembly",
-                          tabName = "gs_screening"
+                          text = "Browse entries",
+                          tabName = "gs_profile"
                         ),
                         menuSubItem(
-                          text = "Resistance Profile",
-                          tabName = "gs_profile"
+                          text = "Screening",
+                          tabName = "gs_screening"
                         )
                       ),
                       menuItem(
@@ -9172,17 +9197,17 @@ server <- function(input, output, session) {
                       icon = icon("gears")
                     ),
                     menuItem(
-                      text = "Gene Screening",
+                      text = "Resistance Profile",
                       tabName = "gene_screening",
                       icon = icon("dna"),
                       startExpanded = TRUE,
                       menuSubItem(
-                        text = "Screen Assembly",
-                        tabName = "gs_screening"
+                        text = "Browse entries",
+                        tabName = "gs_profile"
                       ),
                       menuSubItem(
-                        text = "Resistance Profile",
-                        tabName = "gs_profile"
+                        text = "Screening",
+                        tabName = "gs_screening"
                       )
                     ),
                     menuItem(
@@ -9663,17 +9688,17 @@ server <- function(input, output, session) {
                 icon = icon("gears")
               ),
               menuItem(
-                text = "Gene Screening",
+                text = "Resistance Profile",
                 tabName = "gene_screening",
                 icon = icon("dna"),
                 startExpanded = TRUE,
                 menuSubItem(
-                  text = "Screen Assembly",
-                  tabName = "gs_screening"
+                  text = "Browse entries",
+                  tabName = "gs_profile"
                 ),
                 menuSubItem(
-                  text = "Resistance Profile",
-                  tabName = "gs_profile"
+                  text = "Screening",
+                  tabName = "gs_screening"
                 )
               ),
               menuItem(
@@ -9726,17 +9751,17 @@ server <- function(input, output, session) {
               icon = icon("gears")
             ),
             menuItem(
-              text = "Gene Screening",
+              text = "Resistance Profile",
               tabName = "gene_screening",
               icon = icon("dna"),
               startExpanded = TRUE,
               menuSubItem(
-                text = "Screen Assembly",
-                tabName = "gs_screening"
+                text = "Browse entries",
+                tabName = "gs_profile"
               ),
               menuSubItem(
-                text = "Resistance Profile",
-                tabName = "gs_profile"
+                text = "Screening",
+                tabName = "gs_screening"
               )
             ),
             menuItem(
@@ -9891,11 +9916,7 @@ server <- function(input, output, session) {
   observeEvent(input$reload_db, {
     log_print("Input reload_db")
     
-    cust_var2 <<- DB$cust_var
-    dataa2 <<- DB$data
-    meta_gs2 <<- DB$meta_gs
-    meta2 <<- DB$meta
-    allelic_profile2 <<- DB$allelic_profile
+    test <<- Screening$status_df
     
     if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
       show_toast(
@@ -22537,48 +22558,37 @@ server <- function(input, output, session) {
     )
   })
   
-  output$screening_results <- renderUI({
-    if(!is.null(Screening$results)) {
-      dataTableOutput("screening_table")
-    }
-  })
-  
   observe({
-    if(isTRUE(Screening$fail)) {
-      output$screening_fail <- renderPrint({
-        readLines(paste0(getwd(), "/execute/screening/error.txt"))
-      })
-    } else {
-      output$screening_fail <- NULL
-    }
-  })
-  
-  
-  observe({
-    if(!is.null(Screening$results)) {
-      req(Screening$results)
-      
-      output$screening_table <- renderDataTable(
-        select(Screening$results, c(6, 7, 8, 9, 11)),
-        selection = "single",
-        options = list(pageLength = 10,
-                       columnDefs = list(list(searchable = TRUE,
-                                              targets = "_all")),
-                       initComplete = DT::JS(
-                         "function(settings, json) {",
-                         "$('th:first-child').css({'border-top-left-radius': '5px'});",
-                         "$('th:last-child').css({'border-top-right-radius': '5px'});",
-                         "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                         "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                         "}"
-                       ),
-                       drawCallback = DT::JS(
-                         "function(settings) {",
-                         "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                         "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                         "}"
-                       )))
-    }
+      req(input$screening_res_sel, DB$database, DB$scheme, Screening$status_df)
+      if(length(input$screening_res_sel) > 0) {
+        if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
+          results <- read.delim(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
+                                          input$screening_res_sel, "resProfile.tsv"))
+          
+          output$screening_table <- renderDataTable(
+            select(results, c(6, 7, 8, 9, 11)),
+            selection = "single",
+            options = list(pageLength = 10,
+                           columnDefs = list(list(searchable = TRUE,
+                                                  targets = "_all")),
+                           initComplete = DT::JS(
+                             "function(settings, json) {",
+                             "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                             "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                             "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                             "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                             "}"
+                           ),
+                           drawCallback = DT::JS(
+                             "function(settings) {",
+                             "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                             "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                             "}"
+                           )))
+        } else {output$screening_table <- NULL}
+      } else {
+        output$screening_table <- NULL
+      }
   })
   
   # Availablity feedback
@@ -22639,26 +22649,67 @@ server <- function(input, output, session) {
         fluidRow(
           column(1),
           column(
-            width = 3,
+            width = 4,
             align = "center",
             br(), br(),
             p(
               HTML(
                 paste(
-                  tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Assembly File (FASTA)')
+                  tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Isolates for Screening')
                 )
               )
             ),
-            shinyFilesButton(
-              "genome_file_gs",
-              "Browse" ,
-              icon = icon("file"),
-              title = "Select the assembly in .fasta/.fna/.fa format:",
-              multiple = FALSE,
-              buttonType = "default",
-              class = NULL,
-              root = path_home()
-            ),
+            if(length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) > 0 &
+               length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) > 0) {
+              div(
+                class = "screening_div",
+                pickerInput(
+                  "screening_select",
+                  "",
+                  choices = list(Unscreened = DB$data$`Assembly ID`[which(DB$data$Screened == "No")],
+                                 Screened = DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]),
+                  options = list(
+                    `live-search` = TRUE,
+                    `actions-box` = TRUE,
+                    size = 10,
+                    style = "background-color: white; border-radius: 5px;"
+                  ),
+                  multiple = TRUE
+                ) 
+              )
+            } else if(length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) > 0) {
+              div(
+                class = "screening_div",
+                pickerInput(
+                  "screening_select",
+                  "",
+                  choices = list(Unscreened = DB$data$`Assembly ID`[which(DB$data$Screened == "No")]),
+                  options = list(
+                    `live-search` = TRUE,
+                    `actions-box` = TRUE,
+                    size = 10,
+                    style = "background-color: white; border-radius: 5px;"
+                  ),
+                  multiple = TRUE
+                ) 
+              )
+            } else {
+              div(
+                class = "screening_div",
+                pickerInput(
+                  "screening_select",
+                  "",
+                  choices = list(Screened = DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]),
+                  options = list(
+                    `live-search` = TRUE,
+                    `actions-box` = TRUE,
+                    size = 10,
+                    style = "background-color: white; border-radius: 5px;"
+                  ),
+                  multiple = TRUE
+                )
+              )
+            },
             br(), br(),
             uiOutput("genome_path_gs")
           ),
@@ -22666,18 +22717,33 @@ server <- function(input, output, session) {
           column(
             width = 2,
             uiOutput("screening_start")
-          )
+          ),
+          column(1)
+          # column(
+          #   width = 3,
+          #   align = "left",
+          #   box(
+          #     solidHeader = TRUE,
+          #     status = "primary",
+          #     width = "90%",
+          #     HTML(paste("<span style='color: white; font-size: 17px'>", 
+          #                "AMRFinder Database Status")),
+          #     
+          #   )
+          # )
         ),
         fluidRow(
           column(1),
           column(
             width = 10,
             br(), br(), br(), br(),
-            uiOutput("screening_results"),
-            verbatimTextOutput("screening_fail"),
-            br(), br(), br(), br(), br(), br()
+            uiOutput("screening_result_sel"),
+            br(),
+            uiOutput("screening_result"),
+            br(), br(), br(), br(), br(), br(), br(), br(), br()
           )
-        )
+        ),
+        br(), br(), br(), br(), br(), br(), br(), br()
       )
     }
   })
@@ -22688,86 +22754,49 @@ server <- function(input, output, session) {
   observeEvent(input$screening_reset_bttn, {
     log_print("Reset gene screening")
     Screening$status <- "idle"
-    file.remove(paste0(getwd(), "/execute/screening/output_file.tsv"))
-    file.remove(paste0(getwd(), "/execute/screening/error.txt"))
+    sapply(Screening$status_df$isolate, remove.screening.status)
     Screening$results <- NULL
-    Screening$single_path <- data.frame()
     Screening$fail <- NULL
-  })
-  
-  # Get selected Genome in Single Mode
-  
-  observe({
-    shinyFileChoose(input,
-                    "genome_file_gs",
-                    roots = c(Home = path_home(), Root = "/"),
-                    defaultRoot = "Home",
-                    session = session,
-                    filetypes = c('', 'fasta', 'fna', 'fa'))
-    Screening$single_path <- parseFilePaths(roots = c(Home = path_home(), Root = "/"), input$genome_file_gs)
-    
+    output$screening_table <- NULL
+    Screening$status_df <- NULL
   })
   
   # Get selected assembly
   
   observe({
-    if (nrow(Screening$single_path) < 1) {
+    if (length(input$screening_select) < 1) {
       output$genome_path_gs <- renderUI(HTML(
-        paste("<span style='color: white;'>", "No file selected.")
+        paste("<span style='color: white;'>", length(input$screening_select), " isolates queried for screening.")
       ))
       
       output$screening_start <- NULL
       
-    } else if (nrow(Screening$single_path) > 0) {
+    } else if (length(input$screening_select) > 0) {
       
-      if (str_detect(str_sub(Screening$single_path$name, start = -6), ".fasta") | 
-          str_detect(str_sub(Screening$single_path$name, start = -6), ".fna") | 
-          str_detect(str_sub(Screening$single_path$name, start = -6), ".fa")) {
-        
-        # Render selected assembly path
-        output$genome_path_gs <- renderUI({
-          HTML(
-            paste(
-              "<span style='color: white; font-weight: bolder'>",
-              as.character(Screening$single_path$name)
-            )
-          )
-        })
+      output$screening_start <- renderUI({
         
-        output$screening_start <- renderUI({
-          
-          fluidRow(
-            column(
-              width = 8,
-              br(), br(), 
-              if(Screening$status == "finished") {
-                actionButton(
-                  "screening_reset_bttn",
-                  "Reset",
-                  icon = icon("arrows-rotate")
-                )
-              } else if(Screening$status == "idle") {
-                actionButton(
-                  inputId = "screening_start_button",
-                  label = "Start",
-                  icon = icon("circle-play")
-                )
-              } else if(Screening$status == "started") {
-                HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:22px;color:white;margin-top:37px;position:relative;left:20px"></i>'))
-              }
-            )
+        fluidRow(
+          column(
+            width = 8,
+            br(), br(), 
+            if(Screening$status == "finished") {
+              actionButton(
+                "screening_reset_bttn",
+                "Reset",
+                icon = icon("arrows-rotate")
+              )
+            } else if(Screening$status == "idle") {
+              actionButton(
+                inputId = "screening_start_button",
+                label = "Start",
+                icon = icon("circle-play")
+              )
+            } else if(Screening$status == "started") {
+              HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:22px;color:white;margin-top:37px;position:relative;left:20px"></i>'))
+            }
           )
-        })
-        
-      } else {
-        show_toast(
-          title = "Wrong file type (only fasta/fna/fa)",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
         )
-        
-      }
+      })
     }
   })
   
@@ -22802,58 +22831,135 @@ server <- function(input, output, session) {
         timer = 6000
       )
       
-      screening_df <- data.frame(wd = getwd(),
-                                 assembly_path = Screening$single_path$datapath,
-                                 assembly = as.character(basename(Screening$single_path$name)),
+      Screening$meta_df <- data.frame(wd = getwd(),
+                                 selected = paste(
+                                   file.path(DB$database, gsub(" ", "_", DB$scheme),
+                                             "Isolates", input$screening_select,
+                                             paste0(input$screening_select, ".zip")), 
+                                   collapse = " "),
                                  species = gsub(" ", "_", DB$scheme))
       
-      saveRDS(screening_df, paste0(getwd(), "/execute/screening_meta.rds"))
+      Screening$status_df <- data.frame(isolate = basename(gsub(".zip", "", str_split_1(Screening$meta_df$selected, " "))), 
+                                        status = "unfinished", shown = FALSE)
+      
+      # Reset screening status
+      sapply(Screening$status_df$isolate, remove.screening.status)
+      
+      saveRDS(Screening$meta_df, paste0(getwd(), "/execute/screening_meta.rds"))
       
       # System execution screening.sh
       system(paste("bash", paste0(getwd(), "/execute/screening.sh")), wait = FALSE)
-      
     }
   })
   
   ### Screening Feedback ----
   
   observe({
-    req(Screening$status)
-    if(Screening$status == "started") {
-      shinyjs::disable("genome_file_gs") 
-      check_screening()
-    } else if(Screening$status == "idle") {
-      shinyjs::enable("genome_file_gs") 
-    }
-  })
-  
-  check_screening <- reactive({
-    invalidateLater(2000, session)
-    if(Screening$status == "started"){
-      if(file.exists(paste0(getwd(), "/execute/screening/output_file.tsv"))) {
-        Screening$results <- read.delim(paste0(getwd(), "/execute/screening/output_file.tsv"))
-        Screening$status <- "finished"
-        log_print("Finalized gene screening")
-        show_toast(
-          title = "Successful gene screening",
-          type = "success",
-          position = "bottom-end",
-          timer = 6000
+    req(Screening$status, Screening$status_df, input$screening_res_sel)
+    if(Screening$status != "idle") {
+      if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
+        output$screening_result <- renderUI(
+          dataTableOutput("screening_table") 
         )
-      } else if(file.exists(paste0(getwd(), "/execute/screening/error.txt"))) {
-        Screening$status <- "finished"
-        log_print("Failed gene screening")
-        Screening$fail <- TRUE
-        show_toast(
-          title = "Failed gene screening",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
+      } else {
+        output$screening_result <- renderUI(
+          verbatimTextOutput("screening_fail")
         )
       }
+    } else {
+      output$screening_result <- NULL
+    }
+  })
+  
+  observe({
+    req(req(Screening$status, Screening$status_df, input$screening_res_sel))
+    if(Screening$status != "idle") {
+      if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "fail") {
+        output$screening_fail <- renderPrint({
+          readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
+                              "Isolates", input$screening_res_sel, "status.txt"))
+        })
+      }
     }
   })
   
+   observe({
+     req(Screening$status)
+     if(Screening$status == "started") {
+       
+       # start status screening for user feedback
+       check_screening()
+       
+       if(isTRUE(Screening$first_result)) {
+         output$screening_result_sel <- renderUI(
+           selectInput(
+             "screening_res_sel",
+             "Select Result",
+             choices = ""
+           )
+         )
+         
+         Screening$first_result <- FALSE
+       }
+     } else if(Screening$status == "idle") {
+       output$screening_result_sel <- NULL
+     }
+   })
+    
+   check_screening <- reactive({
+     invalidateLater(2000, session)
+     
+     req(Screening$status_df)
+     
+     if(Screening$status == "started") {
+       
+       Screening$status_df$status <- sapply(Screening$status_df$isolate, check_status)
+       
+       if(any("unfinished" != Screening$status_df$status) &
+          !identical(Screening$choices, Screening$status_df$isolate[which(Screening$status_df$status == "success")])) {
+         
+         status_df <- Screening$status_df[which(Screening$status_df$status != "unfinished"),]
+         
+         Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
+                                                                  Screening$status_df$status == "fail")]
+         
+         if(sum("unfinished" != Screening$status_df$status) == 1) {
+           Screening$first_result <- TRUE
+         }
+         
+         if(tail(status_df$status, 1) == "success") {
+           
+           show_toast(
+             title = paste("Successful screening of", tail(Screening$choices, 1)),
+             type = "success",
+             position = "bottom-end",
+             timer = 6000)
+           
+           updateSelectInput(session = session,
+                             inputId = "screening_res_sel",
+                             choices = Screening$choices,
+                             selected = tail(Screening$choices, 1))
+           
+         } else if(tail(status_df$status, 1) == "fail") {
+           show_toast(
+             title = paste("Failed screening of", tail(status_df$isolate, 1)),
+             type = "error",
+             position = "bottom-end",
+             timer = 6000)
+           
+           updateSelectInput(session = session,
+                             inputId = "screening_res_sel",
+                             choices = Screening$choices,
+                             selected = tail(Screening$choices, 1))
+         }
+         
+         if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+           Screening$status <- "finished"
+         }
+       } 
+     }
+   })
+  
   
   # _______________________ ####
   
diff --git a/execute/screening.sh b/execute/screening.sh
index 75b0351..0a9a0f9 100755
--- a/execute/screening.sh
+++ b/execute/screening.sh
@@ -7,12 +7,9 @@ unset R_HOME
 
 # Set base path
 base_path=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'wd'])")
-path_assembly=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'assembly_path'])")
-assembly=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'assembly'])")
+selected=$(Rscript -e "cat(stringr::str_split_1(readRDS('screening_meta.rds')[,'selected'], ' '))")
 species=$(Rscript -e "cat(readRDS('screening_meta.rds')[,'species'])")
 
-error_file="screening/error.txt"
-
 if [ "$species" = "Escherichia_coli" ]; then
   species="Escherichia"
 fi
@@ -42,22 +39,32 @@ if [ -d "$base_path/execute/screening" ]; then
     rm -r "$base_path/execute/screening"
 fi
 
-mkdir "$base_path/execute/screening"
-
-amrfinder -n "$path_assembly" --plus --organism $species -o "screening/output_file.tsv" > amrfinder_stdout.txt 2> amrfinder_stderr.txt
-status=$?
+isolates=($selected)
 
-# Check if status variable is set and is an integer
-if [ -z "$status" ]; then
-  echo "AMRFinder execution did not set an exit status." > "$base_path/execute/$error_file"
-  exit 1
-fi
+# Loop through the list of file names and copy them to the new folder
+for file in "${isolates[@]}"; do
 
-if [ "$status" -ne 0 ]; then
-  echo "AMRFinder failed with status $status" > "$base_path/execute/$error_file"
-  echo "Error details:" >> "$base_path/execute/$error_file"
-  cat amrfinder_stderr.txt >> "$base_path/execute/$error_file"
-  exit $status
-fi
+    # Get the directory and base name of the zip file
+    zip_dir=$(dirname "$file")
+    zip_base=$(basename "$file" .zip)
+    
+    unzip -o "$file" -d "$zip_dir"
+    
+    amrfinder -n "$zip_dir/$zip_base.fasta" --plus --organism $species -o "$zip_dir/resProfile.tsv" > amrfinder_stdout.txt 2> amrfinder_stderr.txt
+    status=$?
+    
+    # Check exit status 
+    if [ "$status" -ne 0 ]; then
+      echo "AMRFinder failed with status $status" > "$zip_dir/status.txt"
+      echo "Error details:" >> "$zip_dir/status.txt"
+      cat amrfinder_stderr.txt >> "$zip_dir/status.txt"
+    else
+        # Write success message if AMRFinder executed successfully
+        echo "AMRFinder executed successfully for $zip_base" > "$zip_dir/status.txt"
+    fi
+    
+    # Clear unzipped assembly
+    rm -rf "$zip_dir/$zip_base.fasta"
+done
 
-echo "AMRFinder completed successfully"
+echo "AMRFinder finalized"

From ec4217bf01fc9462ca626b759e021d76173ce426 Mon Sep 17 00:00:00 2001
From: marian <marian@fedora.fritz.box>
Date: Mon, 12 Aug 2024 23:40:45 +0200
Subject: [PATCH 44/75] Polished Screening UI; Added Screening Termination

---
 App.R                 | 431 ++++++++++++++++++++++++++++--------------
 execute/kill_multi.sh |   2 +-
 www/body.css          | 346 ++++++++++++++++-----------------
 3 files changed, 465 insertions(+), 314 deletions(-)

diff --git a/App.R b/App.R
index df76356..b028abf 100644
--- a/App.R
+++ b/App.R
@@ -582,7 +582,7 @@ ui <- dashboardPage(
           fluidRow(
             column(
               width = 6,
-              uiOutput("test_yes_pending")
+              uiOutput("pending_typing")
             ),
             column(
               width = 6,
@@ -5320,7 +5320,9 @@ ui <- dashboardPage(
         ),
         br(),
         hr(),
-        uiOutput("screening_interface")
+        fluidRow(
+          uiOutput("screening_interface")
+        )
       ),
       
       ## Tab Resistance Profile -------------------------------------------------------
@@ -5690,13 +5692,19 @@ server <- function(input, output, session) {
   
   # Reset gene screening status
   remove.screening.status <- function(isolate) {
-    file.remove(
-      file.path(DB$database, 
-                gsub(" ", "_", DB$scheme),
-                "Isolates",
-                Screening$status_df$isolate,
-                "status.txt")
-    )
+    if(file.exists(file.path(DB$database, 
+                             gsub(" ", "_", DB$scheme),
+                             "Isolates",
+                             isolate,
+                             "status.txt"))) {
+      file.remove(
+        file.path(DB$database, 
+                  gsub(" ", "_", DB$scheme),
+                  "Isolates",
+                  isolate,
+                  "status.txt")
+      )
+    }
   }
   
   # Function to check for duplicate isolate IDs for multi typing start
@@ -6469,7 +6477,7 @@ server <- function(input, output, session) {
               icon = icon("dna"),
               startExpanded = TRUE,
               menuSubItem(
-                text = "Browse entries",
+                text = "Browse Entries",
                 tabName = "gs_profile"
               ),
               menuSubItem(
@@ -6512,7 +6520,7 @@ server <- function(input, output, session) {
         output$multi_stop <- NULL
         output$metadata_multi_box <- NULL
         output$start_multi_typing_ui <- NULL
-        output$test_yes_pending <- NULL
+        output$pending_typing <- NULL
         output$multi_typing_results <- NULL
         output$single_typing_progress <- NULL
         output$metadata_single_box <- NULL
@@ -6549,7 +6557,7 @@ server <- function(input, output, session) {
         output$multi_stop <- NULL
         output$metadata_multi_box <- NULL
         output$start_multi_typing_ui <- NULL
-        output$test_yes_pending <- NULL
+        output$pending_typing <- NULL
         output$multi_typing_results <- NULL
         output$single_typing_progress <- NULL
         output$metadata_single_box <- NULL
@@ -6647,7 +6655,7 @@ server <- function(input, output, session) {
                   icon = icon("dna"),
                   startExpanded = TRUE,
                   menuSubItem(
-                    text = "Browse entries",
+                    text = "Browse Entries",
                     tabName = "gs_profile"
                   ),
                   menuSubItem(
@@ -6737,7 +6745,7 @@ server <- function(input, output, session) {
                   icon = icon("dna"),
                   startExpanded = TRUE,
                   menuSubItem(
-                    text = "Browse entries",
+                    text = "Browse Entries",
                     tabName = "gs_profile"
                   ),
                   menuSubItem(
@@ -6829,7 +6837,7 @@ server <- function(input, output, session) {
                   icon = icon("dna"),
                   startExpanded = TRUE,
                   menuSubItem(
-                    text = "Browse entries",
+                    text = "Browse Entries",
                     tabName = "gs_profile"
                   ),
                   menuSubItem(
@@ -6950,7 +6958,7 @@ server <- function(input, output, session) {
                     icon = icon("dna"),
                     startExpanded = TRUE,
                     menuSubItem(
-                      text = "Browse entries",
+                      text = "Browse Entries",
                       tabName = "gs_profile"
                     ),
                     menuSubItem(
@@ -7187,7 +7195,7 @@ server <- function(input, output, session) {
                         icon = icon("dna"),
                         startExpanded = TRUE,
                         menuSubItem(
-                          text = "Browse entries",
+                          text = "Browse Entries",
                           tabName = "gs_profile"
                         ),
                         menuSubItem(
@@ -7254,7 +7262,7 @@ server <- function(input, output, session) {
                         icon = icon("dna"),
                         startExpanded = TRUE,
                         menuSubItem(
-                          text = "Browse entries",
+                          text = "Browse Entries",
                           tabName = "gs_profile"
                         ),
                         menuSubItem(
@@ -9202,7 +9210,7 @@ server <- function(input, output, session) {
                       icon = icon("dna"),
                       startExpanded = TRUE,
                       menuSubItem(
-                        text = "Browse entries",
+                        text = "Browse Entries",
                         tabName = "gs_profile"
                       ),
                       menuSubItem(
@@ -9358,7 +9366,7 @@ server <- function(input, output, session) {
                 output$multi_stop <- NULL
                 output$metadata_multi_box <- NULL
                 output$start_multi_typing_ui <- NULL
-                output$test_yes_pending <- NULL
+                output$pending_typing <- NULL
                 output$multi_typing_results <- NULL
                 output$single_typing_progress <- NULL
                 output$metadata_single_box <- NULL
@@ -9693,7 +9701,7 @@ server <- function(input, output, session) {
                 icon = icon("dna"),
                 startExpanded = TRUE,
                 menuSubItem(
-                  text = "Browse entries",
+                  text = "Browse Entries",
                   tabName = "gs_profile"
                 ),
                 menuSubItem(
@@ -9756,7 +9764,7 @@ server <- function(input, output, session) {
               icon = icon("dna"),
               startExpanded = TRUE,
               menuSubItem(
-                text = "Browse entries",
+                text = "Browse Entries",
                 tabName = "gs_profile"
               ),
               menuSubItem(
@@ -22559,7 +22567,8 @@ server <- function(input, output, session) {
   })
   
   observe({
-      req(input$screening_res_sel, DB$database, DB$scheme, Screening$status_df)
+    req(input$screening_res_sel, DB$database, DB$scheme)
+    if(!is.null(Screening$status_df)) {
       if(length(input$screening_res_sel) > 0) {
         if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
           results <- read.delim(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
@@ -22589,6 +22598,10 @@ server <- function(input, output, session) {
       } else {
         output$screening_table <- NULL
       }
+    } else {
+      output$screening_table <- NULL
+    }
+      
   })
   
   # Availablity feedback
@@ -22649,7 +22662,7 @@ server <- function(input, output, session) {
         fluidRow(
           column(1),
           column(
-            width = 4,
+            width = 3,
             align = "center",
             br(), br(),
             p(
@@ -22713,11 +22726,16 @@ server <- function(input, output, session) {
             br(), br(),
             uiOutput("genome_path_gs")
           ),
-          column(1),
           column(
-            width = 2,
+            width = 3,
             uiOutput("screening_start")
           ),
+          column(
+            width = 3,
+            align = "center",
+            br(), br(),
+            uiOutput("screening_result_sel")
+          ),
           column(1)
           # column(
           #   width = 3,
@@ -22736,14 +22754,11 @@ server <- function(input, output, session) {
           column(1),
           column(
             width = 10,
-            br(), br(), br(), br(),
-            uiOutput("screening_result_sel"),
-            br(),
+            br(), br(), 
             uiOutput("screening_result"),
-            br(), br(), br(), br(), br(), br(), br(), br(), br()
+            br(), br(), br(), br()
           )
-        ),
-        br(), br(), br(), br(), br(), br(), br(), br()
+        )
       )
     }
   })
@@ -22753,12 +22768,54 @@ server <- function(input, output, session) {
   # Reset screening 
   observeEvent(input$screening_reset_bttn, {
     log_print("Reset gene screening")
-    Screening$status <- "idle"
+    
+    # reset status file
     sapply(Screening$status_df$isolate, remove.screening.status)
+    
+    # set feedback variables
+    Screening$status <- "idle"
     Screening$results <- NULL
     Screening$fail <- NULL
+    Screening$status_df <- NULL
+    
+    # change reactive UI
     output$screening_table <- NULL
+    output$screening_result <- NULL
+    output$screening_fail <- NULL
+    
+    updatePickerInput(session, "screening_select", selected = character(0))
+    
+    # disable isolate picker
+    shinyjs::runjs("$('#screening_select').prop('disabled', false);")
+    shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
+  })
+  
+  # Cancel screening
+  observeEvent(input$screening_cancel, {
+    log_print("Cancelled gene screening")
+    
+    # terminate screening
+    system(paste("kill $(pgrep -f 'execute/screening.sh')"), wait = FALSE)
+    system(paste("killall -TERM tblastn"), wait = FALSE)
+    
+    # reset status file
+    sapply(Screening$status_df$isolate, remove.screening.status)
+    
+    # set feedback variables
+    Screening$status <- "idle"
+    Screening$results <- NULL
+    Screening$fail <- NULL
     Screening$status_df <- NULL
+    
+    # change reactive UI
+    output$screening_table <- NULL
+    output$screening_result <- NULL
+    
+    updatePickerInput(session, "screening_select", selected = character(0))
+    
+    # disable isolate picker
+    shinyjs::runjs("$('#screening_select').prop('disabled', false);")
+    shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
   })
   
   # Get selected assembly
@@ -22777,22 +22834,91 @@ server <- function(input, output, session) {
         
         fluidRow(
           column(
-            width = 8,
+            width = 12,
             br(), br(), 
-            if(Screening$status == "finished") {
-              actionButton(
-                "screening_reset_bttn",
-                "Reset",
-                icon = icon("arrows-rotate")
+            if(length(input$screening_select) < 1) {
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+                    paste("<span style='color: white; font-style:italic'>", 
+                          "&nbsp Select Isolate(s) for Screening")))
+                )
+              )
+            } else if(Screening$status == "finished") {
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:white"></i>',
+                    paste("<span style='color: white; font-style:italic'>", 
+                          "&nbsp Reset to Perform Screening Again")))
+                ),
+                actionButton(
+                  "screening_reset_bttn",
+                  "Reset",
+                  icon = icon("arrows-rotate")
+                ),
+                if(!is.null(Screening$status_df)) {
+                  p(
+                    HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
+                               sum(Screening$status_df$status != "unfinished"), "/",
+                               nrow(Screening$status_df), " Isolate(s) screened"))
+                  )
+                }
               )
             } else if(Screening$status == "idle") {
-              actionButton(
-                inputId = "screening_start_button",
-                label = "Start",
-                icon = icon("circle-play")
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
+                    paste("<span style='color: white; font-style:italic'>",
+                          "&nbsp Screening Ready")))
+                ),
+                actionButton(
+                  inputId = "screening_start_button",
+                  label = "Start",
+                  icon = icon("circle-play")
+                )
               )
             } else if(Screening$status == "started") {
-              HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:22px;color:white;margin-top:37px;position:relative;left:20px"></i>'))
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-clock" style="font-size:15px;color:white"></i>',
+                    paste("<span style='color: white; font-style:italic'>",
+                          "&nbsp Running Screening ...")))
+                ),
+                fluidRow(
+                  column(3),
+                  column(
+                    width = 3,
+                    actionButton(
+                      inputId = "screening_cancel",
+                      label = "Terminate",
+                      icon = icon("ban")
+                    )
+                  ),
+                  column(
+                    width = 3,
+                    HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:22px;color:white;margin-top:27px;position:relative;left:20px"></i>'))
+                  )
+                ),
+                if(!is.null(Screening$status_df)) {
+                  p(
+                    HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
+                               sum(Screening$status_df$status != "unfinished"), "/",
+                               nrow(Screening$status_df), " Isolate(s) screened"))
+                  )
+                }
+              )
             }
           )
         )
@@ -22824,6 +22950,9 @@ server <- function(input, output, session) {
       
       Screening$status <- "started"
       
+      shinyjs::runjs("$('#screening_select').prop('disabled', true);")
+      shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
+      
       show_toast(
         title = "Gene screening started",
         type = "success",
@@ -22855,16 +22984,28 @@ server <- function(input, output, session) {
   ### Screening Feedback ----
   
   observe({
-    req(Screening$status, Screening$status_df, input$screening_res_sel)
-    if(Screening$status != "idle") {
-      if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
-        output$screening_result <- renderUI(
-          dataTableOutput("screening_table") 
-        )
+    req(Screening$status, input$screening_res_sel)
+    if(!is.null(Screening$status_df)) {
+      if(Screening$status != "idle") {
+        if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
+          output$screening_result <- renderUI(
+            column(
+              width = 12,
+              hr(), br(),
+              dataTableOutput("screening_table") 
+            )
+          )
+        } else {
+          output$screening_result <- renderUI(
+            column(
+              width = 12,
+              hr(), br(),
+              verbatimTextOutput("screening_fail")
+            )
+          )
+        }
       } else {
-        output$screening_result <- renderUI(
-          verbatimTextOutput("screening_fail")
-        )
+        output$screening_result <- NULL
       }
     } else {
       output$screening_result <- NULL
@@ -22872,93 +23013,99 @@ server <- function(input, output, session) {
   })
   
   observe({
-    req(req(Screening$status, Screening$status_df, input$screening_res_sel))
-    if(Screening$status != "idle") {
-      if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "fail") {
-        output$screening_fail <- renderPrint({
-          readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
-                              "Isolates", input$screening_res_sel, "status.txt"))
-        })
+    req(Screening$status, input$screening_res_sel)
+    if(!is.null(Screening$status_df)) {
+      if(Screening$status != "idle") {
+        if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "fail") {
+          output$screening_fail <- renderPrint({
+            cat(paste(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
+                                          "Isolates", input$screening_res_sel, "status.txt")),"\n"))
+          })
+        }
+      } else {
+        output$screening_fail <- NULL
       }
+    } else {
+      output$screening_fail <- NULL
     }
   })
   
-   observe({
-     req(Screening$status)
-     if(Screening$status == "started") {
-       
-       # start status screening for user feedback
-       check_screening()
-       
-       if(isTRUE(Screening$first_result)) {
-         output$screening_result_sel <- renderUI(
-           selectInput(
-             "screening_res_sel",
-             "Select Result",
-             choices = ""
-           )
-         )
-         
-         Screening$first_result <- FALSE
-       }
-     } else if(Screening$status == "idle") {
-       output$screening_result_sel <- NULL
-     }
-   })
-    
-   check_screening <- reactive({
-     invalidateLater(2000, session)
-     
-     req(Screening$status_df)
-     
-     if(Screening$status == "started") {
-       
-       Screening$status_df$status <- sapply(Screening$status_df$isolate, check_status)
-       
-       if(any("unfinished" != Screening$status_df$status) &
-          !identical(Screening$choices, Screening$status_df$isolate[which(Screening$status_df$status == "success")])) {
-         
-         status_df <- Screening$status_df[which(Screening$status_df$status != "unfinished"),]
-         
-         Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
-                                                                  Screening$status_df$status == "fail")]
-         
-         if(sum("unfinished" != Screening$status_df$status) == 1) {
-           Screening$first_result <- TRUE
-         }
-         
-         if(tail(status_df$status, 1) == "success") {
-           
-           show_toast(
-             title = paste("Successful screening of", tail(Screening$choices, 1)),
-             type = "success",
-             position = "bottom-end",
-             timer = 6000)
-           
-           updateSelectInput(session = session,
-                             inputId = "screening_res_sel",
-                             choices = Screening$choices,
-                             selected = tail(Screening$choices, 1))
-           
-         } else if(tail(status_df$status, 1) == "fail") {
-           show_toast(
-             title = paste("Failed screening of", tail(status_df$isolate, 1)),
-             type = "error",
-             position = "bottom-end",
-             timer = 6000)
-           
-           updateSelectInput(session = session,
-                             inputId = "screening_res_sel",
-                             choices = Screening$choices,
-                             selected = tail(Screening$choices, 1))
-         }
-         
-         if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
-           Screening$status <- "finished"
-         }
-       } 
-     }
-   })
+  observe({
+    req(Screening$status)
+    if(Screening$status == "started") {
+      
+      # start status screening for user feedback
+      check_screening()
+      
+      if(isTRUE(Screening$first_result)) {
+        output$screening_result_sel <- renderUI(
+          selectInput(
+            "screening_res_sel",
+            label = h5("Select Result", style = "color:white; margin-bottom: 32px; margin-top: -10px;"),
+            choices = ""
+          )
+        )
+        
+        Screening$first_result <- FALSE
+      }
+    } else if(Screening$status == "idle") {
+      output$screening_result_sel <- NULL
+    }
+  }) 
+    
+  check_screening <- reactive({
+    invalidateLater(2000, session)
+    
+    req(Screening$status_df)
+    
+    if(Screening$status == "started") {
+      
+      Screening$status_df$status <- sapply(Screening$status_df$isolate, check_status)
+      
+      if(any("unfinished" != Screening$status_df$status) &
+         !identical(Screening$choices, Screening$status_df$isolate[which(Screening$status_df$status != "unfinished")])) {
+        
+        status_df <- Screening$status_df[which(Screening$status_df$status != "unfinished"),]
+        
+        Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
+                                                                 Screening$status_df$status == "fail")]
+        
+        if(sum("unfinished" != Screening$status_df$status) == 1) {
+          Screening$first_result <- TRUE
+        }
+        
+        if(tail(status_df$status, 1) == "success") {
+          
+          show_toast(
+            title = paste("Successful screening of", tail(Screening$choices, 1)),
+            type = "success",
+            position = "bottom-end",
+            timer = 6000)
+          
+          updateSelectInput(session = session,
+                            inputId = "screening_res_sel",
+                            choices = Screening$choices,
+                            selected = tail(Screening$choices, 1))
+          
+        } else if(tail(status_df$status, 1) == "fail") {
+          show_toast(
+            title = paste("Failed screening of", tail(status_df$isolate, 1)),
+            type = "error",
+            position = "bottom-end",
+            timer = 6000)
+          
+          updateSelectInput(session = session,
+                            inputId = "screening_res_sel",
+                            choices = Screening$choices,
+                            selected = tail(Screening$choices, 1))
+        }
+        
+        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+          Screening$status <- "finished"
+        }
+      } 
+    }
+  }) 
   
   
   # _______________________ ####
@@ -24703,7 +24850,7 @@ server <- function(input, output, session) {
         )
       })
       
-      output$test_yes_pending <- NULL
+      output$pending_typing <- NULL
       output$multi_typing_results <- NULL
     }
   })
@@ -24735,7 +24882,7 @@ server <- function(input, output, session) {
     
     # Reset User Feedback variable
     Typing$pending_format <- 0
-    output$test_yes_pending <- NULL
+    output$pending_typing <- NULL
     output$multi_typing_results <- NULL
     Typing$failures <- 0
     Typing$successes <- 0
@@ -25066,14 +25213,14 @@ server <- function(input, output, session) {
       
       output$initiate_multi_typing_ui <- NULL
       
-      output$test_yes_pending <- renderUI({
+      output$pending_typing <- renderUI({
         fluidRow(
           fluidRow(
             br(), br(),
             column(width = 2),
             column(
               width = 4,
-              h3(p("Pending Multi Typing ..."), style = "color:white"),
+              h3(p("Pending Typing ..."), style = "color:white"),
               br(), br(),
               fluidRow(
                 column(
@@ -25110,7 +25257,7 @@ server <- function(input, output, session) {
       
       output$initiate_multi_typing_ui <- NULL
       
-      output$test_yes_pending <- renderUI({
+      output$pending_typing <- renderUI({
         
         fluidRow(
           fluidRow(
@@ -25158,7 +25305,7 @@ server <- function(input, output, session) {
         )
       })
     } else if (!grepl("Start Multi Typing", head(readLogFile(), n = 1))){
-      output$test_yes_pending <- NULL
+      output$pending_typing <- NULL
       Typing$multi_result_status <- "idle"
     }
   })
diff --git a/execute/kill_multi.sh b/execute/kill_multi.sh
index 6d1c7e7..2708e6e 100755
--- a/execute/kill_multi.sh
+++ b/execute/kill_multi.sh
@@ -33,4 +33,4 @@ else
   kill "$PID"
 fi
 
-echo 0 > $log_file
\ No newline at end of file
+echo 0 > $log_file
diff --git a/www/body.css b/www/body.css
index a472966..c0652e4 100644
--- a/www/body.css
+++ b/www/body.css
@@ -159,7 +159,7 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
   border: 1px solid #00000000;
   border-width: 1px;
   display: inline-block; /* Make the element inline-block */
-    transition: border-color 0.3s ease; /* Smooth transition for border color */
+  transition: border-color 0.3s ease; /* Smooth transition for border color */
 }
 
 .bttn-material-flat:hover{
@@ -168,20 +168,20 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
 
 .action-button.bttn.bttn-material-flat.bttn-sm.bttn-default.bttn-no-outline.shiny-bound-input {
   background: #282F38 !important;
-    border: 1px solid transparent; /* Default border color */
-    display: inline-block; /* Make the element inline-block */
-    transition: border-color 0.3s ease; /* Smooth transition for border color */
-    border-width: 1px !important;
+  border: 1px solid transparent; /* Default border color */
+  display: inline-block; /* Make the element inline-block */
+  transition: border-color 0.3s ease; /* Smooth transition for border color */
+  border-width: 1px !important;
   border-color: white !important;
   color: white !important;
   transition: background 0.3s ease; /* Smooth transition for border color */
-    transition: color 0.3s ease; /* Smooth transition for border color */
+  transition: color 0.3s ease; /* Smooth transition for border color */
 }
 
 .action-button.bttn.bttn-material-flat.bttn-sm.bttn-default.bttn-no-outline.shiny-bound-input:hover {
   border-color: transparent !important; /* Change border color to white on hover */
-    background: #20E6E5 !important;
-    color: black !important;
+  background: #20E6E5 !important;
+  color: black !important;
 }
 
 .shiny-input-container input[type = "text"]:hover {
@@ -194,14 +194,14 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
 
 .main-sidebar .sidebar .sidebar-menu .treeview-menu li.active a {
   color: #000000 !important; 
-    border-radius: 20px; 
+  border-radius: 20px; 
   margin-top: 7px; 
   margin-bottom: 7px;
 }
 
 .main-sidebar .sidebar .sidebar-menu .treeview-menu li:hover a {
   color: #000000; 
-    border-radius: 20px; 
+  border-radius: 20px; 
   margin-top: 7px; 
   margin-bottom: 7px;
 }
@@ -212,7 +212,7 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
 
 .main-sidebar .sidebar .sidebar-menu li:hover a {
   color: #000000; 
-    border: none;
+  border: none;
 }
 
 file.select {
@@ -221,17 +221,17 @@ file.select {
 
 .box.box-solid.box-info{
   background: #282F38;
-    margin-top: 20px;
+  margin-top: 20px;
   position: relative;
   left: 30px;
 }
 
 .box.box-solid.box-info, .box.box-info {
   border-color: #ffffff;
-    border-left-color: #ffffff;
-    border-right-color: #ffffff;
-    border-top-color: #ffffff;
-    border-radius: 7px;
+  border-left-color: #ffffff;
+  border-right-color: #ffffff;
+  border-top-color: #ffffff;
+  border-radius: 7px;
 }
 
 .selectize-control.single .selectize-input:after {
@@ -1847,108 +1847,108 @@ margin-left: -5px
 }
 
 #nj_tiplab_show, #upgma_tiplab_show {
-margin-top: 17px; 
-margin-left: -5px
+  margin-top: 17px; 
+  margin-left: -5px
 }
 
 #nj_fruit_offset, #upgma_fruit_offset {
-position: relative; 
-top: -20px
+  position: relative; 
+  top: -20px
 }
 
 #nj_layout .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y,
 #upgma_layout .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y{
-margin-bottom: 16px
+  margin-bottom: 16px
 }
 
 #nj_div_tiles, #upgma_div_tiles {
-position: absolute; 
-bottom: 4px; 
-margin-left: -5px
+  position: absolute; 
+  bottom: 4px; 
+  margin-left: -5px
 }
 
 #nj_fruit_offset_2, #upgma_fruit_offset_2 {
-position: relative; 
-top: -20px
+  position: relative; 
+  top: -20px
 }
 
 #nj_layout_2 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y,
 #upgma_layout_2 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y{
-margin-bottom: 16px
+  margin-bottom: 16px
 }
 
 #nj_div_tiles_2, #upgma_div_tiles_2 {
-position: absolute; 
-bottom: 4px; 
-margin-left: -5px
+  position: absolute; 
+  bottom: 4px; 
+  margin-left: -5px
 }
 
 #nj_fruit_offset_3, #upgma_fruit_offset_3 {
-position: relative; 
-top: -20px
+  position: relative; 
+  top: -20px
 }
 
 #nj_layout_3 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y,
 #upgma_layout_3 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y{
-margin-bottom: 16px
+  margin-bottom: 16px
 }
 
 #nj_div_tiles_3, #upgma_div_tiles_3 {
-position: absolute; 
-bottom: 4px; 
-margin-left: -5px
+  position: absolute; 
+  bottom: 4px; 
+  margin-left: -5px
 }
 
 #nj_fruit_offset_4, #upgma_fruit_offset_4 {
-position: relative; 
-top: -20px
+  position: relative; 
+  top: -20px
 }
 
 #nj_layout_4 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y,
 #upgma_layout_4 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y{
-margin-bottom: 16px
+  margin-bottom: 16px
 }
 
 #nj_div_tiles_4, #upgma_div_tiles_4 {
-position: absolute; 
-bottom: 4px; 
-margin-left: -5px
+  position: absolute; 
+  bottom: 4px; 
+  margin-left: -5px
 }
 
 #nj_fruit_offset_5, #upgma_fruit_offset_5 {
-position: relative; 
-top: -20px
+  position: relative; 
+  top: -20px
 }
 
 #nj_layout_5 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y,
 #upgma_layout_5 .shiny-input-select.shinyjs-resettable.selectize-control.single plugin-selectize-plugin-a11y {
-margin-bottom: 16px
+  margin-bottom: 16px
 }
 
 #nj_div_tiles_5, #upgma_div_tiles_5 {
-position: absolute; 
-bottom: 4px; 
-margin-left: -5px
+  position: absolute; 
+  bottom: 4px; 
+  margin-left: -5px
 }
 
 #nj_heatmap_width, #upgma_heatmap_width {
-margin-top: 8px;
+  margin-top: 8px;
 }
 
 #nj_heatmap_offset, #upgma_heatmap_offset {
-margin-top: 4px;
-margin-bottom: 2px;
+  margin-top: 4px;
+  margin-bottom: 2px;
 }
 
 #nj_fruit_width, #nj_fruit_width2, #nj_fruit_width3, #nj_fruit_width4, #nj_fruit_width5,
 #upgma_fruit_width, #upgma_fruit_width2, #upgma_fruit_width3, #upgma_fruit_width4, #upgma_fruit_width5{
-margin-top: -5px;
-margin-bottom: -15px;
+  margin-top: -5px;
+  margin-bottom: -15px;
 }
 
 #nj_heatmap_show, #upgma_heatmap_show {
-margin-top: 18px; 
-margin-left: -5px;
+  margin-top: 18px; 
+  margin-left: -5px;
 }
 
 #nj_nodepoint_show, #nj_tippoint_show, #upgma_nodepoint_show, #upgma_tippoint_show {
@@ -2524,10 +2524,10 @@ background: linear-gradient(to right, #F7FCFD 0%, #F7FCFD 11.1111%, #E0ECF4 11.1
 #upgma_tiles_scale_5 .option[data-value="BuGn"], 
 #upgma_heatmap_scale .option[data-value="BuGn"],
 #upgma_clade_scale .option[data-value="BuGn"] {
-background: linear-gradient(to right, #F7FCFD 0%, #F7FCFD 11.1111%, #E5F5F9 11.1111%, #E5F5F9 22.2222%, #CCECE6 22.2222%, #CCECE6 33.3333%, #99D8C9 33.3333%, #99D8C9 44.4444%, #66C2A4 44.4444%, #66C2A4 55.5556%, #41AE76 55.5556%, #41AE76 66.6667%, #238B45 66.6667%, #238B45 77.7778%, #006D2C 77.7778%, #006D2C 88.8889%, #00441B 88.8889%, #00441B 100%);
-                            color: white;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #F7FCFD 0%, #F7FCFD 11.1111%, #E5F5F9 11.1111%, #E5F5F9 22.2222%, #CCECE6 22.2222%, #CCECE6 33.3333%,   #99D8C9 33.3333%, #99D8C9 44.4444%, #66C2A4 44.4444%, #66C2A4 55.5556%, #41AE76 55.5556%, #41AE76 66.6667%, #238B45 66.6667%, #238B45 77     .7778%, #006D2C 77.7778%, #006D2C 88.8889%, #00441B 88.8889%, #00441B 100%);
+  color: white;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="Blues"], 
 #nj_tippoint_scale .option[data-value="Blues"], 
@@ -2547,10 +2547,10 @@ background: linear-gradient(to right, #F7FCFD 0%, #F7FCFD 11.1111%, #E5F5F9 11.1
 #upgma_tiles_scale_5 .option[data-value="Blues"], 
 #upgma_heatmap_scale .option[data-value="Blues"],
 #upgma_clade_scale .option[data-value="Blues"] {
-background: linear-gradient(to right, #F7FBFF 0%, #F7FBFF 11.1111%, #DEEBF7 11.1111%, #DEEBF7 22.2222%, #C6DBEF 22.2222%, #C6DBEF 33.3333%, #9ECAE1 33.3333%, #9ECAE1 44.4444%, #6BAED6 44.4444%, #6BAED6 55.5556%, #4292C6 55.5556%, #4292C6 66.6667%, #2171B5 66.6667%, #2171B5 77.7778%, #08519C 77.7778%, #08519C 88.8889%, #08306B 88.8889%, #08306B 100%);
-                            color: white;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #F7FBFF 0%, #F7FBFF 11.1111%, #DEEBF7 11.1111%, #DEEBF7 22.2222%, #C6DBEF 22.2222%, #C6DBEF 33.3333%,   #9ECAE1 33.3333%, #9ECAE1 44.4444%, #6BAED6 44.4444%, #6BAED6 55.5556%, #4292C6 55.5556%, #4292C6 66.6667%, #2171B5 66.6667%, #2171B5 77     .7778%, #08519C 77.7778%, #08519C 88.8889%, #08306B 88.8889%, #08306B 100%);
+  color: white;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="magma"], 
 #nj_tippoint_scale .option[data-value="magma"], 
@@ -2568,10 +2568,10 @@ background: linear-gradient(to right, #F7FBFF 0%, #F7FBFF 11.1111%, #DEEBF7 11.1
 #upgma_tiles_scale_4 .option[data-value="magma"], 
 #upgma_tiles_scale_5 .option[data-value="magma"], 
 #upgma_heatmap_scale .option[data-value="magma"] {
-background: linear-gradient(to right, #000004FF, #07071DFF, #160F3BFF, #29115AFF, #400F73FF, #56147DFF, #6B1D81FF, #802582FF, #952C80FF, #AB337CFF, #C03A76FF, #D6456CFF, #E85362FF, #F4685CFF, #FA815FFF, #FD9A6AFF, #FEB37BFF, #FECC8FFF, #FDE4A6FF, #FCFDBFFF);
-                            color: white;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #000004FF, #07071DFF, #160F3BFF, #29115AFF, #400F73FF, #56147DFF, #6B1D81FF, #802582FF, #952C80FF,     #AB337CFF, #C03A76FF, #D6456CFF, #E85362FF, #F4685CFF, #FA815FFF, #FD9A6AFF, #FEB37BFF, #FECC8FFF, #FDE4A6FF, #FCFDBFFF);
+  color: white;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="inferno"], 
 #nj_tippoint_scale .option[data-value="inferno"], 
@@ -2589,10 +2589,10 @@ background: linear-gradient(to right, #000004FF, #07071DFF, #160F3BFF, #29115AFF
 #upgma_tiles_scale_4 .option[data-value="inferno"], 
 #upgma_tiles_scale_5 .option[data-value="inferno"], 
 #upgma_heatmap_scale .option[data-value="inferno"] {
-background: linear-gradient(to right, #000004FF, #08051EFF, #190C3EFF, #300A5BFF, #460B6AFF, #5C126EFF, #711A6EFF, #87216BFF, #9C2964FF, #B1325AFF, #C43C4EFF, #D64B40FF, #E55C30FF, #F17020FF, #F8870EFF, #FCA007FF, #FBB91FFF, #F7D340FF, #F1ED6FFF, #FCFFA4FF);
-                            color: white;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #000004FF, #08051EFF, #190C3EFF, #300A5BFF, #460B6AFF, #5C126EFF, #711A6EFF, #87216BFF, #9C2964FF,     #B1325AFF, #C43C4EFF, #D64B40FF, #E55C30FF, #F17020FF, #F8870EFF, #FCA007FF, #FBB91FFF, #F7D340FF, #F1ED6FFF, #FCFFA4FF);
+  color: white;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="plasma"], 
 #nj_tippoint_scale .option[data-value="plasma"], 
@@ -2610,10 +2610,10 @@ background: linear-gradient(to right, #000004FF, #08051EFF, #190C3EFF, #300A5BFF
 #upgma_tiles_scale_4 .option[data-value="plasma"], 
 #upgma_tiles_scale_5 .option[data-value="plasma"], 
 #upgma_heatmap_scale .option[data-value="plasma"] {
-background: linear-gradient(to right, #0D0887FF, #2D0594FF, #44039EFF, #5901A5FF, #6F00A8FF, #8305A7FF, #9512A1FF, #A72197FF, #B6308BFF, #C5407EFF, #D14E72FF, #DD5E66FF, #E76E5BFF, #EF7F4FFF, #F79044FF, #FBA238FF, #FEB72DFF, #FDCB26FF, #F7E225FF, #F0F921FF);
-                            color: white;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #0D0887FF, #2D0594FF, #44039EFF, #5901A5FF, #6F00A8FF, #8305A7FF, #9512A1FF, #A72197FF, #B6308BFF,     #C5407EFF, #D14E72FF, #DD5E66FF, #E76E5BFF, #EF7F4FFF, #F79044FF, #FBA238FF, #FEB72DFF, #FDCB26FF, #F7E225FF, #F0F921FF);
+  color: white;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="viridis"], 
 #nj_tippoint_scale .option[data-value="viridis"], 
@@ -2631,10 +2631,10 @@ background: linear-gradient(to right, #0D0887FF, #2D0594FF, #44039EFF, #5901A5FF
 #upgma_tiles_scale_4 .option[data-value="viridis"], 
 #upgma_tiles_scale_5 .option[data-value="viridis"], 
 #upgma_heatmap_scale .option[data-value="viridis"] {
-background: linear-gradient(to right, #440154FF, #481568FF, #482677FF, #453781FF, #3F4788FF, #39558CFF, #32648EFF, #2D718EFF, #287D8EFF, #238A8DFF, #1F968BFF, #20A386FF, #29AF7FFF, #3CBC75FF, #56C667FF, #74D055FF, #94D840FF, #B8DE29FF, #DCE318FF, #FDE725FF);
-                            color: white;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #440154FF, #481568FF, #482677FF, #453781FF, #3F4788FF, #39558CFF, #32648EFF, #2D718EFF, #287D8EFF,     #238A8DFF, #1F968BFF, #20A386FF, #29AF7FFF, #3CBC75FF, #56C667FF, #74D055FF, #94D840FF, #B8DE29FF, #DCE318FF, #FDE725FF);
+  color: white;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="cividis"], 
 #nj_tippoint_scale .option[data-value="cividis"], 
@@ -2652,10 +2652,10 @@ background: linear-gradient(to right, #440154FF, #481568FF, #482677FF, #453781FF
 #upgma_tiles_scale_4 .option[data-value="cividis"], 
 #upgma_tiles_scale_5 .option[data-value="cividis"], 
 #upgma_heatmap_scale .option[data-value="cividis"] {
-background: linear-gradient(to right, #00204DFF, #002A64FF, #00336FFF, #1F3C6DFF, #35466BFF, #444F6BFF, #53596CFF, #5F636EFF, #6B6C71FF, #777776FF, #838079FF, #908B79FF, #9D9677FF, #ABA074FF, #B9AC70FF, #C7B76BFF, #D7C463FF, #E5D05AFF, #F5DD4DFF, #FFEA46FF);
-                            color: white;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #00204DFF, #002A64FF, #00336FFF, #1F3C6DFF, #35466BFF, #444F6BFF, #53596CFF, #5F636EFF, #6B6C71FF,     #777776FF, #838079FF, #908B79FF, #9D9677FF, #ABA074FF, #B9AC70FF, #C7B76BFF, #D7C463FF, #E5D05AFF, #F5DD4DFF, #FFEA46FF);
+  color: white;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="rocket"], 
 #nj_tippoint_scale .option[data-value="rocket"], 
@@ -2673,10 +2673,10 @@ background: linear-gradient(to right, #00204DFF, #002A64FF, #00336FFF, #1F3C6DFF
 #upgma_tiles_scale_4 .option[data-value="rocket"], 
 #upgma_tiles_scale_5 .option[data-value="rocket"], 
 #upgma_heatmap_scale .option[data-value="rocket"] {
-background: linear-gradient(to right, #03051AFF, #150E26FF, #281535FF, #3C1A42FF, #511E4DFF, #661F54FF, #7C1F5AFF, #931C5BFF, #AA185AFF, #C11754FF, #D3214BFF, #E33541FF, #ED4E3EFF, #F26847FF, #F4815AFF, #F5986FFF, #F6AE86FF, #F7C2A2FF, #F8D7BFFF, #FAEBDDFF);
-                            color: white;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #03051AFF, #150E26FF, #281535FF, #3C1A42FF, #511E4DFF, #661F54FF, #7C1F5AFF, #931C5BFF, #AA185AFF,     #C11754FF, #D3214BFF, #E33541FF, #ED4E3EFF, #F26847FF, #F4815AFF, #F5986FFF, #F6AE86FF, #F7C2A2FF, #F8D7BFFF, #FAEBDDFF);
+  color: white;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="mako"], 
 #nj_tippoint_scale .option[data-value="mako"], 
@@ -2694,10 +2694,10 @@ background: linear-gradient(to right, #03051AFF, #150E26FF, #281535FF, #3C1A42FF
 #upgma_tiles_scale_4 .option[data-value="mako"], 
 #upgma_tiles_scale_5 .option[data-value="mako"], 
 #upgma_heatmap_scale .option[data-value="mako"]{
-background: linear-gradient(to right, #0B0405FF, #190E19FF, #27182DFF, #312142FF, #3A2C59FF, #3F3770FF, #414388FF, #3C5397FF, #38639DFF, #3573A1FF, #3482A4FF, #3491A8FF, #35A0ABFF, #3AAEADFF, #46BEADFF, #5ACCADFF, #7ED7AFFF, #A4E0BBFF, #C3E9CEFF, #DEF5E5FF);
-                            color: white;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #0B0405FF, #190E19FF, #27182DFF, #312142FF, #3A2C59FF, #3F3770FF, #414388FF, #3C5397FF, #38639DFF,     #3573A1FF, #3482A4FF, #3491A8FF, #35A0ABFF, #3AAEADFF, #46BEADFF, #5ACCADFF, #7ED7AFFF, #A4E0BBFF, #C3E9CEFF, #DEF5E5FF);
+  color: white;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="turbo"], 
 #nj_tippoint_scale .option[data-value="turbo"], 
@@ -2715,9 +2715,9 @@ background: linear-gradient(to right, #0B0405FF, #190E19FF, #27182DFF, #312142FF
 #upgma_tiles_scale_4 .option[data-value="turbo"], 
 #upgma_tiles_scale_5 .option[data-value="turbo"], 
 #upgma_heatmap_scale .option[data-value="turbo"] {
-background: linear-gradient(to right, #30123BFF, #3F3994FF, #455ED2FF, #4681F7FF, #3AA2FCFF, #23C3E4FF, #18DEC1FF, #2CF09EFF, #5BFB72FF, #8EFF49FF, #B5F836FF, #D6E635FF, #EFCD3AFF, #FCB036FF, #FD8A26FF, #F36215FF, #E14209FF, #C82803FF, #A51301FF, #7A0403FF);
-                            color: white;
-                            }
+  background: linear-gradient(to right, #30123BFF, #3F3994FF, #455ED2FF, #4681F7FF, #3AA2FCFF, #23C3E4FF, #18DEC1FF, #2CF09EFF, #5BFB72FF,     #8EFF49FF, #B5F836FF, #D6E635FF, #EFCD3AFF, #FCB036FF, #FD8A26FF, #F36215FF, #E14209FF, #C82803FF, #A51301FF, #7A0403FF);
+  color: white;
+}
 
 #nj_tiplab_scale .option[data-value="Spectral"], 
 #nj_tippoint_scale .option[data-value="Spectral"], 
@@ -2735,10 +2735,10 @@ background: linear-gradient(to right, #30123BFF, #3F3994FF, #455ED2FF, #4681F7FF
 #upgma_tiles_scale_4 .option[data-value="Spectral"], 
 #upgma_tiles_scale_5 .option[data-value="Spectral"], 
 #upgma_heatmap_scale .option[data-value="Spectral"]{
-background: linear-gradient(to right, #9E0142, #D53E4F, #F46D43, #FDAE61, #FEE08B, #FFFFBF, #E6F598, #ABDDA4, #66C2A5, #3288BD, #5E4FA2);
-                            color: black;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #9E0142, #D53E4F, #F46D43, #FDAE61, #FEE08B, #FFFFBF, #E6F598, #ABDDA4, #66C2A5, #3288BD, #5E4FA2);
+  color: black;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="RdYlGn"], 
 #nj_tippoint_scale .option[data-value="RdYlGn"], 
@@ -2756,10 +2756,10 @@ background: linear-gradient(to right, #9E0142, #D53E4F, #F46D43, #FDAE61, #FEE08
 #upgma_tiles_scale_4 .option[data-value="RdYlGn"], 
 #upgma_tiles_scale_5 .option[data-value="RdYlGn"], 
 #upgma_heatmap_scale .option[data-value="RdYlGn"]{
-background: linear-gradient(to right, #A50026, #D73027, #F46D43, #FDAE61, #FEE08B, #FFFFBF, #D9EF8B, #A6D96A, #66BD63, #1A9850, #006837);
-                            color: black;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #A50026, #D73027, #F46D43, #FDAE61, #FEE08B, #FFFFBF, #D9EF8B, #A6D96A, #66BD63, #1A9850, #006837);
+  color: black;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="RdYlBu"], 
 #nj_tippoint_scale .option[data-value="RdYlBu"], 
@@ -2777,10 +2777,10 @@ background: linear-gradient(to right, #A50026, #D73027, #F46D43, #FDAE61, #FEE08
 #upgma_tiles_scale_4 .option[data-value="RdYlBu"], 
 #upgma_tiles_scale_5 .option[data-value="RdYlBu"], 
 #upgma_heatmap_scale .option[data-value="RdYlBu"]{
-background: linear-gradient(to right, #A50026, #D73027, #F46D43, #FDAE61, #FEE090, #FFFFBF, #E0F3F8, #ABD9E9, #74ADD1, #4575B4, #313695);
-                            color: black;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #A50026, #D73027, #F46D43, #FDAE61, #FEE090, #FFFFBF, #E0F3F8, #ABD9E9, #74ADD1, #4575B4, #313695);
+  color: black;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="RdGy"], 
 #nj_tippoint_scale .option[data-value="RdGy"], 
@@ -2798,10 +2798,10 @@ background: linear-gradient(to right, #A50026, #D73027, #F46D43, #FDAE61, #FEE09
 #upgma_tiles_scale_4 .option[data-value="RdGy"], 
 #upgma_tiles_scale_5 .option[data-value="RdGy"], 
 #upgma_heatmap_scale .option[data-value="RdGy"] {
-background: linear-gradient(to right, #67001F, #B2182B, #D6604D, #F4A582, #FDDBC7, #FFFFFF, #E0E0E0, #BABABA, #878787, #4D4D4D, #1A1A1A);
-                            color: black;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #67001F, #B2182B, #D6604D, #F4A582, #FDDBC7, #FFFFFF, #E0E0E0, #BABABA, #878787, #4D4D4D, #1A1A1A);
+  color: black;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="RdBu"], 
 #nj_tippoint_scale .option[data-value="RdBu"], 
@@ -2819,10 +2819,10 @@ background: linear-gradient(to right, #67001F, #B2182B, #D6604D, #F4A582, #FDDBC
 #upgma_tiles_scale_4 .option[data-value="RdBu"], 
 #upgma_tiles_scale_5 .option[data-value="RdBu"], 
 #upgma_heatmap_scale .option[data-value="RdBu"] {
-background: linear-gradient(to right, #67001F, #B2182B, #D6604D, #F4A582, #FDDBC7, #F7F7F7, #D1E5F0, #92C5DE, #4393C3, #2166AC, #053061);
-                            color: black;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #67001F, #B2182B, #D6604D, #F4A582, #FDDBC7, #F7F7F7, #D1E5F0, #92C5DE, #4393C3, #2166AC, #053061);
+  color: black;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="PuOr"], 
 #nj_tippoint_scale .option[data-value="PuOr"], 
@@ -2840,10 +2840,10 @@ background: linear-gradient(to right, #67001F, #B2182B, #D6604D, #F4A582, #FDDBC
 #upgma_tiles_scale_4 .option[data-value="PuOr"], 
 #upgma_tiles_scale_5 .option[data-value="PuOr"], 
 #upgma_heatmap_scale .option[data-value="PuOr"] {
-background: linear-gradient(to right, #7F3B08, #B35806, #E08214, #FDB863, #FEE0B6, #F7F7F7, #D8DAEB, #B2ABD2, #8073AC, #542788, #2D004B);
-                            color: black;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #7F3B08, #B35806, #E08214, #FDB863, #FEE0B6, #F7F7F7, #D8DAEB, #B2ABD2, #8073AC, #542788, #2D004B);
+  color: black;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="PRGn"], 
 #nj_tippoint_scale .option[data-value="PRGn"], 
@@ -2861,10 +2861,10 @@ background: linear-gradient(to right, #7F3B08, #B35806, #E08214, #FDB863, #FEE0B
 #upgma_tiles_scale_4 .option[data-value="PRGn"], 
 #upgma_tiles_scale_5 .option[data-value="PRGn"], 
 #upgma_heatmap_scale .option[data-value="PRGn"] {
-background: linear-gradient(to right, #40004B, #762A83, #9970AB, #C2A5CF, #E7D4E8, #F7F7F7, #D9F0D3, #A6DBA0, #5AAE61, #1B7837, #00441B);
-                            color: black;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #40004B, #762A83, #9970AB, #C2A5CF, #E7D4E8, #F7F7F7, #D9F0D3, #A6DBA0, #5AAE61, #1B7837, #00441B);
+  color: black;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="PiYG"], 
 #nj_tippoint_scale .option[data-value="PiYG"], 
@@ -2882,10 +2882,10 @@ background: linear-gradient(to right, #40004B, #762A83, #9970AB, #C2A5CF, #E7D4E
 #upgma_tiles_scale_4 .option[data-value="PiYG"], 
 #upgma_tiles_scale_5 .option[data-value="PiYG"], 
 #upgma_heatmap_scale .option[data-value="PiYG"] {
-background: linear-gradient(to right, #8E0152, #C51B7D, #DE77AE, #F1B6DA, #FDE0EF, #F7F7F7, #E6F5D0, #B8E186, #7FBC41, #4D9221, #276419);
-                            color: black;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #8E0152, #C51B7D, #DE77AE, #F1B6DA, #FDE0EF, #F7F7F7, #E6F5D0, #B8E186, #7FBC41, #4D9221, #276419);
+  color: black;
+  margin-bottom: 2px;
+}
 
 #nj_tiplab_scale .option[data-value="BrBG"], 
 #nj_tippoint_scale .option[data-value="BrBG"], 
@@ -2903,47 +2903,49 @@ background: linear-gradient(to right, #8E0152, #C51B7D, #DE77AE, #F1B6DA, #FDE0E
 #upgma_tiles_scale_4 .option[data-value="BrBG"], 
 #upgma_tiles_scale_5 .option[data-value="BrBG"], 
 #upgma_heatmap_scale .option[data-value="BrBG"] {
-background: linear-gradient(to right, #543005, #8C510A, #BF812D, #DFC27D, #F6E8C3, #F5F5F5, #C7EAE5, #80CDC1, #35978F, #01665E, #003C30);
-                            color: black;
-                            margin-bottom: 2px;
-                            }
+  background: linear-gradient(to right, #543005, #8C510A, #BF812D, #DFC27D, #F6E8C3, #F5F5F5, #C7EAE5, #80CDC1, #35978F, #01665E, #003C30);
+  color: black;
+  margin-bottom: 2px;
+}
 
 /* Report */
   
-  #shiny-modal > div > div > div.modal-body > div > div > div:nth-child(5) > div > div > div > div > button {
+#shiny-modal > div > div > div.modal-body > div > div > div:nth-child(5) > div > div > div > div > button {
   border: 1px solid black;
 }
 
 #rep_general {
-position: absolute;
-top: -10px;
-left: -110px;
+  position: absolute;
+  top: -10px;
+  left: -110px;
 }
 
 #rep_entrytable {
-position: relative;
-top: -10px;
-left: -96px;
+  position: relative;
+  top: -10px;
+  left: -96px;
 }
 
 #rep_plot_report {
-position: relative;
-top: -15px;
-left: -96px;
+  position: relative;
+  top: -15px;
+  left: -96px;
 }
 
 #rep_analysis {
-position: relative;
-top: -10px;
-left: -45px;
+  position: relative;
+  top: -10px;
+  left: -45px;
 }
 
 #mst_date_general_select {
-margin-top: -14px;
-width: 100px;
+  margin-top: -14px;
+  width: 100px;
 }
 
-.datepicker { z-index: 99999 !important; }
+.datepicker { 
+  z-index: 99999 !important; 
+}
 
 .rep_tab_sel {
   margin-top: -25px;
@@ -2959,7 +2961,7 @@ width: 100px;
 #rep_missval,
 #rep_version,
 #rep_plot_report {
-margin-top: 10px;
+  margin-top: 10px;
 }
 
 #mst_date_general_select .form-control {
@@ -2970,46 +2972,48 @@ margin-top: 7px;
 }
 
 #mst_operator_general_select {
-height: 28px;
-margin-top: -8px;
-position: relative;
-right: -22px;
-width: 250px;
+  height: 28px;
+  margin-top: -8px;
+  position: relative;
+  right: -22px;
+  width: 250px;
 }
 
 #mst_institute_general_select {
-height: 28px;
-margin-top: -8px;
-position: relative;
-right: -22px;
-width: 250px;
+  height: 28px;
+  margin-top: -8px;
+  position: relative;
+  right: -22px;
+  width: 250px;
 }
 
 #mst_comm_general_select {
-margin-top: -8px;
-border-radius: 5px;
-position: relative;
-right: -22px;
-border-color: black;
+  margin-top: -8px;
+  border-radius: 5px;
+  position: relative;
+  right: -22px;
+  border-color: black;
 }
 
 button#download_report_bttn {
-font-size: 14px;
-height: 36px;
-background: #282F38;
+  font-size: 14px;
+  height: 36px;
+  background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-position: relative;
-top: 1px;
-border-radius: 6px;
-margin-left: 10px;
+  position: relative;
+  top: 1px;
+  border-radius: 6px;
+  margin-left: 10px;
 }
 
 /* Gene Screening */
 
 #screening_start_button,
-#screening_reset_bttn {
-  margin-top: 31px;
+#screening_reset_bttn,
+#screening_cancel {
+  margin-top: 20px;
+  border: 1px solid white;
 }
 
 #screening_fail {

From 37c149b5b672f89f3943c2c10e03fdac0f39901b Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Tue, 13 Aug 2024 12:07:54 +0200
Subject: [PATCH 45/75] Fixes in gene screening

---
 App.R | 276 +++++++++++++++++++++++++++++++---------------------------
 1 file changed, 148 insertions(+), 128 deletions(-)

diff --git a/App.R b/App.R
index b028abf..051b729 100644
--- a/App.R
+++ b/App.R
@@ -6279,31 +6279,17 @@ server <- function(input, output, session) {
             )
           )
         } else if(Screening$status == "finished") {
-          if(isTRUE(Screening$fail)) {
-            output$statustext <- renderUI(
-              fluidRow(
-                tags$li(
-                  class = "dropdown", 
-                  tags$span(HTML(
-                    paste('<i class="fa-solid fa-circle-dot" style="color:red !important;"></i>', 
-                          "Status:&nbsp;&nbsp;&nbsp;<i> gene screening failed</i>")), 
-                    style = "color:white;")
-                )
-              )
-            )
-          } else {
-            output$statustext <- renderUI(
-              fluidRow(
-                tags$li(
-                  class = "dropdown", 
-                  tags$span(HTML(
-                    paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
-                          "Status:&nbsp;&nbsp;&nbsp;<i> gene screening finalized</i>")), 
-                    style = "color:white;")
-                )
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> gene screening finalized</i>")), 
+                  style = "color:white;")
               )
             )
-          }
+          )
         } else {
           output$statustext <- renderUI(
             fluidRow(
@@ -7867,7 +7853,7 @@ server <- function(input, output, session) {
                                       valign = "htMiddle",
                                       halign = "htCenter") %>%
                               hot_col(3, readOnly = TRUE) %>%
-                              hot_col(c(1, 5, 10, 11, 12),
+                              hot_col(c(1, 5, 10, 11, 12, 13),
                                       readOnly = TRUE) %>%
                               hot_col(3:(12 + nrow(DB$cust_var)), 
                                       valign = "htMiddle",
@@ -7970,7 +7956,7 @@ server <- function(input, output, session) {
                                         valign = "htMiddle",
                                         halign = "htCenter") %>%
                                 hot_col(3, readOnly = TRUE) %>%
-                                hot_col(c(1, 5, 10, 11, 12),
+                                hot_col(c(1, 5, 10, 11, 12, 13),
                                         readOnly = TRUE) %>%
                                 hot_col(3, validator = "
                                   function(value, callback) {
@@ -8127,7 +8113,7 @@ server <- function(input, output, session) {
                                         valign = "htMiddle",
                                         halign = "htCenter") %>%
                                 hot_col(3, readOnly = TRUE) %>%
-                                hot_col(c(1, 5, 10, 11, 12),
+                                hot_col(c(1, 5, 10, 11, 12, 13),
                                         readOnly = TRUE) %>%
                                 hot_col(3:(12 + nrow(DB$cust_var)), 
                                         valign = "htMiddle",
@@ -8306,7 +8292,7 @@ server <- function(input, output, session) {
                                     }
                                   }
                                 ") %>%
-                                hot_col(c(1, 5, 10, 11, 12),
+                                hot_col(c(1, 5, 10, 11, 12, 13),
                                         readOnly = TRUE) %>%
                                 hot_col(8, type = "dropdown", source = country_names) %>%
                                 hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
@@ -8424,7 +8410,7 @@ server <- function(input, output, session) {
                                         valign = "htMiddle",
                                         halign = "htCenter") %>%
                                 hot_col(3, readOnly = TRUE) %>%
-                                hot_col(c(1, 5, 10, 11, 12),
+                                hot_col(c(1, 5, 10, 11, 12, 13),
                                         readOnly = TRUE) %>%
                                 hot_col(3, validator = "
                                   function(value, callback) {
@@ -9924,8 +9910,6 @@ server <- function(input, output, session) {
   observeEvent(input$reload_db, {
     log_print("Input reload_db")
     
-    test <<- Screening$status_df
-    
     if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
       show_toast(
         title = "Pending Multi Typing",
@@ -10033,7 +10017,7 @@ server <- function(input, output, session) {
                         valign = "htMiddle",
                         halign = "htCenter") %>%
                 hot_col(3, readOnly = TRUE) %>%
-                hot_col(c(1, 5, 10, 11, 12),
+                hot_col(c(1, 5, 10, 11, 12, 13),
                         readOnly = TRUE) %>%
                 hot_col(3:(12 + nrow(DB$cust_var)), 
                         valign = "htMiddle",
@@ -10136,7 +10120,7 @@ server <- function(input, output, session) {
                           valign = "htMiddle",
                           halign = "htCenter") %>%
                   hot_col(3, readOnly = TRUE) %>%
-                  hot_col(c(1, 5, 10, 11, 12),
+                  hot_col(c(1, 5, 10, 11, 12, 13),
                           readOnly = TRUE) %>%
                   hot_col(3:(12 + nrow(DB$cust_var)), 
                           valign = "htMiddle",
@@ -10293,7 +10277,7 @@ server <- function(input, output, session) {
                           valign = "htMiddle",
                           halign = "htCenter") %>%
                   hot_col(3, readOnly = TRUE) %>%
-                  hot_col(c(1, 5, 10, 11, 12),
+                  hot_col(c(1, 5, 10, 11, 12, 13),
                           readOnly = TRUE) %>%
                   hot_col(3:(12 + nrow(DB$cust_var)), 
                           valign = "htMiddle",
@@ -10472,7 +10456,7 @@ server <- function(input, output, session) {
                                     }
                                   }
                                 ") %>%
-                  hot_col(c(1, 5, 10, 11, 12),
+                  hot_col(c(1, 5, 10, 11, 12, 13),
                           readOnly = TRUE) %>%
                   hot_col(8, type = "dropdown", source = country_names) %>%
                   hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
@@ -10589,7 +10573,7 @@ server <- function(input, output, session) {
                   hot_col(1, 
                           valign = "htMiddle",
                           halign = "htCenter") %>%
-                  hot_col(c(1, 5, 10, 11, 12),
+                  hot_col(c(1, 5, 10, 11, 12, 13),
                           readOnly = TRUE) %>%
                   hot_col(3, readOnly = TRUE) %>%
                   hot_col(3, validator = "
@@ -10799,20 +10783,11 @@ server <- function(input, output, session) {
       
       DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "cont"))
     }
-    dataa <<- DB$data
-    cust_var <<- DB$cust_var
     
     DB$meta_gs <- select(DB$data, c(1, 3:13))
-    
-    meta_gs <<- DB$meta_gs
-    
     DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    meta <<- DB$meta
-    
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    
     DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    allelic_profile <<- DB$allelic_profile
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
     
     log_print(paste0("New custom variable added: ", input$new_var_name))
@@ -11056,20 +11031,19 @@ server <- function(input, output, session) {
     }
     DB$remove_iso <- NULL
     
-    Data <<- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
+    Data <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
     
     if ((ncol(Data[["Typing"]]) - 13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
       cust_vars_pre <- select(Data[["Typing"]], 
                               14:(ncol(Data[["Typing"]]) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-      cust_vars_pre <<- names(cust_vars_pre)
+      cust_vars_pre <- names(cust_vars_pre)
     } else {
-      cust_vars_pre <<- character()
+      cust_vars_pre <- character()
     }
     
-    checkpoint <<- select(Data[["Typing"]], -(1:(13 + length(cust_vars_pre))))
     Data[["Typing"]] <- select(Data[["Typing"]], -(1:(13 + length(cust_vars_pre))))
     
-    meta_hot <<- hot_to_r(input$db_entries)
+    meta_hot <- hot_to_r(input$db_entries)
     
     if(length(DB$deleted_entries > 0)) {
       
@@ -11084,7 +11058,6 @@ server <- function(input, output, session) {
     
     # Ensure correct logical data type
     Data[["Typing"]][["Include"]] <- as.logical(Data[["Typing"]][["Include"]])
-    testdata <<- Data
     saveRDS(Data, paste0(
       DB$database, "/",
       gsub(" ", "_", DB$scheme),
@@ -22568,33 +22541,38 @@ server <- function(input, output, session) {
   
   observe({
     req(input$screening_res_sel, DB$database, DB$scheme)
-    if(!is.null(Screening$status_df)) {
+    if(!is.null(Screening$status_df) &
+       !is.null(input$screening_res_sel) & 
+       !is.null(Screening$status_df$status) & 
+       !is.null(Screening$status_df$isolate)) {
       if(length(input$screening_res_sel) > 0) {
-        if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
-          results <- read.delim(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
-                                          input$screening_res_sel, "resProfile.tsv"))
-          
-          output$screening_table <- renderDataTable(
-            select(results, c(6, 7, 8, 9, 11)),
-            selection = "single",
-            options = list(pageLength = 10,
-                           columnDefs = list(list(searchable = TRUE,
-                                                  targets = "_all")),
-                           initComplete = DT::JS(
-                             "function(settings, json) {",
-                             "$('th:first-child').css({'border-top-left-radius': '5px'});",
-                             "$('th:last-child').css({'border-top-right-radius': '5px'});",
-                             "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                             "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                             "}"
-                           ),
-                           drawCallback = DT::JS(
-                             "function(settings) {",
-                             "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                             "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                             "}"
-                           )))
-        } else {output$screening_table <- NULL}
+        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
+          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
+            results <- read.delim(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
+                                            input$screening_res_sel, "resProfile.tsv"))
+            
+            output$screening_table <- renderDataTable(
+              select(results, c(6, 7, 8, 9, 11)),
+              selection = "single",
+              options = list(pageLength = 10,
+                             columnDefs = list(list(searchable = TRUE,
+                                                    targets = "_all")),
+                             initComplete = DT::JS(
+                               "function(settings, json) {",
+                               "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                               "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                               "}"
+                             ),
+                             drawCallback = DT::JS(
+                               "function(settings) {",
+                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                               "}"
+                             )))
+          } else {output$screening_table <- NULL}
+        }
       } else {
         output$screening_table <- NULL
       }
@@ -22774,9 +22752,8 @@ server <- function(input, output, session) {
     
     # set feedback variables
     Screening$status <- "idle"
-    Screening$results <- NULL
-    Screening$fail <- NULL
     Screening$status_df <- NULL
+    Screening$choices <- NULL
     
     # change reactive UI
     output$screening_table <- NULL
@@ -22792,7 +22769,25 @@ server <- function(input, output, session) {
   
   # Cancel screening
   observeEvent(input$screening_cancel, {
+    showModal(
+      modalDialog(
+        paste0(
+          "Gene screening is still pending. Stopping this process will cancel the screening."
+        ),
+        title = "Reset Multi Typing",
+        fade = TRUE,
+        easyClose = TRUE,
+        footer = tagList(
+          modalButton("Cancel"),
+          actionButton("conf_screening_cancel", "Stop", class = "btn btn-danger")
+        )
+      )
+    )
+  })
+  
+  observeEvent(input$conf_screening_cancel, {
     log_print("Cancelled gene screening")
+    removeModal()
     
     # terminate screening
     system(paste("kill $(pgrep -f 'execute/screening.sh')"), wait = FALSE)
@@ -22803,9 +22798,8 @@ server <- function(input, output, session) {
     
     # set feedback variables
     Screening$status <- "idle"
-    Screening$results <- NULL
-    Screening$fail <- NULL
     Screening$status_df <- NULL
+    Screening$choices <- NULL
     
     # change reactive UI
     output$screening_table <- NULL
@@ -22819,11 +22813,10 @@ server <- function(input, output, session) {
   })
   
   # Get selected assembly
-  
   observe({
     if (length(input$screening_select) < 1) {
       output$genome_path_gs <- renderUI(HTML(
-        paste("<span style='color: white;'>", length(input$screening_select), " isolates queried for screening.")
+        paste("<span style='color: white; font-style:italic'>", length(input$screening_select), " isolate(s) queried for screening")
       ))
       
       output$screening_start <- NULL
@@ -22877,7 +22870,7 @@ server <- function(input, output, session) {
                 p(
                   HTML(paste(
                     '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
-                    paste("<span style='color: white; font-style:italic'>",
+                    paste("<span style='color: white;'>",
                           "&nbsp Screening Ready")))
                 ),
                 actionButton(
@@ -22893,7 +22886,7 @@ server <- function(input, output, session) {
                 p(
                   HTML(paste(
                     '<i class="fa-solid fa-clock" style="font-size:15px;color:white"></i>',
-                    paste("<span style='color: white; font-style:italic'>",
+                    paste("<span style='color: white;'>",
                           "&nbsp Running Screening ...")))
                 ),
                 fluidRow(
@@ -22915,7 +22908,7 @@ server <- function(input, output, session) {
                   p(
                     HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
                                sum(Screening$status_df$status != "unfinished"), "/",
-                               nrow(Screening$status_df), " Isolate(s) screened"))
+                               nrow(Screening$status_df), " isolate(s) screened"))
                   )
                 }
               )
@@ -22969,7 +22962,7 @@ server <- function(input, output, session) {
                                  species = gsub(" ", "_", DB$scheme))
       
       Screening$status_df <- data.frame(isolate = basename(gsub(".zip", "", str_split_1(Screening$meta_df$selected, " "))), 
-                                        status = "unfinished", shown = FALSE)
+                                        status = "unfinished")
       
       # Reset screening status
       sapply(Screening$status_df$isolate, remove.screening.status)
@@ -22984,25 +22977,30 @@ server <- function(input, output, session) {
   ### Screening Feedback ----
   
   observe({
-    req(Screening$status, input$screening_res_sel)
-    if(!is.null(Screening$status_df)) {
-      if(Screening$status != "idle") {
-        if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
-          output$screening_result <- renderUI(
-            column(
-              width = 12,
-              hr(), br(),
-              dataTableOutput("screening_table") 
+    req(Screening$status, input$screening_res_sel, Screening$status_df)
+    if(!is.null(Screening$status_df) &
+       !is.null(Screening$status_df$status) & 
+       !is.null(Screening$status_df$isolate) &
+       !is.null(input$screening_res_sel)) {
+      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
+        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
+          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
+            output$screening_result <- renderUI(
+              column(
+                width = 12,
+                hr(), br(),
+                dataTableOutput("screening_table") 
+              )
             )
-          )
-        } else {
-          output$screening_result <- renderUI(
-            column(
-              width = 12,
-              hr(), br(),
-              verbatimTextOutput("screening_fail")
+          } else {
+            output$screening_result <- renderUI(
+              column(
+                width = 12,
+                hr(), br(),
+                verbatimTextOutput("screening_fail")
+              )
             )
-          )
+          }
         }
       } else {
         output$screening_result <- NULL
@@ -23014,13 +23012,18 @@ server <- function(input, output, session) {
   
   observe({
     req(Screening$status, input$screening_res_sel)
-    if(!is.null(Screening$status_df)) {
-      if(Screening$status != "idle") {
-        if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "fail") {
-          output$screening_fail <- renderPrint({
-            cat(paste(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
-                                          "Isolates", input$screening_res_sel, "status.txt")),"\n"))
-          })
+    if(!is.null(Screening$status_df) &
+       !is.null(Screening$status_df$status) & 
+       !is.null(Screening$status_df$isolate) &
+       !is.null(input$screening_res_sel)) {
+      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
+        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
+          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "fail") {
+            output$screening_fail <- renderPrint({
+              cat(paste(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
+                                            "Isolates", input$screening_res_sel, "status.txt")),"\n"))
+            })
+          }
         }
       } else {
         output$screening_fail <- NULL
@@ -23031,25 +23034,26 @@ server <- function(input, output, session) {
   })
   
   observe({
-    req(Screening$status)
-    if(Screening$status == "started") {
-      
-      # start status screening for user feedback
-      check_screening()
-      
-      if(isTRUE(Screening$first_result)) {
-        output$screening_result_sel <- renderUI(
-          selectInput(
-            "screening_res_sel",
-            label = h5("Select Result", style = "color:white; margin-bottom: 32px; margin-top: -10px;"),
-            choices = ""
-          )
-        )
+    if(!is.null(Screening$status)) {
+      if(Screening$status != "idle") {
+        
+        # start status screening for user feedback
+        check_screening()
         
-        Screening$first_result <- FALSE
+        if(isTRUE(Screening$first_result)) {
+          output$screening_result_sel <- renderUI(
+            selectInput(
+              "screening_res_sel",
+              label = h5("Select Result", style = "color:white; margin-bottom: 28px; margin-top: -10px;"),
+              choices = ""
+            )
+          )
+          
+          Screening$first_result <- FALSE
+        }
+      } else if(Screening$status == "idle") {
+        output$screening_result_sel <- NULL
       }
-    } else if(Screening$status == "idle") {
-      output$screening_result_sel <- NULL
     }
   }) 
     
@@ -23065,6 +23069,8 @@ server <- function(input, output, session) {
       if(any("unfinished" != Screening$status_df$status) &
          !identical(Screening$choices, Screening$status_df$isolate[which(Screening$status_df$status != "unfinished")])) {
         
+        # Screening$first_check <- FALSE
+        
         status_df <- Screening$status_df[which(Screening$status_df$status != "unfinished"),]
         
         Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
@@ -23076,6 +23082,11 @@ server <- function(input, output, session) {
         
         if(tail(status_df$status, 1) == "success") {
           
+          #TODO
+          # hjier einfügen laden der rds datenbank, ändern direkt lokal
+          
+          #DB$meta$Screened[which(DB$meta["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
+          
           show_toast(
             title = paste("Successful screening of", tail(Screening$choices, 1)),
             type = "success",
@@ -23088,6 +23099,7 @@ server <- function(input, output, session) {
                             selected = tail(Screening$choices, 1))
           
         } else if(tail(status_df$status, 1) == "fail") {
+          
           show_toast(
             title = paste("Failed screening of", tail(status_df$isolate, 1)),
             type = "error",
@@ -23103,7 +23115,15 @@ server <- function(input, output, session) {
         if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
           Screening$status <- "finished"
         }
-      } 
+      } else {
+        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+          Screening$status <- "finished"
+        }
+      }
+      
+      if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+        Screening$status <- "finished"
+      }
     }
   }) 
   

From 43a51053de597f36a627d304b337ae735987bb3b Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Tue, 13 Aug 2024 19:08:52 +0200
Subject: [PATCH 46/75] Advanced gene screening section; Changes in Resistance
 Profile Tab

---
 App.R        | 201 +++++++++++++++++++++++++++++++++++++++------------
 www/body.css |  19 +++++
 www/head.css |  24 +++++-
 3 files changed, 193 insertions(+), 51 deletions(-)

diff --git a/App.R b/App.R
index 051b729..ebdda86 100644
--- a/App.R
+++ b/App.R
@@ -5351,6 +5351,15 @@ ui <- dashboardPage(
             div(class = "loci_table",
                 dataTableOutput("gs_isolate_table"))
           )
+        ),
+        hr(),
+        fluidRow(
+          column(1),
+          column(
+            width = 10,
+            div(class = "loci_table",
+                DT::dataTableOutput("gs_profile_table"))
+          )
         )
       )
     ) # End tabItems
@@ -5524,7 +5533,7 @@ server <- function(input, output, session) {
   get.entry.table.meta <- reactive({
     if(!is.null(hot_to_r(input$db_entries))){
       table <- hot_to_r(input$db_entries)
-      select(table, 1:(13 + nrow(DB$cust_var)))
+      select(select(table, -13), 1:(12 + nrow(DB$cust_var)))
     }
   })
   
@@ -5722,13 +5731,13 @@ server <- function(input, output, session) {
     invalidateLater(5000, session)
     
     if(!is.null(DB$database)) {
-      if(file_exists(paste0(
-        DB$database, "/",
+      if(file_exists(file.path(
+        DB$database,
         gsub(" ", "_", DB$scheme),
-        "/Typing.rds"
+        "Typing.rds"
       ))) {
         
-        Database <- readRDS(paste0(DB$database, "/", gsub(" ", "_", DB$scheme),"/Typing.rds"))
+        Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
         
         if(is.null(DB$data)) {
           if(nrow(Database[["Typing"]]) >= 1) {
@@ -5831,7 +5840,8 @@ server <- function(input, output, session) {
                            result_list = NULL,
                            status = "") # reactive variables related to typing process
   
-  Screening <- reactiveValues(status = "idle") # reactive variables related to gene screening
+  Screening <- reactiveValues(status = "idle",
+                              picker_status = TRUE) # reactive variables related to gene screening
   
   Vis <- reactiveValues(cluster = NULL, 
                         metadata = list(),
@@ -8572,7 +8582,7 @@ server <- function(input, output, session) {
                             HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px; color:white; margin-top: 10px"></i>'))
                           )
                         )
-                      } else if((DB$change == TRUE) | !identical(get.entry.table.meta(), DB$meta)) {
+                      } else if((DB$change == TRUE) | !identical(get.entry.table.meta(), select(DB$meta, -13))) {
                         if(!is.null(input$db_entries)) {
                           fluidRow(
                             column(
@@ -9910,6 +9920,9 @@ server <- function(input, output, session) {
   observeEvent(input$reload_db, {
     log_print("Input reload_db")
     
+    pick_stat <<- Screening$picker_status
+    ttest <<- input$screening_select
+    
     if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
       show_toast(
         title = "Pending Multi Typing",
@@ -11360,7 +11373,6 @@ server <- function(input, output, session) {
   output$sequence_selector <- renderUI({
     if(!is.null(input$db_loci_rows_selected)) {
       
-      
       req(input$db_loci_rows_selected, DB$database, DB$scheme)
       
       DB$loci <- list.files(
@@ -22513,10 +22525,65 @@ server <- function(input, output, session) {
   
   ### Render UI Elements ----
   
+  # Resistance profile table
+  observe({
+    req(DB$meta_gs, input$gs_isolate_table_rows_selected, DB$database, DB$scheme)
+    
+    if(DB$meta_gs$Screened[input$gs_isolate_table_rows_selected] == "Yes") {
+      iso_select <- DB$meta_gs$`Assembly ID`[input$gs_isolate_table_rows_selected]
+      iso_path <- file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
+                            iso_select, "resProfile.tsv")
+      res_profile <- read.delim(iso_path)
+      
+      colnames(res_profile) <- c(
+        "Protein Identifier",	"Contig ID", "Start", "Stop", "Strand", "Gene Symbol", 
+        "Sequence Name", "Scope", "Element Type",  "Element Subtype", "Class", 
+        "Subclass", "Method", "Target Length", "Reference Sequence Length",	
+        "% Coverage of Reference Sequence", "% Identity to Reference Sequence", 
+        "Alignment Length", "Accession of Closest Sequence", 
+        "Name of Closest Sequence", "HMM ID", "HMM Description")
+      
+      
+      res_profile <- res_profile %>%
+        relocate(c("Gene Symbol", "Sequence Name", "Element Subtype", "Class", 
+                   "Subclass", "Scope", "Contig ID", "Target Length", "Alignment Length",
+                   "Start", "Stop", "Strand"))
+      
+      # Generate gene profile table
+      output$gs_profile_table <- DT::renderDataTable(
+        res_profile,
+        selection = "single",
+        rownames= FALSE,
+        options = list(pageLength = 10, scrollX = TRUE,
+                       autoWidth = TRUE,
+                       columnDefs = list(list(width = '400px', targets = c("Sequence Name"))),
+                       columnDefs = list(list(searchable = TRUE,
+                                              targets = "_all")),
+                       initComplete = DT::JS(
+                         "function(settings, json) {",
+                         "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                         "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                         # "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                         # "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                         "}"
+                       ),
+                       drawCallback = DT::JS(
+                         "function(settings) {",
+                         # "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                         # "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                         "}"
+                       ))
+      )
+    } else {
+      output$gs_profile_table <- NULL
+    }
+  })
+
+  #Resistance profile selection table
   observe({
     req(DB$meta)
     output$gs_isolate_table <- renderDataTable(
-      DB$meta_gs,
+      select(DB$meta_gs, -c(2, 4, 10, 11, 12)),
       selection = "single",
       rownames= FALSE,
       options = list(pageLength = 10,
@@ -22633,7 +22700,7 @@ server <- function(input, output, session) {
   
   # Screening Interface
   
-  output$screening_interface <- renderUI({
+  output$screening_interface <- renderUI(
     if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
       column(
         width = 12,
@@ -22650,31 +22717,30 @@ server <- function(input, output, session) {
                 )
               )
             ),
-            if(length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) > 0 &
-               length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) > 0) {
+            if(Screening$picker_status) {
               div(
                 class = "screening_div",
                 pickerInput(
                   "screening_select",
                   "",
-                  choices = list(Unscreened = DB$data$`Assembly ID`[which(DB$data$Screened == "No")],
-                                 Screened = DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]),
-                  options = list(
-                    `live-search` = TRUE,
-                    `actions-box` = TRUE,
-                    size = 10,
-                    style = "background-color: white; border-radius: 5px;"
+                  choices = list(
+                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
+                    },
+                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+                    }
+                  ),
+                  choicesOpt = list(
+                    disabled = c(
+                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]))
+                    )
                   ),
-                  multiple = TRUE
-                ) 
-              )
-            } else if(length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) > 0) {
-              div(
-                class = "screening_div",
-                pickerInput(
-                  "screening_select",
-                  "",
-                  choices = list(Unscreened = DB$data$`Assembly ID`[which(DB$data$Screened == "No")]),
                   options = list(
                     `live-search` = TRUE,
                     `actions-box` = TRUE,
@@ -22682,7 +22748,7 @@ server <- function(input, output, session) {
                     style = "background-color: white; border-radius: 5px;"
                   ),
                   multiple = TRUE
-                ) 
+                )
               )
             } else {
               div(
@@ -22690,7 +22756,8 @@ server <- function(input, output, session) {
                 pickerInput(
                   "screening_select",
                   "",
-                  choices = list(Screened = DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]),
+                  choices = Screening$picker_choices,
+                  selected = Screening$picker_selected,
                   options = list(
                     `live-search` = TRUE,
                     `actions-box` = TRUE,
@@ -22698,7 +22765,7 @@ server <- function(input, output, session) {
                     style = "background-color: white; border-radius: 5px;"
                   ),
                   multiple = TRUE
-                )
+                ) 
               )
             },
             br(), br(),
@@ -22739,7 +22806,7 @@ server <- function(input, output, session) {
         )
       )
     }
-  })
+  )
   
   ### Screening Events ----
   
@@ -22754,6 +22821,7 @@ server <- function(input, output, session) {
     Screening$status <- "idle"
     Screening$status_df <- NULL
     Screening$choices <- NULL
+    Screening$picker_status <- TRUE
     
     # change reactive UI
     output$screening_table <- NULL
@@ -22800,6 +22868,7 @@ server <- function(input, output, session) {
     Screening$status <- "idle"
     Screening$status_df <- NULL
     Screening$choices <- NULL
+    Screening$picker_status <- TRUE
     
     # change reactive UI
     output$screening_table <- NULL
@@ -22816,7 +22885,7 @@ server <- function(input, output, session) {
   observe({
     if (length(input$screening_select) < 1) {
       output$genome_path_gs <- renderUI(HTML(
-        paste("<span style='color: white; font-style:italic'>", length(input$screening_select), " isolate(s) queried for screening")
+        paste("<span style='color: white; font-style:italic'>", length(input$screening_select), " Isolate(s) queried for screening")
       ))
       
       output$screening_start <- NULL
@@ -22942,9 +23011,22 @@ server <- function(input, output, session) {
       log_print("Started gene screening")
       
       Screening$status <- "started"
-      
-      shinyjs::runjs("$('#screening_select').prop('disabled', true);")
-      shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
+      Screening$picker_choices <- list(
+        Unscreened = if (sum(DB$data$Screened == "No") == 1) {
+          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
+        } else {
+          DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
+        },
+        Screened =  if (sum(DB$data$Screened == "Yes") == 1) {
+          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
+        } else {
+          DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+        }
+      )
+      pick_choices <<- Screening$picker_choices
+      Screening$picker_selected <- input$screening_select
+      okayy <<- Screening$picker_selected
+      Screening$picker_status <- FALSE
       
       show_toast(
         title = "Gene screening started",
@@ -22964,11 +23046,15 @@ server <- function(input, output, session) {
       Screening$status_df <- data.frame(isolate = basename(gsub(".zip", "", str_split_1(Screening$meta_df$selected, " "))), 
                                         status = "unfinished")
       
-      # Reset screening status
+       # Reset screening status
       sapply(Screening$status_df$isolate, remove.screening.status)
       
       saveRDS(Screening$meta_df, paste0(getwd(), "/execute/screening_meta.rds"))
       
+      # Disable pickerInput
+      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').prop('disabled', true);"))
+      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').selectpicker('refresh');"))
+    
       # System execution screening.sh
       system(paste("bash", paste0(getwd(), "/execute/screening.sh")), wait = FALSE)
     }
@@ -23042,10 +23128,27 @@ server <- function(input, output, session) {
         
         if(isTRUE(Screening$first_result)) {
           output$screening_result_sel <- renderUI(
-            selectInput(
-              "screening_res_sel",
-              label = h5("Select Result", style = "color:white; margin-bottom: 28px; margin-top: -10px;"),
-              choices = ""
+            column(
+              width = 12,
+              align = "center",
+              selectInput(
+                "screening_res_sel",
+                label = h5("Select Result", style = "color:white; margin-bottom: 28px; margin-top: -10px;"),
+                choices = ""
+              ),
+              if(!is.null(Screening$status_df)) {
+                p(HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
+                             if(sum(Screening$status_df$status == "success") == 1) {
+                               "1 success &nbsp / &nbsp"
+                             } else {
+                               paste0(sum(Screening$status_df$status == "success"), " successes &nbsp / &nbsp")
+                             },
+                             if(sum(Screening$status_df$status == "fail") == 1) {
+                               "1 failure"
+                             } else {
+                               paste0(sum(Screening$status_df$status == "fail"), " failures")
+                             })))
+              }
             )
           )
           
@@ -23069,8 +23172,6 @@ server <- function(input, output, session) {
       if(any("unfinished" != Screening$status_df$status) &
          !identical(Screening$choices, Screening$status_df$isolate[which(Screening$status_df$status != "unfinished")])) {
         
-        # Screening$first_check <- FALSE
-        
         status_df <- Screening$status_df[which(Screening$status_df$status != "unfinished"),]
         
         Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
@@ -23082,11 +23183,15 @@ server <- function(input, output, session) {
         
         if(tail(status_df$status, 1) == "success") {
           
-          #TODO
-          # hjier einfügen laden der rds datenbank, ändern direkt lokal
-          
-          #DB$meta$Screened[which(DB$meta["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
+          # Changing "Screened" metadata variable in database
+          Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
           
+          Database[["Typing"]]$Screened[which(Database[["Typing"]]["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
+
+          saveRDS(Database, file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+
+          DB$data$Screened[which(DB$data["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
+
           show_toast(
             title = paste("Successful screening of", tail(Screening$choices, 1)),
             type = "success",
diff --git a/www/body.css b/www/body.css
index c0652e4..21ec938 100644
--- a/www/body.css
+++ b/www/body.css
@@ -411,6 +411,12 @@ table.dataTable tbody tr {
   border-radius: 5px !important;
 }
 
+#gs_profile_table table.dataTable tbody tr {
+  background-color: transparent;
+  border-bottom-left-radius: 0px !important;
+  border-bottom-right-radius: 0px !important;
+}
+
 table.dataTable.stripe>tbody>tr.odd.selected>*, table.dataTable.display>tbody>tr.odd.selected>* {
   box-shadow: inset 0 0 0 9999px #282F38;
   box-shadow: inset 0 0 0 9999px #282F38;
@@ -530,6 +536,10 @@ left: -6px;
 
 /* Icons */
 
+.bootstrap-select.show-tick .dropdown-menu .selected span.check-mark {
+  right: 0px !important;
+}
+
 i.fa-solid .fa-arrow-right-long {
   font-size: 30px;
   color: white;
@@ -3009,6 +3019,15 @@ button#download_report_bttn {
 
 /* Gene Screening */
 
+.dataTables_wrapper.no-footer .dataTables_scrollBody {
+  border-bottom: none;
+}
+
+#DataTables_Table_8_wrapper > div.dataTables_scroll > div.dataTables_scrollBody,
+.display .dataTable .no-footer,
+#DataTables_Table_8,
+.dataTables_scrollBody
+
 #screening_start_button,
 #screening_reset_bttn,
 #screening_cancel {
diff --git a/www/head.css b/www/head.css
index 962b17d..c9e4b51 100644
--- a/www/head.css
+++ b/www/head.css
@@ -93,8 +93,20 @@ div#bs-select-12::-webkit-scrollbar-track,
 .selectize-dropdown-content::-webkit-scrollbar-track,
 #mst_comm_general_select::-webkit-scrollbar-track,
 .sF-dirInfo>div::-webkit-scrollbar-track{
-background: #F0F0F0;
-  }
+  background: #F0F0F0;
+}
+  
+#DataTables_Table_8_wrapper > div.dataTables_scroll > div.dataTables_scrollBody::-webkit-scrollbar-track,
+.display .dataTable .no-footer::-webkit-scrollbar-track,
+#DataTables_Table_8::-webkit-scrollbar-track,
+.dataTables_scrollBody::-webkit-scrollbar-track,
+div#gs_profile_table::-webkit-scrollbar-track,
+#gs_profile_table::-webkit-scrollbar-track {
+  background: #F0F0F0;
+  border-bottom-right-radius: 5px;
+  border-bottom-left-radius: 5px;
+}
+  
 
 .wtHolder::-webkit-scrollbar-thumb,
 div#bs-select-1::-webkit-scrollbar-thumb,
@@ -114,7 +126,13 @@ div#bs-select-12::-webkit-scrollbar-thumb,
 #screening_fail::-webkit-scrollbar-thumb,
 .selectize-dropdown-content::-webkit-scrollbar-thumb,
 #mst_comm_general_select::-webkit-scrollbar-thumb,
-.sF-dirInfo>div::-webkit-scrollbar-thumb {
+.sF-dirInfo>div::-webkit-scrollbar-thumb,
+#DataTables_Table_8_wrapper > div.dataTables_scroll > div.dataTables_scrollBody::-webkit-scrollbar-thumb,
+.display .dataTable .no-footer::-webkit-scrollbar-thumb,
+#DataTables_Table_8::-webkit-scrollbar-thumb,
+.dataTables_scrollBody::-webkit-scrollbar-thumb,
+#gs_profile_table::-webkit-scrollbar-thumb,
+div#gs_profile_table::-webkit-scrollbar-thumb {
   background: #bcbcbc;
   border: 2px solid #F0F0F0;
   min-width: 100px;

From 4f2f1657d40176728ca9819fda261873a5db6098 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Wed, 14 Aug 2024 09:30:02 +0200
Subject: [PATCH 47/75] Added spinner while downloading scheme

---
 App.R | 35 ++++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/App.R b/App.R
index 67289fa..c8f41e8 100644
--- a/App.R
+++ b/App.R
@@ -737,7 +737,10 @@ ui <- dashboardPage(
               "download_cgMLST",
               label = "Download",
               icon = icon("download")
-            )
+            ),
+            shinyjs::hidden(
+              div(id = "loading",
+                  HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>')))
           )
         ),
         fluidRow(
@@ -11444,6 +11447,21 @@ server <- function(input, output, session) {
   observeEvent(input$download_cgMLST, {
     log_print(paste0("Started download of scheme for ", Scheme$folder_name))
     
+    shinyjs::hide("download_cgMLST")
+    shinyjs::show("loading")
+    
+    output$statustext <- renderUI(
+      fluidRow(
+        tags$li(
+          class = "dropdown", 
+          tags$span(HTML(
+            paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                  "Status:&nbsp;&nbsp;&nbsp; <i>Downloading scheme...</i>")),
+            style = "color:white;")
+        )
+      )
+    )
+    
     show_toast(
       title = "Download started",
       type = "success",
@@ -11600,6 +11618,21 @@ server <- function(input, output, session) {
     
     DB$exist <- length(dir_ls(DB$database)) == 0
     
+    shinyjs::show("download_cgMLST")
+    shinyjs::hide("loading")
+    
+    output$statustext <- renderUI(
+      fluidRow(
+        tags$li(
+          class = "dropdown", 
+          tags$span(HTML(
+            paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                  "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
+            style = "color:white;")
+        )
+      )
+    )
+    
     show_toast(
       title = "Download successful",
       type = "success",

From c9f879d56cd4d417368af622463f8199971c4ec2 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Wed, 14 Aug 2024 20:25:05 +0200
Subject: [PATCH 48/75] Added gene resistance profile legend

---
 App.R | 30 ++++++++++++++++++++++--------
 1 file changed, 22 insertions(+), 8 deletions(-)

diff --git a/App.R b/App.R
index ebdda86..da8d1e0 100644
--- a/App.R
+++ b/App.R
@@ -5358,7 +5358,17 @@ ui <- dashboardPage(
           column(
             width = 10,
             div(class = "loci_table",
-                DT::dataTableOutput("gs_profile_table"))
+                DT::dataTableOutput("gs_profile_table")),
+            br(),
+            HTML(
+              paste0("<span style='color: white; font-size: 12px'>", 
+                     '<strong>RSL</strong> = <em>Reference Sequence Length</em>&nbsp&nbsp|&nbsp&nbsp',
+                     '<strong>%CRS</strong> = <em>% Coverage of Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                     '<strong>%IRS</strong> = <em>% Identity to Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                     '<strong>ACS</strong> = <em>Accession of Closest Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                     '<strong>NCS</strong> = <em>Name of Closest Sequence</em>')
+              
+            )
           )
         )
       )
@@ -22534,15 +22544,17 @@ server <- function(input, output, session) {
       iso_path <- file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
                             iso_select, "resProfile.tsv")
       res_profile <- read.delim(iso_path)
-      
+      # 
+      # colnames(res_profile) <- c(
+      #   "Protein Identifier",	"Contig ID", "Start", "Stop", "Strand", "Gene Symbol", 
+      #   "Sequence Name", "Scope", "Element Type",  "Element Subtype", "Class", 
+      #   "Subclass", "Method", "Target Length", "RSL",	"%CRS", "%IRS", "Alignment Length", 
+      #   "ACS", "NCS", "HMM ID", "HMM Description")
       colnames(res_profile) <- c(
         "Protein Identifier",	"Contig ID", "Start", "Stop", "Strand", "Gene Symbol", 
         "Sequence Name", "Scope", "Element Type",  "Element Subtype", "Class", 
-        "Subclass", "Method", "Target Length", "Reference Sequence Length",	
-        "% Coverage of Reference Sequence", "% Identity to Reference Sequence", 
-        "Alignment Length", "Accession of Closest Sequence", 
-        "Name of Closest Sequence", "HMM ID", "HMM Description")
-      
+        "Subclass", "Method", "Target Length", "RSL",	"%CRS", "%IRS", 
+        "Alignment Length", "ACS", "Name of Closest Sequence", "HMM ID", "HMM Description")
       
       res_profile <- res_profile %>%
         relocate(c("Gene Symbol", "Sequence Name", "Element Subtype", "Class", 
@@ -22556,7 +22568,9 @@ server <- function(input, output, session) {
         rownames= FALSE,
         options = list(pageLength = 10, scrollX = TRUE,
                        autoWidth = TRUE,
-                       columnDefs = list(list(width = '400px', targets = c("Sequence Name"))),
+                       columnDefs = list(list(width = '400px', targets = c("Sequence Name",
+                                                                           "Name of Closest Sequence"))),
+                       columnDefs = list(list(width = 'auto', targets = "_all")),
                        columnDefs = list(list(searchable = TRUE,
                                               targets = "_all")),
                        initComplete = DT::JS(

From a9b3f0e0d03be465c409f50b4cf9b1105176fce2 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Thu, 15 Aug 2024 12:48:40 +0200
Subject: [PATCH 49/75] Screening UI refinements

---
 App.R        | 293 +++++++++++++++++++++++++++++++++++++++++----------
 www/body.css |  14 +++
 www/head.css |   3 +-
 3 files changed, 254 insertions(+), 56 deletions(-)

diff --git a/App.R b/App.R
index da8d1e0..99c860d 100644
--- a/App.R
+++ b/App.R
@@ -52,7 +52,7 @@ options(ignore.negative.edge=TRUE)
 
 ui <- dashboardPage(
   
-  title = "PhyloTrace 1.4.1",
+  title = "PhyloTrace 1.5.0",
   
   # Title
   dashboardHeader(
@@ -113,6 +113,10 @@ ui <- dashboardPage(
       conditionalPanel(
         "input.tabs==='visualization'",
         uiOutput("visualization_sidebar")
+      ),
+      conditionalPanel(
+        "input.tabs==='gs_profile'",
+        uiOutput("screening_sidebar")
       )
     )
   ),
@@ -5344,32 +5348,10 @@ ui <- dashboardPage(
         br(),
         hr(),
         br(), br(),
+        uiOutput("gs_table_selection"),
         fluidRow(
           column(1),
-          column(
-            width = 10,
-            div(class = "loci_table",
-                dataTableOutput("gs_isolate_table"))
-          )
-        ),
-        hr(),
-        fluidRow(
-          column(1),
-          column(
-            width = 10,
-            div(class = "loci_table",
-                DT::dataTableOutput("gs_profile_table")),
-            br(),
-            HTML(
-              paste0("<span style='color: white; font-size: 12px'>", 
-                     '<strong>RSL</strong> = <em>Reference Sequence Length</em>&nbsp&nbsp|&nbsp&nbsp',
-                     '<strong>%CRS</strong> = <em>% Coverage of Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
-                     '<strong>%IRS</strong> = <em>% Identity to Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
-                     '<strong>ACS</strong> = <em>Accession of Closest Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
-                     '<strong>NCS</strong> = <em>Name of Closest Sequence</em>')
-              
-            )
-          )
+          uiOutput("gs_profile_display")
         )
       )
     ) # End tabItems
@@ -5382,7 +5364,7 @@ ui <- dashboardPage(
 
 server <- function(input, output, session) {
   
-  phylotraceVersion <- paste("1.4.1")
+  phylotraceVersion <- paste("1.5.0")
   
   #TODO Enable this, or leave disabled
   # Kill server on session end
@@ -9930,9 +9912,6 @@ server <- function(input, output, session) {
   observeEvent(input$reload_db, {
     log_print("Input reload_db")
     
-    pick_stat <<- Screening$picker_status
-    ttest <<- input$screening_select
-    
     if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
       show_toast(
         title = "Pending Multi Typing",
@@ -22535,35 +22514,227 @@ server <- function(input, output, session) {
   
   ### Render UI Elements ----
   
+  # Rendering results table
+  output$gs_results_table <- renderUI({
+    if(!is.null(Screening$selected_isolate)) {
+      if(length(Screening$selected_isolate) > 0) {
+        fluidRow(
+          div(class = "loci_table",
+              DT::dataTableOutput("gs_profile_table")),
+          br(),
+          HTML(
+            paste0("<span style='color: white; font-size: 12px'>", 
+                   '<strong>RSL</strong> = <em>Reference Sequence Length</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>%CRS</strong> = <em>% Coverage of Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>%IRS</strong> = <em>% Identity to Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>ACS</strong> = <em>Accession of Closest Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>NCS</strong> = <em>Name of Closest Sequence</em>')
+            
+          )
+        )
+      } else {
+        fluidRow(
+          br(), br(),
+          p(
+            HTML(
+              paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
+                     'Select entry from the table to display resistance profile')
+              
+            )
+          )
+        )
+      }
+    } else {
+      fluidRow(
+        br(), br(),
+        p(
+          HTML(
+            paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
+                   'Select entry from the table to display resistance profile')
+            
+          )
+        )
+      )
+    }
+  })
+  
+  # Gene screening download button
+  output$gs_download <- renderUI({
+    if(!is.null(Screening$selected_isolate)) {
+      if(length(Screening$selected_isolate) > 0) {
+        fluidRow(
+          downloadBttn(
+            "download_resistance_profile",
+            style = "simple",
+            label = "Profile Table",
+            size = "sm",
+            icon = icon("download"),
+            color = "primary"
+          ),
+          bsTooltip("download_resistance_profile_bttn", 
+                    HTML(paste0("Save resistance profile table for</br>",
+                                Screening$selected_isolate)), 
+                    placement = "bottom", trigger = "hover")
+        )
+      } else {NULL}
+    } else {NULL}
+  })
+  
+  # Conditionally render table selectiom interface
+  output$gs_table_selection <- renderUI({
+    req(input$gs_view)
+    if(input$gs_view == "Table") {
+      fluidRow(
+        column(1),
+        column(
+          width = 10,
+          div(class = "loci_table",
+              dataTableOutput("gs_isolate_table"))
+        )
+      )
+    } else {NULL}
+  })
+  
+  # Resistance profile table output display
+  output$gs_profile_display <- renderUI({
+    if(!is.null(DB$meta_gs) & !is.null(input$gs_view)) {
+      if(input$gs_view == "Table") {
+        column(
+          width = 10,
+          hr(), 
+          fluidRow(
+            column(
+              width = 4,
+              p(
+                HTML(
+                  paste0("<span style='color: white; font-size: 18px'>", 
+                         "Gene Screening Results</br>",
+                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
+                         "Comprising genes for resistance, virulence, stress, etc.")
+                )
+              )
+            ),
+            column(
+              width = 4,
+              uiOutput("gs_download")
+            )
+          ),
+          br(),
+          uiOutput("gs_results_table")
+        )
+      } else {
+        column(
+          width = 10,
+          fluidRow(
+            column(
+              width = 4,
+              p(
+                HTML(
+                  paste0("<span style='color: white; font-size: 18px'>", 
+                         "Gene Screening Results</br>",
+                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
+                         "Comprising genes for resistance, virulence, stress, etc.")
+                )
+              )
+            ),
+            column(
+              width = 4,
+              div(
+                class = "gs-picker",
+                pickerInput(
+                  "gs_profile_select",
+                  "",
+                  choices = list(
+                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+                    },
+                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
+                    }
+                  ),
+                  choicesOpt = list(
+                    disabled = c(
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
+                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]))
+                    )
+                  ),
+                  options = list(
+                    `live-search` = TRUE,
+                    size = 10,
+                    style = "background-color: white; border-radius: 5px;"
+                  )
+                )
+              )
+            ),
+            column(
+              width = 3,
+              uiOutput("gs_download")
+            )
+          ),
+          br(),
+          uiOutput("gs_results_table")
+        )
+      }
+    } else {NULL}
+  })
+  
+  # Screening sidebar
+  output$screening_sidebar <- renderUI({
+    if(!is.null(DB$meta_gs)) {
+      column(
+        width = 12,
+        align = "center",
+        br(), br(),
+        p(
+          HTML(
+            paste(
+              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Toggle View')
+            )
+          )
+        ),
+        radioGroupButtons(
+          inputId = "gs_view",
+          choices = c("Picker", "Table"),
+          selected = "Picker",
+          checkIcon = list(
+            yes = icon("square-check"),
+            no = icon("square")
+          )
+        ),
+        br()
+      )
+    } else {NULL}
+  })
+  
   # Resistance profile table
   observe({
-    req(DB$meta_gs, input$gs_isolate_table_rows_selected, DB$database, DB$scheme)
+    req(DB$meta_gs, Screening$selected_isolate, DB$database, DB$scheme)
     
-    if(DB$meta_gs$Screened[input$gs_isolate_table_rows_selected] == "Yes") {
-      iso_select <- DB$meta_gs$`Assembly ID`[input$gs_isolate_table_rows_selected]
+    if(length(Screening$selected_isolate) > 0 & any(Screening$selected_isolate %in% DB$data$`Assembly ID`)) {
+      iso_select <- Screening$selected_isolate
       iso_path <- file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
                             iso_select, "resProfile.tsv")
+      
       res_profile <- read.delim(iso_path)
-      # 
-      # colnames(res_profile) <- c(
-      #   "Protein Identifier",	"Contig ID", "Start", "Stop", "Strand", "Gene Symbol", 
-      #   "Sequence Name", "Scope", "Element Type",  "Element Subtype", "Class", 
-      #   "Subclass", "Method", "Target Length", "RSL",	"%CRS", "%IRS", "Alignment Length", 
-      #   "ACS", "NCS", "HMM ID", "HMM Description")
+      
       colnames(res_profile) <- c(
         "Protein Identifier",	"Contig ID", "Start", "Stop", "Strand", "Gene Symbol", 
         "Sequence Name", "Scope", "Element Type",  "Element Subtype", "Class", 
         "Subclass", "Method", "Target Length", "RSL",	"%CRS", "%IRS", 
         "Alignment Length", "ACS", "Name of Closest Sequence", "HMM ID", "HMM Description")
       
-      res_profile <- res_profile %>%
+      Screening$res_profile <- res_profile %>%
         relocate(c("Gene Symbol", "Sequence Name", "Element Subtype", "Class", 
                    "Subclass", "Scope", "Contig ID", "Target Length", "Alignment Length",
                    "Start", "Stop", "Strand"))
       
       # Generate gene profile table
       output$gs_profile_table <- DT::renderDataTable(
-        res_profile,
+        Screening$res_profile,
         selection = "single",
         rownames= FALSE,
         options = list(pageLength = 10, scrollX = TRUE,
@@ -22597,7 +22768,7 @@ server <- function(input, output, session) {
   observe({
     req(DB$meta)
     output$gs_isolate_table <- renderDataTable(
-      select(DB$meta_gs, -c(2, 4, 10, 11, 12)),
+      select(DB$meta_gs, -c(3, 4, 10, 11, 12)),
       selection = "single",
       rownames= FALSE,
       options = list(pageLength = 10,
@@ -22796,18 +22967,6 @@ server <- function(input, output, session) {
             uiOutput("screening_result_sel")
           ),
           column(1)
-          # column(
-          #   width = 3,
-          #   align = "left",
-          #   box(
-          #     solidHeader = TRUE,
-          #     status = "primary",
-          #     width = "90%",
-          #     HTML(paste("<span style='color: white; font-size: 17px'>", 
-          #                "AMRFinder Database Status")),
-          #     
-          #   )
-          # )
         ),
         fluidRow(
           column(1),
@@ -22824,6 +22983,32 @@ server <- function(input, output, session) {
   
   ### Screening Events ----
   
+  observe({
+    req(input$gs_view)
+    if(input$gs_view == "Table") {
+      Screening$selected_isolate <- DB$meta_gs$`Assembly ID`[input$gs_isolate_table_rows_selected]
+    } else if(input$gs_view == "Picker") {
+      Screening$selected_isolate <- input$gs_profile_select
+    }
+  })
+  
+  output$download_resistance_profile <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save resistance profile table ", Screening$selected_isolate, "_Profile.csv"))
+      
+      paste0(format(Sys.Date()), "_", Screening$selected_isolate, "_Profile.csv")
+    },
+    content = function(file) {
+      write.table(
+        Screening$res_profile,
+        file, 
+        sep = ";",
+        row.names = FALSE, 
+        quote = FALSE
+      ) 
+    }
+  )
+  
   # Reset screening 
   observeEvent(input$screening_reset_bttn, {
     log_print("Reset gene screening")
@@ -23037,9 +23222,7 @@ server <- function(input, output, session) {
           DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
         }
       )
-      pick_choices <<- Screening$picker_choices
       Screening$picker_selected <- input$screening_select
-      okayy <<- Screening$picker_selected
       Screening$picker_status <- FALSE
       
       show_toast(
diff --git a/www/body.css b/www/body.css
index 21ec938..ffae73c 100644
--- a/www/body.css
+++ b/www/body.css
@@ -3019,6 +3019,20 @@ button#download_report_bttn {
 
 /* Gene Screening */
 
+.gs-picker {
+  margin-top: -13px;
+}
+
+button#download_resistance_profile_bttn {
+    background: #282F38;
+    color: #ffffff;
+    border: 1px solid white;
+    transition: border-color 0.3s ease;
+    opacity: 1;
+    font-size: 15px;
+    margin-top: 10px;
+}
+
 .dataTables_wrapper.no-footer .dataTables_scrollBody {
   border-bottom: none;
 }
diff --git a/www/head.css b/www/head.css
index c9e4b51..ff46edc 100644
--- a/www/head.css
+++ b/www/head.css
@@ -87,6 +87,7 @@ div#bs-select-9::-webkit-scrollbar-track,
 div#bs-select-10::-webkit-scrollbar-track,
 div#bs-select-11::-webkit-scrollbar-track,
 div#bs-select-12::-webkit-scrollbar-track,
+div#bs-select-17::-webkit-scrollbar-track,
 #logText::-webkit-scrollbar-track, 
 #logTextFull::-webkit-scrollbar-track,
 #screening_fail::-webkit-scrollbar-track,
@@ -107,7 +108,6 @@ div#gs_profile_table::-webkit-scrollbar-track,
   border-bottom-left-radius: 5px;
 }
   
-
 .wtHolder::-webkit-scrollbar-thumb,
 div#bs-select-1::-webkit-scrollbar-thumb,
 div#bs-select-2::-webkit-scrollbar-thumb,
@@ -121,6 +121,7 @@ div#bs-select-9::-webkit-scrollbar-thumb,
 div#bs-select-10::-webkit-scrollbar-thumb,
 div#bs-select-11::-webkit-scrollbar-thumb,
 div#bs-select-12::-webkit-scrollbar-thumb,
+div#bs-select-17::-webkit-scrollbar-thumb,
 #logText::-webkit-scrollbar-thumb, 
 #logTextFull::-webkit-scrollbar-thumb,
 #screening_fail::-webkit-scrollbar-thumb,

From c55cdb280bb26389067733bbfd04df2ca2c5ac52 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Thu, 15 Aug 2024 20:48:11 +0200
Subject: [PATCH 50/75] Fixed and robustified AMRFinder feature

---
 App.R                 | 186 ++++++++++++++++++++++++------------------
 execute/multi_eval.R  |   8 +-
 execute/single_eval.R |   8 +-
 www/body.css          |   6 +-
 www/head.css          |  18 +++-
 5 files changed, 140 insertions(+), 86 deletions(-)

diff --git a/App.R b/App.R
index 99c860d..b14aaf1 100644
--- a/App.R
+++ b/App.R
@@ -6148,6 +6148,21 @@ server <- function(input, output, session) {
   
   observeEvent(input$load, {
     
+    # Reset reactive screening variables 
+    output$screening_start <- NULL
+    output$screening_result_sel <- NULL
+    output$screening_result <- NULL
+    output$screening_fail <- NULL
+    Screening$status_df <- NULL
+    Screening$choices <- NULL
+    Screening$picker_status <- TRUE
+    Screening$status <- "idle"
+    if(!is.null(input$screening_select)) {
+      if(!is.null(DB$data)) {
+        updatePickerInput(session, "screening_select", selected = character(0))
+      }
+    }
+    
     log_print("Input load")
     
     # set typing start control variable
@@ -6263,7 +6278,7 @@ server <- function(input, output, session) {
                 class = "dropdown", 
                 tags$span(HTML(
                   paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp;<i> running typing</i>")), 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> pending typing</i>")), 
                   style = "color:white;")
               )
             )
@@ -6275,7 +6290,7 @@ server <- function(input, output, session) {
                 class = "dropdown", 
                 tags$span(HTML(
                   paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp;<i> running gene screening</i>")), 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> pending gene screening</i>")), 
                   style = "color:white;")
               )
             )
@@ -6370,19 +6385,12 @@ server <- function(input, output, session) {
         log_print(paste0("New database created in ", DB$new_database))
         
         DB$check_new_entries <- TRUE
-        
         DB$data <- NULL
-        
         DB$meta_gs <- NULL
-        
         DB$meta <- NULL
-        
         DB$meta_true <- NULL
-        
         DB$allelic_profile <- NULL
-        
         DB$allelic_profile_true <- NULL
-        
         DB$scheme <- input$scheme_db
         
         # null Distance matrix, entry table and plots
@@ -6513,6 +6521,7 @@ server <- function(input, output, session) {
         output$single_typing_progress <- NULL
         output$metadata_single_box <- NULL
         output$start_typing_ui <- NULL
+        
       }
     } else {
       log_print(paste0("Loading existing ", input$scheme_db, " database from ", DB$database))
@@ -6975,12 +6984,9 @@ server <- function(input, output, session) {
               ))))) {
                 
                 # Load database from files  
-                Database <-
-                  readRDS(paste0(
-                    DB$database, "/",
-                    gsub(" ", "_", DB$scheme),
-                    "/Typing.rds"
-                  ))
+                Database <- readRDS(file.path(DB$database, 
+                                              gsub(" ", "_", DB$scheme), 
+                                              "Typing.rds"))
                 
                 DB$data <- Database[["Typing"]]
                 
@@ -6994,15 +7000,10 @@ server <- function(input, output, session) {
                 }
                 
                 DB$change <- FALSE
-                
                 DB$meta_gs <- select(DB$data, c(1, 3:13))
-                
                 DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-                
                 DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-                
                 DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-                
                 DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
                 
                 # Null pipe 
@@ -7015,25 +7016,15 @@ server <- function(input, output, session) {
                 
                 # Reset other reactive typing variables
                 Typing$progress_format_end <- 0 
-                
                 Typing$progress_format_start <- 0
-                
                 Typing$pending_format <- 0
-                
                 Typing$entry_added <- 0
-                
                 Typing$progress <- 0
-                
                 Typing$progress_format <- 900000
-                
                 output$single_typing_progress <- NULL
-                
                 output$typing_fin <- NULL
-                
                 output$single_typing_results <- NULL
-                
                 output$typing_formatting <- NULL
-                
                 Typing$single_path <- data.frame()
                 
                 # Null multi typing feedback variable
@@ -9145,15 +9136,10 @@ server <- function(input, output, session) {
                 # null underlying database
                 
                 DB$data <- NULL
-                
                 DB$meta <- NULL
-                
                 DB$meta_gs <- NULL
-                
                 DB$meta_true <- NULL
-                
                 DB$allelic_profile <- NULL
-                
                 DB$allelic_profile_true <- NULL
                 
                 # Render menu without missing values tab
@@ -9926,6 +9912,13 @@ server <- function(input, output, session) {
         position = "bottom-end",
         timer = 6000
       )
+    } else if(Screening$status == "started") {
+      show_toast(
+        title = "Pending Screening",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
     } else {
       showModal(
         modalDialog(
@@ -9985,21 +9978,13 @@ server <- function(input, output, session) {
     }
     
     DB$change <- FALSE
-    
     DB$count <- 0
-    
     DB$no_na_switch <- TRUE
-    
     DB$meta_gs <- select(DB$data, c(1, 3:13))
-    
     DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    
     DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-    
     DB$deleted_entries <- character(0)
     
     observe({
@@ -10855,17 +10840,11 @@ server <- function(input, output, session) {
     log_print(paste0("Variable ", input$del_which_var, " removed"))
     
     DB$cust_var <- DB$cust_var[-which(DB$cust_var$Variable == input$del_which_var),]
-    
     DB$data <- select(DB$data, -(input$del_which_var))
-    
     DB$meta_gs <- select(DB$data, c(1, 3:13))
-    
     DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    
     DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
   })
   
@@ -11076,8 +11055,6 @@ server <- function(input, output, session) {
     
     DB$data <- Database[["Typing"]]
     
-    dataa <- DB$data
-    
     if(!is.null(DB$data)){
       if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
         cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
@@ -11088,21 +11065,13 @@ server <- function(input, output, session) {
     }
     
     DB$change <- FALSE
-    
     DB$count <- 0
-    
     DB$no_na_switch <- TRUE
-    
     DB$meta_gs <- select(DB$data, c(1, 3:13))
-    
     DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    
     DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-    
     DB$deleted_entries <- character(0)
     
     removeModal()
@@ -22516,6 +22485,7 @@ server <- function(input, output, session) {
   
   # Rendering results table
   output$gs_results_table <- renderUI({
+    req(DB$data)
     if(!is.null(Screening$selected_isolate)) {
       if(length(Screening$selected_isolate) > 0) {
         fluidRow(
@@ -22560,6 +22530,7 @@ server <- function(input, output, session) {
   
   # Gene screening download button
   output$gs_download <- renderUI({
+    req(DB$data)
     if(!is.null(Screening$selected_isolate)) {
       if(length(Screening$selected_isolate) > 0) {
         fluidRow(
@@ -22582,7 +22553,7 @@ server <- function(input, output, session) {
   
   # Conditionally render table selectiom interface
   output$gs_table_selection <- renderUI({
-    req(input$gs_view)
+    req(DB$data, input$gs_view)
     if(input$gs_view == "Table") {
       fluidRow(
         column(1),
@@ -22597,6 +22568,7 @@ server <- function(input, output, session) {
   
   # Resistance profile table output display
   output$gs_profile_display <- renderUI({
+    req(DB$data)
     if(!is.null(DB$meta_gs) & !is.null(input$gs_view)) {
       if(input$gs_view == "Table") {
         column(
@@ -22654,12 +22626,18 @@ server <- function(input, output, session) {
                       as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
                     } else {
                       DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
+                    },
+                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
                     }
                   ),
                   choicesOpt = list(
                     disabled = c(
+                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
                       rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
-                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]))
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
                     )
                   ),
                   options = list(
@@ -22684,6 +22662,7 @@ server <- function(input, output, session) {
   
   # Screening sidebar
   output$screening_sidebar <- renderUI({
+    req(DB$data)
     if(!is.null(DB$meta_gs)) {
       column(
         width = 12,
@@ -22712,7 +22691,7 @@ server <- function(input, output, session) {
   
   # Resistance profile table
   observe({
-    req(DB$meta_gs, Screening$selected_isolate, DB$database, DB$scheme)
+    req(DB$meta_gs, Screening$selected_isolate, DB$database, DB$scheme, DB$data)
     
     if(length(Screening$selected_isolate) > 0 & any(Screening$selected_isolate %in% DB$data$`Assembly ID`)) {
       iso_select <- Screening$selected_isolate
@@ -22766,9 +22745,9 @@ server <- function(input, output, session) {
 
   #Resistance profile selection table
   observe({
-    req(DB$meta)
+    req(DB$meta, DB$data)
     output$gs_isolate_table <- renderDataTable(
-      select(DB$meta_gs, -c(3, 4, 10, 11, 12)),
+      select(DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ], -c(3, 4, 10, 11, 12)),
       selection = "single",
       rownames= FALSE,
       options = list(pageLength = 10,
@@ -22792,7 +22771,7 @@ server <- function(input, output, session) {
   })
   
   observe({
-    req(input$screening_res_sel, DB$database, DB$scheme)
+    req(input$screening_res_sel, DB$database, DB$scheme, DB$data)
     if(!is.null(Screening$status_df) &
        !is.null(input$screening_res_sel) & 
        !is.null(Screening$status_df$status) & 
@@ -22836,6 +22815,7 @@ server <- function(input, output, session) {
   
   # Availablity feedback
   output$gene_screening_info <- renderUI({
+    req(DB$data)
     if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
       p(
         HTML(
@@ -22860,6 +22840,7 @@ server <- function(input, output, session) {
   })
   
   output$gene_resistance_info <- renderUI({
+    req(DB$data)
     if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
       p(
         HTML(
@@ -22885,7 +22866,8 @@ server <- function(input, output, session) {
   
   # Screening Interface
   
-  output$screening_interface <- renderUI(
+  output$screening_interface <- renderUI({
+    req(DB$data)
     if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
       column(
         width = 12,
@@ -22918,12 +22900,18 @@ server <- function(input, output, session) {
                       as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
                     } else {
                       DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+                    },
+                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
                     }
                   ),
                   choicesOpt = list(
                     disabled = c(
                       rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
-                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]))
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
                     )
                   ),
                   options = list(
@@ -22979,14 +22967,15 @@ server <- function(input, output, session) {
         )
       )
     }
-  )
+  })
   
   ### Screening Events ----
   
   observe({
-    req(input$gs_view)
+    req(DB$data, input$gs_view)
     if(input$gs_view == "Table") {
-      Screening$selected_isolate <- DB$meta_gs$`Assembly ID`[input$gs_isolate_table_rows_selected]
+      meta_gs <- DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ]
+      Screening$selected_isolate <- meta_gs$`Assembly ID`[input$gs_isolate_table_rows_selected]
     } else if(input$gs_view == "Picker") {
       Screening$selected_isolate <- input$gs_profile_select
     }
@@ -23056,6 +23045,13 @@ server <- function(input, output, session) {
     log_print("Cancelled gene screening")
     removeModal()
     
+    show_toast(
+      title = "Gene Screening Terminated",
+      type = "warning",
+      position = "bottom-end",
+      timer = 6000
+    )
+    
     # terminate screening
     system(paste("kill $(pgrep -f 'execute/screening.sh')"), wait = FALSE)
     system(paste("killall -TERM tblastn"), wait = FALSE)
@@ -23082,9 +23078,10 @@ server <- function(input, output, session) {
   
   # Get selected assembly
   observe({
+    req(DB$data, Screening$status)
     if (length(input$screening_select) < 1) {
       output$genome_path_gs <- renderUI(HTML(
-        paste("<span style='color: white; font-style:italic'>", length(input$screening_select), " Isolate(s) queried for screening")
+        paste("<span style='color: white; font-style:italic'>", length(input$screening_select), " isolate(s) queried for screening")
       ))
       
       output$screening_start <- NULL
@@ -23184,7 +23181,7 @@ server <- function(input, output, session) {
           )
         )
       })
-    }
+    } else {NULL}
   })
   
   #### Running Screening ----
@@ -23220,6 +23217,11 @@ server <- function(input, output, session) {
           as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
         } else {
           DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+        },
+        `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
+          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
+        } else {
+          DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
         }
       )
       Screening$picker_selected <- input$screening_select
@@ -23257,10 +23259,8 @@ server <- function(input, output, session) {
     }
   })
   
-  ### Screening Feedback ----
-  
   observe({
-    req(Screening$status, input$screening_res_sel, Screening$status_df)
+    req(DB$data, Screening$status, input$screening_res_sel, Screening$status_df)
     if(!is.null(Screening$status_df) &
        !is.null(Screening$status_df$status) & 
        !is.null(Screening$status_df$isolate) &
@@ -23294,7 +23294,7 @@ server <- function(input, output, session) {
   })
   
   observe({
-    req(Screening$status, input$screening_res_sel)
+    req(DB$data, Screening$status, input$screening_res_sel)
     if(!is.null(Screening$status_df) &
        !is.null(Screening$status_df$status) & 
        !is.null(Screening$status_df$isolate) &
@@ -23317,6 +23317,7 @@ server <- function(input, output, session) {
   })
   
   observe({
+    req(DB$data)
     if(!is.null(Screening$status)) {
       if(Screening$status != "idle") {
         
@@ -23374,7 +23375,7 @@ server <- function(input, output, session) {
         Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
                                                                  Screening$status_df$status == "fail")]
         
-        if(sum("unfinished" != Screening$status_df$status) == 1) {
+        if(sum(Screening$status_df$status != "unfinished") == 1) {
           Screening$first_result <- TRUE
         }
         
@@ -23388,7 +23389,11 @@ server <- function(input, output, session) {
           saveRDS(Database, file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
 
           DB$data$Screened[which(DB$data["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
-
+          
+          DB$meta_gs <- select(DB$data, c(1, 3:13))
+          DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+          DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+          
           show_toast(
             title = paste("Successful screening of", tail(Screening$choices, 1)),
             type = "success",
@@ -23415,15 +23420,24 @@ server <- function(input, output, session) {
         }
         
         if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+          if(sum(Screening$status_df$status != "unfinished") == 1) {
+            Screening$first_result <- TRUE
+          }
           Screening$status <- "finished"
         }
       } else {
         if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+          if(sum(Screening$status_df$status != "unfinished") == 1) {
+            Screening$first_result <- TRUE
+          }
           Screening$status <- "finished"
         }
       }
       
       if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+        if(sum(Screening$status_df$status != "unfinished") == 1) {
+          Screening$first_result <- TRUE
+        }
         Screening$status <- "finished"
       }
     }
@@ -24194,7 +24208,7 @@ server <- function(input, output, session) {
         position = "bottom-end",
         timer = 6000
       )
-    }  else if (ass_id == "") {
+    } else if (ass_id == "") {
     show_toast(
       title = "Empty Assembly ID",
       type = "error",
@@ -24215,6 +24229,13 @@ server <- function(input, output, session) {
         position = "bottom-end",
         timer = 3000
       )
+    } else if(Screening$status == "started") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
     } else {
       
       log_print("Single typing metadata confirmed")
@@ -25004,6 +25025,13 @@ server <- function(input, output, session) {
         position = "bottom-end",
         timer = 6000
       )
+    } else if(Screening$status == "started") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
     } else {
       
       log_print("Multi typing metadata confirmed")
diff --git a/execute/multi_eval.R b/execute/multi_eval.R
index eba5b90..8742546 100644
--- a/execute/multi_eval.R
+++ b/execute/multi_eval.R
@@ -172,6 +172,8 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
         ncol = 13 + length(psl_files)
       ))
     
+    if(!save_assembly) {screen <- "NA"} else {screen <- "No"}
+    
     metadata <-
       c(
         1,
@@ -186,7 +188,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
         as.character(meta_info$append_analysisdate),
         length(allele_vector) - sum(sapply(allele_vector, is.na)),
         sum(sapply(allele_vector, is.na)),
-        "No"
+        screen
       )
     
     new_row <- c(metadata, allele_vector)
@@ -229,6 +231,8 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
     
     Database <- readRDS(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Typing.rds"))
     
+    if(!save_assembly) {screen <- "NA"} else {screen <- "No"}
+    
     metadata <-
       data.frame(
         nrow(Database[["Typing"]]) + 1,
@@ -243,7 +247,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
         as.character(meta_info$append_analysisdate),
         length(allele_vector) - sum(sapply(allele_vector, is.na)),
         sum(sapply(allele_vector, is.na)),
-        "No"
+        screen
       )
     
     if ((ncol(Database$Typing)-13) != length(allele_vector)) {
diff --git a/execute/single_eval.R b/execute/single_eval.R
index 1fb70a3..3dea406 100644
--- a/execute/single_eval.R
+++ b/execute/single_eval.R
@@ -152,6 +152,8 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
     
     Typing <- data.frame(matrix(NA, nrow = 0, ncol = 13 + length(psl_files)))
     
+    if(!save_assembly) {screen <- "NA"} else {screen <- "No"}
+    
     metadata <- c(
       1,
       TRUE,
@@ -165,7 +167,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
       as.character(meta_info$append_analysisdate),
       length(allele_vector) - sum(sapply(allele_vector, is.na)),
       sum(sapply(allele_vector, is.na)),
-      "No"
+      screen
     )
     
     new_row <- c(metadata, allele_vector)
@@ -207,6 +209,8 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
     
     Database <- readRDS(paste0(db_path, "/", gsub(" ", "_", meta_info$cgmlst_typing), "/Typing.rds"))
     
+    if(!save_assembly) {screen <- "NA"} else {screen <- "No"}
+    
     metadata <-
       data.frame(
         nrow(Database[["Typing"]]) + 1,
@@ -221,7 +225,7 @@ if(sum(unname(base::sapply(psl_files, file.size)) <= 427) / length(psl_files) <=
         as.character(meta_info$append_analysisdate),
         length(allele_vector) - sum(sapply(allele_vector, is.na)),
         sum(sapply(allele_vector, is.na)),
-        "No"
+        screen
       )
     
     if ((ncol(Database$Typing)-13) != length(allele_vector)) {
diff --git a/www/body.css b/www/body.css
index ffae73c..4f31873 100644
--- a/www/body.css
+++ b/www/body.css
@@ -3045,10 +3045,14 @@ button#download_resistance_profile_bttn {
 #screening_start_button,
 #screening_reset_bttn,
 #screening_cancel {
-  margin-top: 20px;
+  margin-top: 20px !important;
   border: 1px solid white;
 }
 
+#screening_start_button {
+  margin-top: 20px !important;
+}
+
 #screening_fail {
   max-width: 1000px;
 }
\ No newline at end of file
diff --git a/www/head.css b/www/head.css
index ff46edc..06bfdad 100644
--- a/www/head.css
+++ b/www/head.css
@@ -87,13 +87,20 @@ div#bs-select-9::-webkit-scrollbar-track,
 div#bs-select-10::-webkit-scrollbar-track,
 div#bs-select-11::-webkit-scrollbar-track,
 div#bs-select-12::-webkit-scrollbar-track,
+div#bs-select-13::-webkit-scrollbar-track,
+div#bs-select-14::-webkit-scrollbar-track,
+div#bs-select-15::-webkit-scrollbar-track,
+div#bs-select-16::-webkit-scrollbar-track,
 div#bs-select-17::-webkit-scrollbar-track,
+div#bs-select-18::-webkit-scrollbar-track,
+div#bs-select-19::-webkit-scrollbar-track,
 #logText::-webkit-scrollbar-track, 
 #logTextFull::-webkit-scrollbar-track,
 #screening_fail::-webkit-scrollbar-track,
 .selectize-dropdown-content::-webkit-scrollbar-track,
 #mst_comm_general_select::-webkit-scrollbar-track,
-.sF-dirInfo>div::-webkit-scrollbar-track{
+.sF-dirInfo>div::-webkit-scrollbar-track,
+[id^="bs-select-"]::-webkit-scrollbar-thumb{
   background: #F0F0F0;
 }
   
@@ -121,7 +128,13 @@ div#bs-select-9::-webkit-scrollbar-thumb,
 div#bs-select-10::-webkit-scrollbar-thumb,
 div#bs-select-11::-webkit-scrollbar-thumb,
 div#bs-select-12::-webkit-scrollbar-thumb,
+div#bs-select-13::-webkit-scrollbar-thumb,
+div#bs-select-14::-webkit-scrollbar-thumb,
+div#bs-select-15::-webkit-scrollbar-thumb,
+div#bs-select-16::-webkit-scrollbar-thumb,
 div#bs-select-17::-webkit-scrollbar-thumb,
+div#bs-select-18::-webkit-scrollbar-thumb,
+div#bs-select-19::-webkit-scrollbar-thumb,
 #logText::-webkit-scrollbar-thumb, 
 #logTextFull::-webkit-scrollbar-thumb,
 #screening_fail::-webkit-scrollbar-thumb,
@@ -133,7 +146,8 @@ div#bs-select-17::-webkit-scrollbar-thumb,
 #DataTables_Table_8::-webkit-scrollbar-thumb,
 .dataTables_scrollBody::-webkit-scrollbar-thumb,
 #gs_profile_table::-webkit-scrollbar-thumb,
-div#gs_profile_table::-webkit-scrollbar-thumb {
+div#gs_profile_table::-webkit-scrollbar-thumb,
+[id^="bs-select-"]::-webkit-scrollbar-thumb {
   background: #bcbcbc;
   border: 2px solid #F0F0F0;
   min-width: 100px;

From 965a8651d64fd9e03a81a18f3b06e9e0a1649c18 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Fri, 16 Aug 2024 13:20:26 +0200
Subject: [PATCH 51/75] Minor change in screening UI rendering

---
 App.R | 23 ++++++++++-------------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/App.R b/App.R
index a942ae6..e52e431 100644
--- a/App.R
+++ b/App.R
@@ -5836,7 +5836,8 @@ server <- function(input, output, session) {
                            status = "") # reactive variables related to typing process
   
   Screening <- reactiveValues(status = "idle",
-                              picker_status = TRUE) # reactive variables related to gene screening
+                              picker_status = TRUE,
+                              first_result = NULL) # reactive variables related to gene screening
   
   Vis <- reactiveValues(cluster = NULL, 
                         metadata = list(),
@@ -6160,6 +6161,7 @@ server <- function(input, output, session) {
     Screening$choices <- NULL
     Screening$picker_status <- TRUE
     Screening$status <- "idle"
+    Screening$first_result <- NULL
     if(!is.null(input$screening_select)) {
       if(!is.null(DB$data)) {
         updatePickerInput(session, "screening_select", selected = character(0))
@@ -23104,6 +23106,7 @@ server <- function(input, output, session) {
     Screening$status_df <- NULL
     Screening$choices <- NULL
     Screening$picker_status <- TRUE
+    Screening$first_result <- NULL
     
     # change reactive UI
     output$screening_table <- NULL
@@ -23158,6 +23161,7 @@ server <- function(input, output, session) {
     Screening$status_df <- NULL
     Screening$choices <- NULL
     Screening$picker_status <- TRUE
+    Screening$first_result <- NULL
     
     # change reactive UI
     output$screening_table <- NULL
@@ -23453,7 +23457,7 @@ server <- function(input, output, session) {
   }) 
     
   check_screening <- reactive({
-    invalidateLater(2000, session)
+    invalidateLater(500, session)
     
     req(Screening$status_df)
     
@@ -23469,8 +23473,10 @@ server <- function(input, output, session) {
         Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
                                                                  Screening$status_df$status == "fail")]
         
-        if(sum(Screening$status_df$status != "unfinished") == 1) {
-          Screening$first_result <- TRUE
+        if(sum(Screening$status_df$status != "unfinished") > 0) {
+          if(is.null(Screening$first_result)) {
+            Screening$first_result <- TRUE
+          }
         }
         
         if(tail(status_df$status, 1) == "success") {
@@ -23514,24 +23520,15 @@ server <- function(input, output, session) {
         }
         
         if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
-          if(sum(Screening$status_df$status != "unfinished") == 1) {
-            Screening$first_result <- TRUE
-          }
           Screening$status <- "finished"
         }
       } else {
         if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
-          if(sum(Screening$status_df$status != "unfinished") == 1) {
-            Screening$first_result <- TRUE
-          }
           Screening$status <- "finished"
         }
       }
       
       if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
-        if(sum(Screening$status_df$status != "unfinished") == 1) {
-          Screening$first_result <- TRUE
-        }
         Screening$status <- "finished"
       }
     }

From 3e921574d9d40a3811905d1eec8474025fcd7a13 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Fri, 16 Aug 2024 13:41:14 +0200
Subject: [PATCH 52/75] Adapted entry table locus column properties

---
 App.R | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/App.R b/App.R
index e52e431..9d4e246 100644
--- a/App.R
+++ b/App.R
@@ -7947,9 +7947,10 @@ server <- function(input, output, session) {
                                 highlightRow = TRUE,
                                 contextMenu = FALSE
                               )  %>%
-                                hot_col((13 + nrow(DB$cust_var)):((12 + nrow(DB$cust_var)) + length(input$compare_select)), 
+                                hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
                                         valign = "htMiddle",
                                         halign = "htCenter",
+                                        readOnly = TRUE,
                                         renderer = htmlwidgets::JS(
                                           "function(instance, td, row, col, prop, value, cellProperties) {
                                             if (value.length > 8) {
@@ -8259,7 +8260,7 @@ server <- function(input, output, session) {
                                 highlightCol = TRUE, 
                                 highlightRow = TRUE
                               ) %>%
-                                hot_col((13 + nrow(DB$cust_var)):((12 + nrow(DB$cust_var)) + length(input$compare_select)),
+                                hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
                                         readOnly = TRUE, 
                                         valign = "htMiddle",
                                         halign = "htCenter",
@@ -10146,9 +10147,10 @@ server <- function(input, output, session) {
                   highlightRow = TRUE,
                   contextMenu = FALSE
                 )  %>%
-                  hot_col((13 + nrow(DB$cust_var)):((12 + nrow(DB$cust_var)) + length(input$compare_select)), 
+                  hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
                           valign = "htMiddle",
                           halign = "htCenter",
+                          readOnly = TRUE,
                           renderer = htmlwidgets::JS(
                             "function(instance, td, row, col, prop, value, cellProperties) {
                                             if (value.length > 8) {
@@ -10457,7 +10459,7 @@ server <- function(input, output, session) {
                   highlightCol = TRUE, 
                   highlightRow = TRUE
                 ) %>%
-                  hot_col((13 + nrow(DB$cust_var)):((12 + nrow(DB$cust_var)) + length(input$compare_select)),
+                  hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
                           readOnly = TRUE, 
                           valign = "htMiddle",
                           halign = "htCenter",

From c9e4862c130a36de8efa4159e318cd657a6b60e0 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Fri, 16 Aug 2024 14:40:49 +0200
Subject: [PATCH 53/75] Added feedback for Hash a directory function

---
 App.R | 66 ++++++++++++++++++++++++++++++++++-------------------------
 1 file changed, 38 insertions(+), 28 deletions(-)

diff --git a/App.R b/App.R
index 9d4e246..84ea7fa 100644
--- a/App.R
+++ b/App.R
@@ -529,7 +529,8 @@ ui <- dashboardPage(
             ),
             shinyjs::hidden(
               div(id = "loading",
-                  HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>')))
+                  HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
+            )
           )
         ),
         fluidRow(
@@ -5288,11 +5289,17 @@ ui <- dashboardPage(
           align = "left",
           shinyDirButton(
             "hash_dir",
-            "Hash folder with loci",
-            title = "Locate the folder with loci",
+            "Choose folder with .fasta files",
+            title = "Locate folder with loci",
             buttonType = "default",
             style = "border-color: white; margin: 10px; min-width: 200px; text-align: center"
           ),
+          actionButton("hash_start", "Start Hashing", icon = icon("circle-play")),
+          shinyjs::hidden(
+            div(id = "hash_loading",
+                HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
+          )
+        )
           # br(),
           # actionButton(
           #   "backup_database",
@@ -5305,7 +5312,6 @@ ui <- dashboardPage(
           #   "Restore backup",
           #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
           # )
-        )
       ),
       
       
@@ -25818,33 +25824,37 @@ server <- function(input, output, session) {
                    defaultRoot = "Home",
                    session = session,
                    filetypes = c('', 'fasta', 'fna', 'fa'))
-    
+  })
+  
+  observeEvent(input$hash_start, {
     dir_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$hash_dir)
-    req(dir_path)
-    log_print("Hashing directory using utilities")
-    output$statustext <- renderUI(
-      fluidRow(
-        tags$li(
-          class = "dropdown", 
-          tags$span(HTML(
-            paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                  "Status:&nbsp;&nbsp;&nbsp; <i>hashing directory</i>")),
-            style = "color:white;")
-        )
+    if (!is_empty(list.files(dir_path)) && all(endsWith(list.files(dir_path), ".fasta"))) {
+      log_print("Hashing directory using utilities")
+      shinyjs::hide("hash_start")
+      shinyjs::show("hash_loading")
+      show_toast(
+        title = "Hashing started!",
+        type = "success",
+        position = "bottom-end",
+        timer = 6000
       )
-    )
-    hash_database(dir_path)
-    output$statustext <- renderUI(
-      fluidRow(
-        tags$li(
-          class = "dropdown", 
-          tags$span(HTML(
-            paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
-                  "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
-            style = "color:white;")
-        )
+      hash_database(dir_path)
+      shinyjs::hide("hash_loading")
+      shinyjs::show("hash_start")
+      show_toast(
+        title = "Hashing completed!",
+        type = "success",
+        position = "bottom-end",
+        timer = 6000
       )
-    )
+    } else {
+      show_toast(
+        title = "Incorrect folder selected!",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    }
   })
   
 } # end server

From 28038e6a4f9850e62d18e3340b8053f7efa33975 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Sat, 17 Aug 2024 22:53:18 +0200
Subject: [PATCH 54/75] Revised distance matrix generation

---
 App.R | 91 ++++++++++++++++++++++++++++++++++-------------------------
 1 file changed, 53 insertions(+), 38 deletions(-)

diff --git a/App.R b/App.R
index 84ea7fa..4a3afbd 100644
--- a/App.R
+++ b/App.R
@@ -5556,17 +5556,30 @@ server <- function(input, output, session) {
     return(varying_columns)
   }
   
-  # Functions to compute Hamming distance between two vectors
-  hamming_distance <- function(x, y) {
+  # Functions to compute hamming distances dependent on missing value handling
+  hamming.dist <- function(x, y) {
     sum(x != y)
   }
   
-  hamming_distance_ignore <- function(x, y) {
+  hamming.distIgnore <- function(x, y) {
     sum( (x != y) & !is.na(x) & !is.na(y) )
   }
   
-  hamming_distance_category <- function(x, y) {
-    sum( ( (x != y) | (is.na(x) & !is.na(y)) | (!is.na(x) & is.na(y)) ) & !(is.na(x) & is.na(y))  )
+  hamming.distCategory <- function(x, y) {
+    sum((x != y | xor(is.na(x), is.na(y))) & !(is.na(x) & is.na(y)))
+  }
+  
+  compute.distMatrix <- function(profile, hamming.method) {
+    mat <- as.matrix(profile)
+    n <- nrow(mat)
+    dist_mat <- matrix(0, n, n)
+    for (i in 1:(n-1)) {
+      for (j in (i+1):n) {
+        dist_mat[i, j] <- hamming.method(x = mat[i, ], y = mat[j, ])
+        dist_mat[j, i] <- dist_mat[i, j]
+      }
+    }
+    return(dist_mat)
   }
   
   # Function to determine entry table height
@@ -11291,7 +11304,6 @@ server <- function(input, output, session) {
   ### Distance Matrix ---- 
   
   hamming_df <- reactive({
-    # Create a custom proxy object for Hamming distance
     if(input$distmatrix_true == TRUE) {
       if(anyNA(DB$allelic_profile)) {
         if(input$na_handling == "omit") {
@@ -11299,54 +11311,57 @@ server <- function(input, output, session) {
           
           allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
           
-          DB$hamming_proxy <- proxy::dist(allelic_profile_noNA_true, method = hamming_distance)
+          hamming_mat <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
           
         } else if(input$na_handling == "ignore_na"){
-          DB$hamming_proxy <- proxy::dist(DB$allelic_profile_true, method = hamming_distance_ignore)
+          hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
           
         } else {
-          DB$hamming_proxy <- proxy::dist(DB$allelic_profile_true, method = hamming_distance_category)
+          hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
           
         } 
       } else {
-        DB$hamming_proxy <- proxy::dist(DB$allelic_profile_true, method = hamming_distance)
+        hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
       }
     } else {
       if(anyNA(DB$allelic_profile)) {
         if(input$na_handling == "omit") {
           allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
-          DB$hamming_proxy <- proxy::dist(allelic_profile_noNA, method = hamming_distance)
+          hamming_mat <- compute.distMatrix(allelic_profile_noNA, hamming.dist)
         } else if(input$na_handling == "ignore_na"){
-          DB$hamming_proxy <- proxy::dist(DB$allelic_profile, method = hamming_distance_ignore)
+          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distIgnore)
         } else {
-          DB$hamming_proxy <- proxy::dist(DB$allelic_profile, method = hamming_distance_category)
+          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distCategory)
         }  
       } else {
-        DB$hamming_proxy <- proxy::dist(DB$allelic_profile, method = hamming_distance)
+        hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.dist)
       }
     }
     
-    hamming_matrix <- as.matrix(DB$hamming_proxy)
-    
-    DB$matrix_min <- min(hamming_matrix, na.rm = TRUE)
-    DB$matrix_max <- max(hamming_matrix, na.rm = TRUE)
+    # Extreme values for distance matrix heatmap display
+    DB$matrix_min <- min(hamming_mat, na.rm = TRUE)
+    DB$matrix_max <- max(hamming_mat, na.rm = TRUE)
     
     if(input$distmatrix_triangle == FALSE) {
-      hamming_matrix[upper.tri(hamming_matrix, diag = !input$distmatrix_diag)] <- NA
+      hamming_mat[upper.tri(hamming_mat, diag = !input$distmatrix_diag)] <- NA
     } 
     
-    # Rownames change
-    rownames(hamming_matrix) <- select(DB$data, 1:(12 + nrow(DB$cust_var)))[rownames(select(DB$data, 1:(12 + nrow(DB$cust_var)))) %in% rownames(hamming_matrix), 
-                                                                            input$distmatrix_label]
-    colnames(hamming_matrix) <- rownames(hamming_matrix)
+    # Row- and colnames change
+    if(input$distmatrix_true == TRUE) {
+      rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label][which(DB$data$Include == TRUE),])
+    } else {
+      rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label])
+    }
+    colnames(hamming_mat) <- rownames(hamming_mat)
     
-    mode(hamming_matrix) <- "integer"
+    mode(hamming_mat) <- "integer"
     
-    DB$ham_matrix <- hamming_matrix %>%
+    DB$ham_matrix <- hamming_mat %>%
       as.data.frame() %>%
-      mutate(Index = colnames(hamming_matrix)) %>%
+      mutate(Index = colnames(hamming_mat)) %>%
       relocate(Index)
     DB$distancematrix_nrow <- nrow(DB$ham_matrix)
+    
     DB$ham_matrix
   })
   
@@ -21195,16 +21210,16 @@ server <- function(input, output, session) {
         
         allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
         
-        proxy::dist(allelic_profile_noNA_true, method = hamming_distance)
+        compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
         
       } else if(input$na_handling == "ignore_na"){
-        proxy::dist(DB$allelic_profile_true, method = hamming_distance_ignore)
+        compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
         
       } else {
-        proxy::dist(DB$allelic_profile_true, method = hamming_distance_category)
+        compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
       } 
       
-    } else {proxy::dist(DB$allelic_profile_true, method = hamming_distance)}
+    } else {compute.distMatrix(DB$allelic_profile_true, hamming.dist)}
   })
   
   hamming_mst <- reactive({
@@ -21214,15 +21229,15 @@ server <- function(input, output, session) {
         
         allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
         
-        dist <- proxy::dist(allelic_profile_noNA_true, method = hamming_distance)
+        dist <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
         
       } else if (input$na_handling == "ignore_na") {
-        dist <- proxy::dist(DB$allelic_profile_true, method = hamming_distance_ignore)
+        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
       } else {
-        dist <- proxy::dist(DB$allelic_profile_true, method = hamming_distance_category)
+        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
       }
     } else {
-      dist <- proxy::dist(DB$allelic_profile_true, method = hamming_distance)
+      dist <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
     }
     
     # Find indices of pairs with a distance of 0
@@ -21507,13 +21522,13 @@ server <- function(input, output, session) {
       if(anyNA(DB$allelic_profile)){
         if(input$na_handling == "omit") {
           allelic_profile_clean_noNA_names <- allelic_profile_clean[, colSums(is.na(allelic_profile_clean)) == 0]
-          proxy::dist(allelic_profile_clean_noNA_names, method = hamming_distance)
+          compute.distMatrix(allelic_profile_clean_noNA_names, hamming.dist)
         } else if (input$na_handling == "ignore_na") {
-          proxy::dist(allelic_profile_clean, method = hamming_distance_ignore)
+          compute.distMatrix(allelic_profile_clean, hamming.distIgnore)
         } else {
-          proxy::dist(allelic_profile_clean, method = hamming_distance_category)
+          compute.distMatrix(allelic_profile_clean, hamming.distCategory)
         }
-      } else {proxy::dist(allelic_profile_clean, method = hamming_distance)}
+      } else {compute.distMatrix(allelic_profile_clean, hamming.dist)}
       
       
     } else {

From 3b05d06941bc21d40041e4c4e04fd5ba5ab5d25f Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Sat, 17 Aug 2024 23:13:07 +0200
Subject: [PATCH 55/75] Fixes in MST creation

---
 App.R | 64 +++++++++++++++++++++++++++++------------------------------
 1 file changed, 31 insertions(+), 33 deletions(-)

diff --git a/App.R b/App.R
index 4a3afbd..e4251c7 100644
--- a/App.R
+++ b/App.R
@@ -17927,9 +17927,8 @@ server <- function(input, output, session) {
   #### MST ----
   
   mst_tree <- reactive({
-    log_print("Generating visNetwork")
-    Typing$data <- toVisNetworkData(Vis$ggraph_1)
-    Typing$data$nodes <- mutate(Typing$data$nodes, 
+    data <- toVisNetworkData(Vis$ggraph_1)
+    data$nodes <- mutate(data$nodes, 
                                 label = label_mst(),
                                 value = mst_node_scaling(),
                                 opacity = node_opacity())
@@ -18005,7 +18004,7 @@ server <- function(input, output, session) {
                             };
                         }")
     
-    Typing$var_cols <- NULL
+    Vis$var_cols <- NULL
     
     # Generate pie charts as nodes
     if(input$mst_color_var == TRUE & (!is.null(input$mst_col_var))) {
@@ -18015,33 +18014,33 @@ server <- function(input, output, session) {
         group[i] <- unique(Vis$meta_mst[[input$mst_col_var]])[i]
       }
       
-      Typing$data$nodes <- cbind(Typing$data$nodes, data.frame(metadata = character(nrow(Typing$data$nodes))))
+      data$nodes <- cbind(data$nodes, data.frame(metadata = character(nrow(data$nodes))))
       
-      if(length(which(Typing$data$nodes$group == "")) != 0) {
-        Typing$data$nodes$group[which(Typing$data$nodes$group == "")] <- Typing$data$nodes$group[1]
+      if(length(which(data$nodes$group == "")) != 0) {
+        data$nodes$group[which(data$nodes$group == "")] <- data$nodes$group[1]
       }
       
       if(is.null(input$mst_col_scale)) {
-        Typing$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
+        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
                                       color = viridis(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
       } else if (input$mst_col_scale == "Rainbow") {
-        Typing$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
+        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
                                       color = rainbow(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
       } else if (input$mst_col_scale == "Viridis") {
-        Typing$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
+        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
                                       color = viridis(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
       }
       
-      for(i in 1:nrow(Typing$data$nodes)) {
+      for(i in 1:nrow(data$nodes)) {
         
-        iso_subset <- strsplit(Typing$data$nodes$label[i], split = "\n")[[1]]
+        iso_subset <- strsplit(data$nodes$label[i], split = "\n")[[1]]
         variable <- Vis$meta_mst[[input$mst_col_var]]
         values <- variable[which(Vis$meta_mst$`Assembly Name` %in% iso_subset)]
         
         for(j in 1:length(unique(values))) {
           
           share <- sum(unique(values)[j] == values) / length(values) * 100
-          color <- Typing$var_cols$color[Typing$var_cols$value == unique(values)[j]]
+          color <- Vis$var_cols$color[Vis$var_cols$value == unique(values)[j]]
           
           if(j == 1) {
             pie_vec <- paste0('{"value":', share,',"color":"', color,'"}')
@@ -18050,26 +18049,26 @@ server <- function(input, output, session) {
           }
         }
         
-        Typing$data$nodes$metadata[i] <- paste0('[', pie_vec, ']')
+        data$nodes$metadata[i] <- paste0('[', pie_vec, ']')
       }
     }
     
-    Typing$data$edges <- mutate(Typing$data$edges,
+    data$edges <- mutate(data$edges,
                                 length = if(input$mst_scale_edges == FALSE) {
                                   input$mst_edge_length
                                 } else {
-                                  Typing$data$edges$weight * input$mst_edge_length_scale
+                                  data$edges$weight * input$mst_edge_length_scale
                                 },
-                                label = as.character(Typing$data$edges$weight),
+                                label = as.character(data$edges$weight),
                                 opacity = input$mst_edge_opacity)
     
     if (input$mst_show_clusters) {
-      Typing$data$nodes$group <- compute_clusters(Typing$data$nodes, Typing$data$edges, input$mst_cluster_threshold)
+      data$nodes$group <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
     }
     
-    updateSliderInput(session, "mst_cluster_threshold", max = max(Typing$data$edges$weight))
+    updateSliderInput(session, "mst_cluster_threshold", max = max(data$edges$weight))
     
-    visNetwork_graph <- visNetwork(Typing$data$nodes, Typing$data$edges,
+    visNetwork_graph <- visNetwork(data$nodes, data$edges,
                                    main = mst_title(),
                                    background = mst_background_color(),
                                    submain = mst_subtitle()) %>%
@@ -18108,16 +18107,15 @@ server <- function(input, output, session) {
           visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
       }
     }
-    log_print("Plotting MST graph")
     visNetwork_graph
   })
   
   # MST legend
   legend_col <- reactive({
-    if(!is.null(Typing$var_cols)) {
-      if(nrow(Typing$var_cols) > 10) {
+    if(!is.null(Vis$var_cols)) {
+      if(nrow(Vis$var_cols) > 10) {
         3
-      } else if(nrow(Typing$var_cols) > 5) {
+      } else if(nrow(Vis$var_cols) > 5) {
         2
       } else {
         1
@@ -18126,10 +18124,10 @@ server <- function(input, output, session) {
   })
   
   mst_legend <- reactive({
-    if(is.null(Typing$var_cols)) {
+    if(is.null(Vis$var_cols)) {
       NULL
     } else {
-      legend <- Typing$var_cols
+      legend <- Vis$var_cols
       names(legend)[1] <- "label"
       mutate(legend, shape = "dot",
              font.color = input$mst_legend_color,
@@ -18391,7 +18389,7 @@ server <- function(input, output, session) {
                                           hjust = input$nj_h,
                                           vjust = input$nj_v)  
       
-      Typing$nj_true <- TRUE
+      Vis$nj_true <- TRUE
       
       # Correct background color if zoomed out
       cowplot::ggdraw(Vis$nj_plot) + 
@@ -21763,7 +21761,7 @@ server <- function(input, output, session) {
               nj_tree()
             })
             
-            Typing$nj_true <- TRUE
+            Vis$nj_true <- TRUE
           }
         } else if (input$tree_algo == "UPGMA") {
           
@@ -21918,7 +21916,7 @@ server <- function(input, output, session) {
               upgma_tree()
             })
             
-            Typing$upgma_true <- TRUE
+            Vis$upgma_true <- TRUE
           }
         } else {
           
@@ -21961,7 +21959,7 @@ server <- function(input, output, session) {
             mst_tree()
           })
           
-          Typing$mst_true <- TRUE
+          Vis$mst_true <- TRUE
         }
       }
     }
@@ -21988,9 +21986,9 @@ server <- function(input, output, session) {
   
   observeEvent(input$create_rep, {
     
-    if((input$tree_algo == "Minimum-Spanning" & isTRUE(Typing$mst_true)) |
-       (input$tree_algo == "UPGMA" & isTRUE(Typing$upgma_true)) |
-       (input$tree_algo == "Neighbour-Joining" & isTRUE(Typing$nj_true))) {
+    if((input$tree_algo == "Minimum-Spanning" & isTRUE(Vis$mst_true)) |
+       (input$tree_algo == "UPGMA" & isTRUE(Vis$upgma_true)) |
+       (input$tree_algo == "Neighbour-Joining" & isTRUE(Vis$nj_true))) {
       # Get currently selected missing value handling option
       if(input$na_handling == "ignore_na") {
         na_handling <- "Ignore missing values for pairwise comparison"

From 9a06ed876d70ed436b346596841a6503eeff475a Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Sun, 18 Aug 2024 17:25:48 +0200
Subject: [PATCH 56/75] Slight adaptions in clustering controls for MST

---
 App.R        | 83 ++++++++++++++++++++++++++++++---------------
 www/body.css | 96 ++++++++++++++++++++++++++++++++++------------------
 2 files changed, 119 insertions(+), 60 deletions(-)

diff --git a/App.R b/App.R
index e4251c7..511f1ca 100644
--- a/App.R
+++ b/App.R
@@ -991,7 +991,7 @@ ui <- dashboardPage(
                             column(
                               width = 2,
                               bslib::tooltip(
-                                bsicons::bs_icon("info-circle", title = "Only categorical variables can \nbe mapped to the node color.", color = "white", 
+                                bsicons::bs_icon("info-circle", title = "Only categorical variables can \nbe mapped to the node color", color = "white", 
                                                  height = "12px", width = "12px", position = "relative", top = "27px", right = "56px"),
                                 "Text shown in the tooltip.",
                                 show = FALSE,
@@ -1377,20 +1377,35 @@ ui <- dashboardPage(
                     width = 6,
                     fluidRow(
                       column(
-                        width = 12,
+                        width = 6,
                         align = "left",
-                        h4(p("Clustering"), style = "color:white; text-align: left;")
+                        h4(p("Clustering"), style = "color:white; text-align: left; position: relative; right: -15px")
+                      ),
+                      column(
+                        width = 2,
+                        bslib::tooltip(
+                          bsicons::bs_icon("info-circle", 
+                                           title = "Cluster threshold according to species-specific\nComplex Type Distance (cgMLST.org)", 
+                                           color = "white", height = "14px", width = "14px", 
+                                           position = "relative", top = "9px", right = "28px"),
+                          "Text shown in the tooltip.",
+                          show = FALSE,
+                          id = "mst_cluster_info"
+                        )
                       )
                     ),
                     br(),
                     fluidRow(
                       column(
                         width = 9,
-                        materialSwitch(
-                          "mst_show_clusters",
-                          h5(p("Show Clusters"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                          value = FALSE,
-                          right = TRUE
+                        div(
+                          class = "mst-cluster-switch",
+                          materialSwitch(
+                            "mst_show_clusters",
+                            h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
                         )
                       ),
                       column(
@@ -1422,20 +1437,24 @@ ui <- dashboardPage(
                         width = 4,
                         HTML(
                           paste(
-                            tags$span(style='color: white; text-align: left; font-size: 14px; margin: 10px', 'Threshold')
+                            tags$span(style='color: white; text-align: left; font-size: 14px; margin-left: 15px', 'Threshold')
                           )
                         )
                       ),
                       column(
-                        width = 8,
-                        sliderInput(
-                          inputId = "mst_cluster_threshold",
-                          label = NULL,
-                          min = 0,
-                          max = 20,
-                          value = 4,
-                          ticks = FALSE
-                        )
+                        width = 4,
+                        uiOutput("mst_cluster")
+                      ),
+                      column(
+                        width = 4,
+                        actionButton(
+                          "mst_cluster_reset",
+                          label = "",
+                          icon = icon("rotate")
+                        ),
+                        bsTooltip("mst_cluster_reset", 
+                                  HTML("Reset to default Complex Type Distance"), 
+                                  placement = "top", trigger = "hover")
                       )
                     )
                   ),
@@ -12098,13 +12117,6 @@ server <- function(input, output, session) {
     }
   })
   
-  observe({
-    req(DB$schemeinfo)
-    updateSliderInput(session, "mst_cluster_threshold",
-                      max = as.numeric(DB$schemeinfo[[7,2]]) * 2,
-                      value = as.numeric(DB$schemeinfo[[7,2]]))
-  })
-  
   # Custom Labels
   
   # Add custom label
@@ -17803,8 +17815,19 @@ server <- function(input, output, session) {
   
   #### MST controls ----
   
-  # Mst color mapping
+  # Clustering UI
+  output$mst_cluster <- renderUI({
+    req(DB$schemeinfo)
+    numericInput(
+      inputId = "mst_cluster_threshold",
+      label = NULL,
+      value = as.numeric(DB$schemeinfo[7, 2]),
+      min = 1,
+      max = 99
+    )
+  })
   
+  # MST color mapping
   output$mst_color_mapping <- renderUI({
     if(input$mst_color_var == FALSE) {
       fluidRow(
@@ -18066,8 +18089,6 @@ server <- function(input, output, session) {
       data$nodes$group <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
     }
     
-    updateSliderInput(session, "mst_cluster_threshold", max = max(data$edges$weight))
-    
     visNetwork_graph <- visNetwork(data$nodes, data$edges,
                                    main = mst_title(),
                                    background = mst_background_color(),
@@ -21088,6 +21109,12 @@ server <- function(input, output, session) {
   
   ### Reactive Events ----
   
+  # MST cluster reset button
+  observeEvent(input$mst_cluster_reset, {
+    if(!is.null(DB$schemeinfo))
+    updateNumericInput(session, "mst_cluster_threshold", value = as.numeric(DB$schemeinfo[7, 2]))
+  })
+  
   # Shut off "Align Labels" control for UPGMA trees
   shinyjs::disable('upgma_align')
   shinyjs::disable('upgma_tiplab_linesize')
diff --git a/www/body.css b/www/body.css
index 4f31873..9563a5c 100644
--- a/www/body.css
+++ b/www/body.css
@@ -945,10 +945,25 @@ border-color: white;
 
 /* Visualization MST */
   
-  #mst_title_color {
+#mst_title_color {
   margin-bottom: 21px;
 }
 
+#mst_cluster_reset i.fas.fa-rotate {
+position: relative; 
+left: -6px;
+top: -3px;
+}
+
+button#mst_cluster_reset.btn.btn-default.action-button.shiny-bound-input {
+height: 27px; 
+width: 27px; 
+position: relative; 
+left: -5px;
+top: -3px;
+border: 1px solid white;
+}
+
 .mat-switch-mst-mult {
   margin-top: 10px;
   margin-left: 2px;
@@ -965,18 +980,27 @@ border-color: white;
 }
 
 #maindivtree_mst, #graphtree_mst {
-border-radius: 10px;
+  border-radius: 10px;
+}
+
+.mst-cluster-switch {
+  margin-top: 6px;
+  margin-left: 20px;
+}
+
+#mst_cluster_threshold {
+  margin-top: -7px;
 }
 
 button#create_tree {
-position: relative;
-overflow: hidden;
-box-shadow: 0px 0px 20px 10px rgba(255, 255, 255, 0.23);
-transition: box-shadow 0.3s ease;
-left: -15px;
-border: none;
-height: 45px;
-z-index: 0;
+  position: relative;
+  overflow: hidden;
+  box-shadow: 0px 0px 20px 10px rgba(255, 255, 255, 0.23);
+  transition: box-shadow 0.3s ease;
+  left: -15px;
+  border: none;
+  height: 45px;
+  z-index: 0;
 }
 
 button#create_tree:hover {
@@ -986,8 +1010,8 @@ box-shadow: 0px 0px 20px 15px rgba(40, 47, 56, 1);
 }
 
 #button-wrapper {
-position: relative;
-display: inline-block;
+  position: relative;
+  display: inline-block;
 }
 
 .icon {
@@ -1002,17 +1026,17 @@ display: inline-block;
 }
 
 #button-wrapper:hover .icon {
-transform: scale(1.2);
-width: 43px;
-height: auto;
-top: -2px;
-left: -7px;
+  transform: scale(1.2);
+  width: 43px;
+  height: auto;
+  top: -2px;
+  left: -7px;
 }
 
 #mst_ratio {
-position: absolute; 
-right: 36px; 
-top: 23px;
+  position: absolute; 
+  right: 36px; 
+  top: 23px;
 }
 
 button#mst_general_menu {
@@ -1052,33 +1076,41 @@ background: #20E6E5;
 }
 
 button#mst_title_menu {
-height: 34px; 
-margin-top: 20px; 
-border-radius: 5px
+  height: 34px; 
+  margin-top: 20px; 
+  border-radius: 5px
 }
 
 button#mst_edgelabel_menu {
-height: 34px; 
-background: #20E6E5; 
+  height: 34px; 
+  background: #20E6E5; 
   color: #000000; 
   margin-top: 37px; 
-border-radius: 5px
+  border-radius: 5px
+}
+
+button#mst_cluster_col_menu {
+  height: 34px;
+  background: #20E6E5;
+  color: #000000;
+  border-radius: 5px;
+  margin-left: -32px;
 }
 
 button#mst_edgecolor_menu {
-height: 34px; 
-background: #20E6E5; 
+  height: 34px; 
+  background: #20E6E5; 
   color: #000000; 
   margin-top: 20px; 
-border-radius: 5px
+  border-radius: 5px
 }
 
 button#mst_subtitle_menu {
-height: 34px; 
-background: #20E6E5; 
+  height: 34px; 
+  background: #20E6E5; 
   color: #000000; 
   margin-top: 20px; 
-border-radius: 5px
+  border-radius: 5px
 }
 
 button#mst_legend_menu {

From f6366f1a5921f8a6aa8db8c30487b09cce2ac304 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Sun, 18 Aug 2024 18:30:39 +0200
Subject: [PATCH 57/75] Fixed PB-19: New entries button appearing after failed
 typing

---
 App.R                    | 107 +++++++++++++++++++--------------------
 execute/single_typing.sh |   1 +
 www/resources.R          |   2 -
 3 files changed, 53 insertions(+), 57 deletions(-)

diff --git a/App.R b/App.R
index 511f1ca..d7191f5 100644
--- a/App.R
+++ b/App.R
@@ -5764,11 +5764,7 @@ server <- function(input, output, session) {
     invalidateLater(5000, session)
     
     if(!is.null(DB$database)) {
-      if(file_exists(file.path(
-        DB$database,
-        gsub(" ", "_", DB$scheme),
-        "Typing.rds"
-      ))) {
+      if(file_exists(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))) {
         
         Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
         
@@ -9320,7 +9316,7 @@ server <- function(input, output, session) {
                         )
                       )
                     } else {
-                      if(is.null(Typing$entry_added)) {
+                      #if(is.null(Typing$entry_added)) {
                         output$db_no_entries <- renderUI(
                           column(
                             width = 12,
@@ -9341,55 +9337,56 @@ server <- function(input, output, session) {
                             )
                           )
                         )
-                      } else {
-                        if(Typing$entry_added == 999999) {
-                          output$db_no_entries <- renderUI(
-                            column(
-                              width = 12,
-                              fluidRow(
-                                column(1),
-                                column(
-                                  width = 3,
-                                  align = "left",
-                                  HTML(
-                                    paste(
-                                      tags$span(style='color: white; font-size: 15px; position: absolute; bottom: -30px; right: -5px', 'New entries - reload database')
-                                    )
-                                  )
-                                ),
-                                column(
-                                  width = 4,
-                                  actionButton(
-                                    "load",
-                                    "",
-                                    icon = icon("rotate"),
-                                    class = "pulsating-button"
-                                  )
-                                )
-                              )
-                            )
-                          )
-                        } else {
-                          output$db_no_entries <- renderUI(
-                            column(
-                              width = 12,
-                              fluidRow(
-                                column(1),
-                                column(
-                                  width = 11,
-                                  align = "left",
-                                  HTML(paste(
-                                    "<span style='color: white;'>",
-                                    "No Entries for this scheme available.",
-                                    "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
-                                    sep = '<br/>'
-                                  ))
-                                )
-                              )
-                            )
-                          )
-                        }
-                      }
+                      #} 
+                      # else {
+                      #   if(Typing$entry_added == 999999) {
+                      #     output$db_no_entries <- renderUI(
+                      #       column(
+                      #         width = 12,
+                      #         fluidRow(
+                      #           column(1),
+                      #           column(
+                      #             width = 3,
+                      #             align = "left",
+                      #             HTML(
+                      #               paste(
+                      #                 tags$span(style='color: white; font-size: 15px; position: absolute; bottom: -30px; right: -5px', 'New entries - reload database')
+                      #               )
+                      #             )
+                      #           ),
+                      #           column(
+                      #             width = 4,
+                      #             actionButton(
+                      #               "load",
+                      #               "",
+                      #               icon = icon("rotate"),
+                      #               class = "pulsating-button"
+                      #             )
+                      #           )
+                      #         )
+                      #       )
+                      #     )
+                      #   } else {
+                      #     output$db_no_entries <- renderUI(
+                      #       column(
+                      #         width = 12,
+                      #         fluidRow(
+                      #           column(1),
+                      #           column(
+                      #             width = 11,
+                      #             align = "left",
+                      #             HTML(paste(
+                      #               "<span style='color: white;'>",
+                      #               "No Entries for this scheme available.",
+                      #               "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
+                      #               sep = '<br/>'
+                      #             ))
+                      #           )
+                      #         )
+                      #       )
+                      #     )
+                      #   }
+                      # }
                     }
                   }
                 })
diff --git a/execute/single_typing.sh b/execute/single_typing.sh
index 92d05ed..c8b5595 100755
--- a/execute/single_typing.sh
+++ b/execute/single_typing.sh
@@ -45,6 +45,7 @@ genome="$base_path/execute/blat_single/$genome_name"
 mv "$genome" "$base_path/execute/blat_single/$rename_file.fasta"
 
 # Run parallelized BLAT
+#TODO remove X
 find "$alleles" -type f \( -name "*.fasta" -o -name "*.fa" -o -name "*.fna" \) | parallel pblat "$base_path/execute/blat_single/$rename_file.fasta" {} "$results/{/.}.psl" > /dev/null 2>&1
 
 # Start appending results
diff --git a/www/resources.R b/www/resources.R
index 812f092..fc46c7f 100644
--- a/www/resources.R
+++ b/www/resources.R
@@ -1,9 +1,7 @@
 # Resources
 
-#TODO remove B pertussis from list
 amrfinder_species <- c(
   "Acinetobacter_baumannii", "Burkholderia_cepacia", "Burkholderia_mallei_FLI", 
-  "Bordetella_pertussis",
   "Burkholderia_mallei_RKI", "Burkholderia_pseudomallei", "Campylobacter_jejuni_coli",
   "Citrobacter_freundii", "Clostridioides_difficile", "Corynebacterium_diphtheriae", 
   "Enterobacter_asburiae", "Enterobacter_cloacae", "Enterococcus_faecalis", 

From b8154fd3e0046ab8184c4200e0067435b8811a02 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Sun, 18 Aug 2024 19:02:46 +0200
Subject: [PATCH 58/75] Fixed PB-20: Scheme present if new DB created

---
 App.R | 89 ++++++++++++++---------------------------------------------
 1 file changed, 21 insertions(+), 68 deletions(-)

diff --git a/App.R b/App.R
index d7191f5..a2dadbd 100644
--- a/App.R
+++ b/App.R
@@ -6430,7 +6430,9 @@ server <- function(input, output, session) {
         DB$meta_true <- NULL
         DB$allelic_profile <- NULL
         DB$allelic_profile_true <- NULL
-        DB$scheme <- input$scheme_db
+        if(!DB$select_new) {
+          DB$scheme <- input$scheme_db
+        }
         
         # null Distance matrix, entry table and plots
         output$db_distancematrix <- NULL 
@@ -6580,7 +6582,9 @@ server <- function(input, output, session) {
         DB$meta_true <- NULL
         DB$allelic_profile <- NULL
         DB$allelic_profile_true <- NULL
-        DB$scheme <- input$scheme_db
+        if(!DB$select_new) {
+          DB$scheme <- input$scheme_db
+        }
         
         # null Distance matrix, entry table and plots
         output$db_distancematrix <- NULL 
@@ -9316,77 +9320,26 @@ server <- function(input, output, session) {
                         )
                       )
                     } else {
-                      #if(is.null(Typing$entry_added)) {
-                        output$db_no_entries <- renderUI(
-                          column(
-                            width = 12,
-                            fluidRow(
-                              column(1),
-                              column(
-                                width = 11,
-                                align = "left",
-                                HTML(
-                                  paste(
-                                    "<span style='color: white;'>",
-                                    "No Entries for this scheme available.\n",
-                                    "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
-                                    sep = '<br/>'
-                                  )
+                      output$db_no_entries <- renderUI(
+                        column(
+                          width = 12,
+                          fluidRow(
+                            column(1),
+                            column(
+                              width = 11,
+                              align = "left",
+                              HTML(
+                                paste(
+                                  "<span style='color: white;'>",
+                                  "No Entries for this scheme available.\n",
+                                  "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
+                                  sep = '<br/>'
                                 )
                               )
                             )
                           )
                         )
-                      #} 
-                      # else {
-                      #   if(Typing$entry_added == 999999) {
-                      #     output$db_no_entries <- renderUI(
-                      #       column(
-                      #         width = 12,
-                      #         fluidRow(
-                      #           column(1),
-                      #           column(
-                      #             width = 3,
-                      #             align = "left",
-                      #             HTML(
-                      #               paste(
-                      #                 tags$span(style='color: white; font-size: 15px; position: absolute; bottom: -30px; right: -5px', 'New entries - reload database')
-                      #               )
-                      #             )
-                      #           ),
-                      #           column(
-                      #             width = 4,
-                      #             actionButton(
-                      #               "load",
-                      #               "",
-                      #               icon = icon("rotate"),
-                      #               class = "pulsating-button"
-                      #             )
-                      #           )
-                      #         )
-                      #       )
-                      #     )
-                      #   } else {
-                      #     output$db_no_entries <- renderUI(
-                      #       column(
-                      #         width = 12,
-                      #         fluidRow(
-                      #           column(1),
-                      #           column(
-                      #             width = 11,
-                      #             align = "left",
-                      #             HTML(paste(
-                      #               "<span style='color: white;'>",
-                      #               "No Entries for this scheme available.",
-                      #               "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
-                      #               sep = '<br/>'
-                      #             ))
-                      #           )
-                      #         )
-                      #       )
-                      #     )
-                      #   }
-                      # }
+                      )
                     }
                   }
                 })

From de346fe191916914b5b6f02bb8ccf26241129751 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Mon, 19 Aug 2024 12:00:51 +0200
Subject: [PATCH 59/75] Minor correction PB-20; syntax polishing css files

---
 App.R        |  19 ++-
 www/body.css | 324 +++++++++++++++++++++++++--------------------------
 www/head.css |  36 ++++--
 3 files changed, 196 insertions(+), 183 deletions(-)

diff --git a/App.R b/App.R
index a2dadbd..a4b4368 100644
--- a/App.R
+++ b/App.R
@@ -5916,14 +5916,14 @@ server <- function(input, output, session) {
           DB$available <- gsub("_", " ", basename(dir_ls(DB$database))) # List of local schemes available
         }
         
-      } else if (DB$select_new ==  TRUE) {
-        DB$database <- paste0(DB$new_database, "/Database")
+      } else if (DB$select_new == TRUE) {
+        DB$database <- file.path(DB$new_database, "Database")
         
       }
     } else {
-      if(!is.null(DB$last_db) & file.exists(paste0(getwd(), "/execute/last_db.rds"))) {
+      if(!is.null(DB$last_db) & file.exists(file.path(getwd(), "execute/last_db.rds"))) {
         
-        DB$database <- readRDS(paste0(getwd(), "/execute/last_db.rds")) 
+        DB$database <- readRDS(file.path(getwd(), "execute/last_db.rds")) 
         
         if(dir_exists(DB$database)) {
           DB$exist <- (length(dir_ls(DB$database)) == 0)  # Logical any local database present
@@ -6407,7 +6407,7 @@ server <- function(input, output, session) {
     
     # Load app elements based on database availability and missing value presence
     if(!is.null(DB$select_new)) {
-      if(DB$select_new & (paste0(DB$new_database, "/Database") %in% dir_ls(DB$new_database))) {
+      if(DB$select_new & (file.path(DB$new_database, "Database") %in% dir_ls(DB$new_database))) {
         
         log_print("Directory already contains a database")
         
@@ -6430,9 +6430,6 @@ server <- function(input, output, session) {
         DB$meta_true <- NULL
         DB$allelic_profile <- NULL
         DB$allelic_profile_true <- NULL
-        if(!DB$select_new) {
-          DB$scheme <- input$scheme_db
-        }
         
         # null Distance matrix, entry table and plots
         output$db_distancematrix <- NULL 
@@ -6466,7 +6463,7 @@ server <- function(input, output, session) {
         DB$load_selected <- FALSE
         
         # Declare database path
-        DB$database <- paste0(DB$new_database, "/Database")
+        DB$database <- file.path(DB$new_database, "Database")
         
         # Set database availability screening variables to present database
         DB$block_db <- TRUE
@@ -6582,9 +6579,7 @@ server <- function(input, output, session) {
         DB$meta_true <- NULL
         DB$allelic_profile <- NULL
         DB$allelic_profile_true <- NULL
-        if(!DB$select_new) {
-          DB$scheme <- input$scheme_db
-        }
+        DB$scheme <- input$scheme_db
         
         # null Distance matrix, entry table and plots
         output$db_distancematrix <- NULL 
diff --git a/www/body.css b/www/body.css
index 9563a5c..96c94e3 100644
--- a/www/body.css
+++ b/www/body.css
@@ -3,7 +3,7 @@
 /* General */
   
 h1, h2, h3, h4, h5, p, body {
-    font-family: 'Liberation Sans', sans-serif;
+  font-family: 'Liberation Sans', sans-serif;
 }
 
 label {
@@ -57,8 +57,8 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
 
 .btn-primary.focus, .btn-primary:active:focus {
   color: #ffffff;
-    background-color: #282F38;  
-    border-color: white;  
+  background-color: #282F38;  
+  border-color: white;  
 }
 
 #conf_delete .btn-default:hover {
@@ -67,8 +67,8 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
 
 .datepicker table tr td.active:active, .datepicker table tr td.active.active, .datepicker table tr td.active.highlighted:active, .datepicker table tr td.active.highlighted.active {
   color: #000000;
-    background-color: #20E6E5;  
-    border-color: #20E6E5;  
+  background-color: #20E6E5;  
+  border-color: #20E6E5;  
 }
 
 .table>caption+thead>tr:first-child>td, .table>caption+thead>tr:first-child>th, .table>colgroup+thead>tr:first-child>td, .table>colgroup+thead>tr:first-child>th, .table>thead:first-child>tr:first-child>td, .table>thead:first-child>tr:first-child>th,
@@ -79,7 +79,7 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
 
 .dropdown-menu>li.selected {
   color: #ffffff;
-    background-color: #282F38;  
+  background-color: #282F38;  
 }
 
 .dropdown-menu>li>a.selected{
@@ -91,13 +91,13 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
 }
 
 .dropdown-menu>li>a:hover {
-  color: #000000;
-    background-color: #20E6E5;  
+  Color: #000000;
+  background-color: #20E6E5;  
 }
 
 .selectize-dropdown .selected {
   background-color: #20E6E5;
-    color: black;
+  color: black;
 }
 
 .bs-searchbox .form-control {
@@ -135,7 +135,7 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
 
 .main-sidebar .sidebar .sidebar-menu .treeview-menu a {
   color: #ffffff !important; 
-    margin-left: 25px; 
+  margin-left: 25px; 
   border-radius: 20px; 
   margin-top: 7px; 
   margin-bottom: 7px;
@@ -259,17 +259,17 @@ font-size: 12px;
 }
 
 #reload_db i.fas.fa-rotate {
-position: relative; 
-left: -7px;
-top: -3px;
+  position: relative; 
+  left: -7px;
+  top: -3px;
 }
 
 button#reload_db.btn.btn-default.action-button.shiny-bound-input {
-height: 27px; 
-width: 27px; 
-position: relative; 
-left: -20px;
-border: 1px solid white;
+  height: 27px; 
+  width: 27px; 
+  position: relative; 
+  left: -20px;
+  border: 1px solid white;
 }
 
 #db_location {
@@ -443,18 +443,18 @@ table.dataTable.display>tbody>tr:hover>* {
   color: white !important;
   border: 1px solid #111;
   background-color: #20E6E5;
-    background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, #585858), color-stop(100%, #111));
-                                                                           background: -webkit-linear-gradient(top, #585858 0%, #111 100%);
-                                                                                                               background: -moz-linear-gradient(top, #585858 0%, #111 100%);
-                                                                                                                                                background: -ms-linear-gradient(top, #585858 0%, #111 100%);
-                                                                                                                                                                                background: -o-linear-gradient(top, #585858 0%, #111 100%);
-                                                                                                                                                                                                               background: linear-gradient(to bottom, #585858 0%, #111 100%);
+  background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, #585858), color-stop(100%, #111));
+  background: -webkit-linear-gradient(top, #585858 0%, #111 100%);
+  background: -moz-linear-gradient(top, #585858 0%, #111 100%);
+  background: -ms-linear-gradient(top, #585858 0%, #111 100%);
+  background: -o-linear-gradient(top, #585858 0%, #111 100%);
+  background: linear-gradient(to bottom, #585858 0%, #111 100%);
 }
 
 .dataTables_wrapper .dataTables_paginate .paginate_button.disabled, .dataTables_wrapper .dataTables_paginate .paginate_button.disabled:hover, .dataTables_wrapper .dataTables_paginate .paginate_button.disabled:active {
   cursor: default;
   color: #fff !important;
-    border: 1px solid transparent;
+  border: 1px solid transparent;
   background: transparent;
   box-shadow: none;
 }
@@ -463,7 +463,7 @@ table.dataTable.display>tbody>tr:hover>* {
   color: black !important;
   border: 1px solid rgb(255 255 255 / 0%);
   background-color: #20E6E5 !important;
-    border-radius: 5px;
+  border-radius: 5px;
   background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, rgba(230, 230, 230, 0.05)), color-stop(100%, rgba(0, 0, 0, 0.05)));
   background: -webkit-linear-gradient(top, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
   background: -moz-linear-gradient(top, rgba(230, 230, 230, 0.05) 0%, rgba(0, 0, 0, 0.05) 100%);
@@ -476,12 +476,12 @@ table.dataTable.display>tbody>tr:hover>* {
   color: white !important;
   border: 1px solid #00f3ff;
   background-color: #111;
-    background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, #585858), color-stop(100%, #111));
-                                                                           background: -webkit-linear-gradient(top, #585858 0%, #111 100%);
-                                                                                                               background: -moz-linear-gradient(top, #585858 0%, #111 100%);
-                                                                                                                                                background: -ms-linear-gradient(top, #585858 0%, #111 100%);
-                                                                                                                                                                                background: -o-linear-gradient(top, #585858 0%, #111 100%);
-                                                                                                                                                                                                               background: transparent;
+  background: -webkit-gradient(linear, left top, left bottom, color-stop(0%, #585858), color-stop(100%, #111));
+  background: -webkit-linear-gradient(top, #585858 0%, #111 100%);
+  background: -moz-linear-gradient(top, #585858 0%, #111 100%);
+  background: -ms-linear-gradient(top, #585858 0%, #111 100%);
+  background: -o-linear-gradient(top, #585858 0%, #111 100%);
+  background: transparent;
 }
 
 input.form-control.pickr-color {
@@ -512,26 +512,26 @@ input.form-control.pickr-color {
 }
 
 button#copy_seq {
-background: #282F38;
+  background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-transition: border-color 0.3s ease;
+  transition: border-color 0.3s ease;
 }
 
 button#get_locus_bttn {
-background: #282F38;
+  background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-transition: border-color 0.3s ease;
-opacity: 1;
-font-size: 15px;
-width: 147px;
+  transition: border-color 0.3s ease;
+  opacity: 1;
+  font-size: 15px;
+  width: 147px;
 }
 
 button#get_locus_bttn i.fas.fa-download {
-position: relative;
-top: -1px;
-left: -6px;
+  position: relative;
+  top: -1px;
+  left: -6px;
 }
 
 /* Icons */
@@ -609,22 +609,22 @@ i.far.fa-pen-to-square {
   #table_missing_values > div > div > div > div > table > tbody > tr > td,
   #multi_select_table > div > div > div > div > table > tbody > tr > td,
   #multi_typing_result_table > div > div > div > div > table > tbody > tr > td,
-  #typing_result_table > div > div > div > div > table > tbody > tr > td{
+  #typing_result_table > div > div > div > div > table > tbody > tr > td {
   color: black !important;
 }
 
 .miss_val_box,
-#table_missing_values{
-margin-left: 50px;
+#table_missing_values {
+  margin-left: 50px;
 }
 
 #download_na_matrix_bttn > i {
-top: 1px !important;
+  top: 1px !important;
 }
 
 #sel_all_entries, #desel_all_entries, #typing_start, #start_typ_multi, 
 #undo_changes, #genome_file, #genome_file_multi, #reset_multi, #save_cust {
-border-color: white;
+  border-color: white;
 }
 
 #genome_file_multi,
@@ -637,24 +637,24 @@ border-color: white;
 }
 
 #cgmlst_scheme {
-margin-top: 41px;
+  margin-top: 41px;
 }
 
 .dropdown-menu>.active>a, .dropdown-menu>.active>a:focus, .dropdown-menu>.active>a:hover {
   color: #ffffff !important;
-    background-color: #282F38 !important;
+  background-color: #282F38 !important;
 }
 
 #shiny-tab-db_browse_entries > div:nth-child(11) > div.col-sm-1,
 #shiny-tab-init > div:nth-child(4) > div.col-sm-1,
 #shiny-tab-init > div:nth-child(3) > div.col-sm-1 {
-width: 4.333333%;
+  width: 4.333333%;
 }
 
 .bttn-simple:hover {
   border-color: #20E6E5 !important;
-    background: #20E6E5 !important;
-    color: black !important;
+  background: #20E6E5 !important;
+  color: black !important;
   opacity: 1;
 }
 
@@ -677,143 +677,143 @@ width: 4.333333%;
 
 #db_entries, #db_distancematrix, #table_missing_values, 
 #multi_select_table, #typing_result_table, #multi_typing_result_table {
-border-radius: 8px;
-color: black;
+  border-radius: 8px;
+  color: black;
 }
 
 #multi_typing_result_table {
-margin-top: -15px;
+  margin-top: -15px;
 }
 
 #add_new_variable {
-background: green; 
-height: 35px; 
-width: 38px;
-margin-left: -5px;
-margin-top: 19px;
+  background: green; 
+  height: 35px; 
+  width: 38px;
+  margin-left: -5px;
+  margin-top: 19px;
 }
 
 #delete_new_variable {
-background: #FF5964; 
+  background: #FF5964; 
   height: 35px; 
-width: 38px;
-margin-left: -5px;
-margin-top: 20px;
+  width: 38px;
+  margin-left: -5px;
+  margin-top: 20px;
 }
 
 #new_var_name {
-height: 33px;
-margin-left: -6px;
-width: 123px;
-margin-top: -12px;
+  height: 33px;
+  margin-left: -6px;
+  width: 123px;
+  margin-top: -12px;
 }
 
 #cust_var_select {
-margin-top: -40px;
+  margin-top: -40px;
 }
 
 #cust_var_select .selectize-dropdown-content {
-max-height: 80px;
+  max-height: 80px;
 }
 
 div#db_distancematrix.rhandsontable {
-font-size: 11px;
+  font-size: 11px;
 }
 
 button#download_cgMLST {
-font-size: 14px; 
-height: 34px; 
-background: #282F38;
+  font-size: 14px; 
+  height: 34px; 
+  background: #282F38;
   color: #ffffff;
   border: 1px solid white;
 }
 
 .btn-primary:hover {
   background-color: #20e6e5;
-    border-color: #20e6e5;
-    color: black;
+  border-color: #20e6e5;
+  color: black;
   border-radius: 5px;
   height: 35px;
 }
 
 .btn-primary {
   background: #282F38;
-    color: #ffffff;
-    border-color: #282F38;
-    border-radius: 5px;
+  color: #ffffff;
+  border-color: #282F38;
+  border-radius: 5px;
   height: 35px;
   padding: 6px 12px;
 }
 
 .btn-default:hover {
   border-color: #20e6e5 !important;
-    background: #20e6e5 !important;
-    color: black !important;
+  background: #20e6e5 !important;
+  color: black !important;
 }
 
 button#download_cgMLST i.fas.fa-download {
-margin-right: 5px !important
+  margin-right: 5px !important
 }
 
 #show_cust_var {
-color:black; 
-font-size: 14px;
-margin-left: 15px;
+  color:black; 
+  font-size: 14px;
+  margin-left: 15px;
 }
 
 button#download_distmatrix_bttn {
-font-size: 14px;
-height: 34px;
-background: #282F38;
+  font-size: 14px;
+  height: 34px;
+  background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-position: absolute;
-top: -50px;
-transition: border-color 0.3s ease; /* Smooth transition for border color */
-  }
+  position: absolute;
+  top: -50px;
+  transition: border-color 0.3s ease; /* Smooth transition for border color */
+}
 
 button#download_entry_table_bttn {
-height: 34px; 
-background: #282F38;
+  height: 34px; 
+  background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-transition: border-color 0.3s ease; /* Smooth transition for border color */
-  }
+  transition: border-color 0.3s ease; 
+}
 
 button#download_schemeinfo_bttn {
-height: 28px;
-background: #282F38;
+  height: 28px;
+  background: #282F38;
   color: #ffffff;
   margin-top: 19px;
-border: 1px solid white;
-margin-left: 10px;
-transition: border-color 0.3s ease; /* Smooth transition for border color */
+  border: 1px solid white;
+  margin-left: 10px;
+  transition: border-color 0.3s ease; 
   }
 
 button#download_loci_info_bttn {
-height: 28px;
-background: #282F38;
+  height: 28px;
+  background: #282F38;
   color: #ffffff;
   margin-top: 19px;
-border: 1px solid white;
-margin-left: 10px;
-transition: border-color 0.3s ease;
+  border: 1px solid white;
+  margin-left: 10px;
+  transition: border-color 0.3s ease;
 }
 
 button#download_na_matrix_bttn {
-height: 34px; 
-background: #282F38;
+  height: 34px; 
+  background: #282F38;
   color: #ffffff;
   border: 1px solid white;
-margin-top: 14px; 
-margin-left: 10px;
-transition: border-color 0.3s ease;
+  margin-top: 14px; 
+  margin-left: 10px;
+  transition: border-color 0.3s ease;
 }
 
 button#edit_button.btn.btn-default.action-button.shiny-bound-input {
-background: #20E6E5; 
+  background: #20E6E5; 
   color: #000000;
-  }
+}
 
 /* Typing */
 
@@ -856,7 +856,7 @@ background: #20E6E5;
 body > div.htDatepickerHolder > div > div > table > tbody > tr > td.is-today.is-selected > button{
   color: white;
   background: #282F38;
-    border-radius: 5px;
+  border-radius: 5px;
   box-shadow: inset 0 1px 3px rgb(0 0 0)
 }
 
@@ -865,7 +865,7 @@ body > div.htDatepickerHolder > div > div > table > tbody > tr > td.is-selected,
 .is-selected .pika-button {
   color: white;
   background: #282F38;
-    border-radius: 5px;
+  border-radius: 5px;
   box-shadow: inset 0 1px 3px rgb(0 0 0)
 }
 
@@ -888,23 +888,23 @@ body > div.htDatepickerHolder > div > div > table > tbody > tr > td.is-today > b
 
 body > div.datepicker.datepicker-dropdown.dropdown-menu.datepicker-orient-left.datepicker-orient-top > div.datepicker-days > table > tbody > tr > td.active.day {
   background: #282F38;
-    color: white;
+  color: white;
   
 }
 
 .datepicker table tr td.day:hover, 
 .datepicker table tr td.focused {
   color: #000;
-    background: rgba(0,255,213,1);
+  background: rgba(0,255,213,1);
   cursor: pointer;
 }
 
 #print_log {
-border-color: white;
+  border-color: white;
 }
 
 #logText, #logTextFull {
-margin-top: 5px;
+  margin-top: 5px;
 }
 
 .append_table {
@@ -923,14 +923,14 @@ margin-top: 5px;
 
 
 span#progress_bar-title.progress-text {
-color: white; 
-font-size: 13px; 
-font-weight: normal;
+  color: white; 
+  font-size: 13px; 
+  font-weight: normal;
 }
 
 div#progress_bar.progress-bar {
-font-size:13px; 
-line-height: 30px;
+  font-size:13px; 
+  line-height: 30px;
 }
 
 .progress {
@@ -950,18 +950,18 @@ border-color: white;
 }
 
 #mst_cluster_reset i.fas.fa-rotate {
-position: relative; 
-left: -6px;
-top: -3px;
+  position: relative; 
+  left: -6px;
+  top: -3px;
 }
 
 button#mst_cluster_reset.btn.btn-default.action-button.shiny-bound-input {
-height: 27px; 
-width: 27px; 
-position: relative; 
-left: -5px;
-top: -3px;
-border: 1px solid white;
+  height: 27px; 
+  width: 27px; 
+  position: relative; 
+  left: -5px;
+  top: -3px;
+  border: 1px solid white;
 }
 
 .mat-switch-mst-mult {
@@ -1004,9 +1004,9 @@ button#create_tree {
 }
 
 button#create_tree:hover {
-background: #3c8c56 !important; 
+  background: #3c8c56 !important; 
   border: none;
-box-shadow: 0px 0px 20px 15px rgba(40, 47, 56, 1);
+  box-shadow: 0px 0px 20px 15px rgba(40, 47, 56, 1);
 }
 
 #button-wrapper {
@@ -1040,37 +1040,37 @@ box-shadow: 0px 0px 20px 15px rgba(40, 47, 56, 1);
 }
 
 button#mst_general_menu {
-height: 27px; 
-width: 27px; 
-background: #20E6E5; 
+  height: 27px; 
+  width: 27px; 
+  background: #20E6E5; 
   color: #000000; 
   border-radius: 5px; 
-margin-top: 2px;
+  margin-top: 2px;
 }
 
 button#mst_analysis_menu {
-height: 27px; 
-width: 27px; 
-background: #20E6E5; 
+  height: 27px; 
+  width: 27px; 
+  background: #20E6E5; 
   color: #000000; 
   border-radius: 5px; 
-margin-top: -17px;
-position: relative;
-top: -10px;
+  margin-top: -17px;
+  position: relative;
+  top: -10px;
 }
 
 button#mst_node_menu {
-height: 34px; 
-background: #20E6E5; 
+  height: 34px; 
+  background: #20E6E5; 
   color: #000000; 
   border-radius: 5px; 
-margin-top: 10px;
-margin-bottom: -1px;
+  margin-top: 10px;
+  margin-bottom: -1px;
 }
 
 button#mst_edge_menu {
-height: 34px; 
-background: #20E6E5; 
+  height: 34px; 
+  background: #20E6E5; 
   color: #000000; 
   border-radius: 5px;
 }
@@ -3007,10 +3007,10 @@ background: linear-gradient(to right, #F7FCFD 0%, #F7FCFD 11.1111%, #E0ECF4 11.1
 }
 
 #mst_date_general_select .form-control {
-height: 28px; 
-position: relative; 
-right: -22px;
-margin-top: 7px;
+  height: 28px; 
+  position: relative; 
+  right: -22px;
+  margin-top: 7px;
 }
 
 #mst_operator_general_select {
@@ -3056,13 +3056,13 @@ button#download_report_bttn {
 }
 
 button#download_resistance_profile_bttn {
-    background: #282F38;
-    color: #ffffff;
-    border: 1px solid white;
-    transition: border-color 0.3s ease;
-    opacity: 1;
-    font-size: 15px;
-    margin-top: 10px;
+  background: #282F38;
+  Color: #ffffff;
+  border: 1px solid white;
+  transition: border-color 0.3s ease;
+  opacity: 1;
+  font-size: 15px;
+  margin-top: 10px;
 }
 
 .dataTables_wrapper.no-footer .dataTables_scrollBody {
diff --git a/www/head.css b/www/head.css
index 06bfdad..2359336 100644
--- a/www/head.css
+++ b/www/head.css
@@ -45,10 +45,22 @@
 }
 
 /* Style sequence display*/
-  .base-a { color: black; text-shadow: 0px 0px 4px red; }
-.base-t { color: black; text-shadow: 0px 0px 4px green; }
-.base-g { color: black; text-shadow: 0px 0px 4px blue; }
-.base-c { color: black; text-shadow: 0px 0px 4px orange; }
+.base-a { 
+  color: black; 
+  text-shadow: 0px 0px 4px red; 
+}
+.base-t { 
+  color: black; 
+  text-shadow: 0px 0px 4px green; 
+}
+.base-g { 
+  color: black; 
+  text-shadow: 0px 0px 4px blue; 
+}
+.base-c { 
+  color: black; 
+  text-shadow: 0px 0px 4px orange; 
+}
 
 .sequence { 
   font-family: monospace; 
@@ -58,10 +70,15 @@
   right: 160px;
 }
 
-.clipboard-button { margin-left: 10px; cursor: pointer; border: none; background: none;}
+.clipboard-button { 
+  margin-left: 10px; 
+  cursor: pointer; 
+  border: none; 
+  background: none;
+}
 
 #loci_sequences {
-color: white;
+  color: white;
 }
 
 /* Scrollbar Styling */
@@ -167,10 +184,11 @@ div#gs_profile_table::-webkit-scrollbar-thumb,
 }
 
 /* Other */
-  #currentTime {
+
+#currentTime {
   padding: 50px;
-position: relative;
-top: 15px;
+  position: relative;
+  top: 15px;
 }
 
 #statustext {

From 1b9d8896c034ca8778235330084b1f0e5cf8a9d5 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Mon, 19 Aug 2024 15:17:40 +0200
Subject: [PATCH 60/75] Changed truncated hash display

---
 App.R | 103 ++++++++++++++++++++++++++++------------------------------
 1 file changed, 49 insertions(+), 54 deletions(-)

diff --git a/App.R b/App.R
index a4b4368..a5b8c99 100644
--- a/App.R
+++ b/App.R
@@ -5749,6 +5749,13 @@ server <- function(input, output, session) {
     }
   }
   
+  # Truncate hashes
+  truncHash <- function(hash) {
+    if(!is.na(hash)) {
+      paste0(str_sub(hash, 1, 4), "...", str_sub(hash, nchar(hash) - 3, nchar(hash))) 
+    } else {NA}
+  }
+  
   # Function to check for duplicate isolate IDs for multi typing start
   dupl_mult_id <- reactive({
     req(Typing$multi_sel_table)
@@ -5916,14 +5923,14 @@ server <- function(input, output, session) {
           DB$available <- gsub("_", " ", basename(dir_ls(DB$database))) # List of local schemes available
         }
         
-      } else if (DB$select_new == TRUE) {
-        DB$database <- file.path(DB$new_database, "Database")
+      } else if (DB$select_new ==  TRUE) {
+        DB$database <- paste0(DB$new_database, "/Database")
         
       }
     } else {
-      if(!is.null(DB$last_db) & file.exists(file.path(getwd(), "execute/last_db.rds"))) {
+      if(!is.null(DB$last_db) & file.exists(paste0(getwd(), "/execute/last_db.rds"))) {
         
-        DB$database <- readRDS(file.path(getwd(), "execute/last_db.rds")) 
+        DB$database <- readRDS(paste0(getwd(), "/execute/last_db.rds"))
         
         if(dir_exists(DB$database)) {
           DB$exist <- (length(dir_ls(DB$database)) == 0)  # Logical any local database present
@@ -6407,7 +6414,7 @@ server <- function(input, output, session) {
     
     # Load app elements based on database availability and missing value presence
     if(!is.null(DB$select_new)) {
-      if(DB$select_new & (file.path(DB$new_database, "Database") %in% dir_ls(DB$new_database))) {
+      if(DB$select_new & (paste0(DB$new_database, "/Database") %in% dir_ls(DB$new_database))) {
         
         log_print("Directory already contains a database")
         
@@ -6429,6 +6436,7 @@ server <- function(input, output, session) {
         DB$meta <- NULL
         DB$meta_true <- NULL
         DB$allelic_profile <- NULL
+        DB$allelic_profile_trunc <- NULL
         DB$allelic_profile_true <- NULL
         
         # null Distance matrix, entry table and plots
@@ -6578,6 +6586,7 @@ server <- function(input, output, session) {
         DB$meta <- NULL
         DB$meta_true <- NULL
         DB$allelic_profile <- NULL
+        DB$allelic_profile_trunc <- NULL
         DB$allelic_profile_true <- NULL
         DB$scheme <- input$scheme_db
         
@@ -7042,6 +7051,7 @@ server <- function(input, output, session) {
                 DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
                 DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
                 DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+                DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
                 DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
                 
                 # Null pipe 
@@ -7968,8 +7978,13 @@ server <- function(input, output, session) {
                         if (length(input$compare_select) > 0) {
                           if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
                             output$db_entries <- renderRHandsontable({
+                              
+                              entry_data <- DB$data %>%
+                                select(1:(13 + nrow(DB$cust_var))) %>%
+                                add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                              
                               rhandsontable(
-                                select(DB$data, 1:(13 + nrow(DB$cust_var)), input$compare_select),
+                                entry_data,
                                 col_highlight = diff_allele() - 1,
                                 dup_names_high = duplicated_names() - 1,
                                 dup_ids_high = duplicated_ids() - 1,
@@ -7983,18 +7998,7 @@ server <- function(input, output, session) {
                                 hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
                                         valign = "htMiddle",
                                         halign = "htCenter",
-                                        readOnly = TRUE,
-                                        renderer = htmlwidgets::JS(
-                                          "function(instance, td, row, col, prop, value, cellProperties) {
-                                            if (value.length > 8) {
-                                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                                            }
-                                            td.innerHTML = value;
-                                            td.style.textAlign = 'center';
-                                            return td;
-                                           }"
-                                          )
-                                        ) %>%
+                                        readOnly = TRUE) %>%
                                 hot_col(1, 
                                         valign = "htMiddle",
                                         halign = "htCenter") %>%
@@ -8280,8 +8284,13 @@ server <- function(input, output, session) {
                         if (length(input$compare_select) > 0) {
                           if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
                             output$db_entries <- renderRHandsontable({
+                              
+                              entry_data <- DB$data %>%
+                                select(1:(13 + nrow(DB$cust_var))) %>%
+                                add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                              
                               rhandsontable(
-                                select(DB$data, 1:(13 + nrow(DB$cust_var)), input$compare_select),
+                                entry_data,
                                 col_highlight = diff_allele() - 1,
                                 rowHeaders = NULL,
                                 height = table_height(),
@@ -8296,17 +8305,7 @@ server <- function(input, output, session) {
                                 hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
                                         readOnly = TRUE, 
                                         valign = "htMiddle",
-                                        halign = "htCenter",
-                                        renderer = htmlwidgets::JS(
-                                          "function(instance, td, row, col, prop, value, cellProperties) {
-                                            if (value.length > 8) {
-                                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                                            }
-                                            td.innerHTML = value;
-                                            td.style.textAlign = 'center';
-                                            return td;
-                                           }")
-                                        ) %>%
+                                        halign = "htCenter") %>%
                                 hot_col(3:(12 + nrow(DB$cust_var)), 
                                         valign = "htMiddle",
                                         halign = "htLeft") %>%
@@ -8626,6 +8625,7 @@ server <- function(input, output, session) {
                           )
                         )
                       } else if((DB$change == TRUE) | !identical(get.entry.table.meta(), select(DB$meta, -13))) {
+                        
                         if(!is.null(input$db_entries)) {
                           fluidRow(
                             column(
@@ -9220,6 +9220,7 @@ server <- function(input, output, session) {
                 DB$meta_gs <- NULL
                 DB$meta_true <- NULL
                 DB$allelic_profile <- NULL
+                DB$allelic_profile_trunc <- NULL
                 DB$allelic_profile_true <- NULL
                 
                 # Render menu without missing values tab
@@ -10014,6 +10015,7 @@ server <- function(input, output, session) {
     DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
     DB$deleted_entries <- character(0)
     
@@ -10118,8 +10120,13 @@ server <- function(input, output, session) {
           if (length(input$compare_select) > 0) {
             if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
               output$db_entries <- renderRHandsontable({
+                
+                entry_data <- DB$data %>%
+                  select(1:(13 + nrow(DB$cust_var))) %>%
+                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                
                 rhandsontable(
-                  select(DB$data, 1:(13 + nrow(DB$cust_var)), input$compare_select),
+                  entry_data,
                   col_highlight = diff_allele() - 1,
                   dup_names_high = duplicated_names() - 1,
                   dup_ids_high = duplicated_ids() - 1,
@@ -10133,17 +10140,7 @@ server <- function(input, output, session) {
                   hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
                           valign = "htMiddle",
                           halign = "htCenter",
-                          readOnly = TRUE,
-                          renderer = htmlwidgets::JS(
-                            "function(instance, td, row, col, prop, value, cellProperties) {
-                                            if (value.length > 8) {
-                                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                                            }
-                                            td.innerHTML = value;
-                                            td.style.textAlign = 'center';
-                                            return td;
-                                           }")
-                          ) %>%
+                          readOnly = TRUE) %>%
                   hot_col(1, 
                           valign = "htMiddle",
                           halign = "htCenter") %>%
@@ -10429,8 +10426,13 @@ server <- function(input, output, session) {
           if (length(input$compare_select) > 0) {
             if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
               output$db_entries <- renderRHandsontable({
+                
+                entry_data <- DB$data %>%
+                  select(1:(13 + nrow(DB$cust_var))) %>%
+                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                
                 rhandsontable(
-                  select(DB$data, 1:(13 + nrow(DB$cust_var)), input$compare_select),
+                  entry_data,
                   col_highlight = diff_allele() - 1,
                   rowHeaders = NULL,
                   height = table_height(),
@@ -10445,17 +10447,7 @@ server <- function(input, output, session) {
                   hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
                           readOnly = TRUE, 
                           valign = "htMiddle",
-                          halign = "htCenter",
-                          renderer = htmlwidgets::JS(
-                            "function(instance, td, row, col, prop, value, cellProperties) {
-                                            if (value.length > 8) {
-                                              value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                                            }
-                                            td.innerHTML = value;
-                                            td.style.textAlign = 'center';
-                                            return td;
-                                           }")
-                          ) %>%
+                          halign = "htCenter") %>%
                   hot_col(3:(12 + nrow(DB$cust_var)), 
                           valign = "htMiddle",
                           halign = "htLeft") %>%
@@ -10896,6 +10888,7 @@ server <- function(input, output, session) {
     DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
   })
   
@@ -11122,6 +11115,7 @@ server <- function(input, output, session) {
     DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
     DB$deleted_entries <- character(0)
     
@@ -11242,6 +11236,7 @@ server <- function(input, output, session) {
     DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
     DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
     DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
     DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
     
     # User feedback

From 4886c7c887ea01335751ee1ef878592674344b5e Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Mon, 19 Aug 2024 15:51:03 +0200
Subject: [PATCH 61/75] Small fixes for entry table

---
 App.R        | 54 ++++++++++++++++++++++++----------------------------
 www/body.css |  9 ++++++++-
 2 files changed, 33 insertions(+), 30 deletions(-)

diff --git a/App.R b/App.R
index a5b8c99..05028db 100644
--- a/App.R
+++ b/App.R
@@ -5563,13 +5563,13 @@ server <- function(input, output, session) {
     varying_columns <- c()
     
     for (col in 1:ncol(dataframe)) {
-      if(class(dataframe[, col]) == "integer") {
+      #if(class(dataframe[, col]) == "integer") {
         unique_values <- unique(dataframe[, col])
         
         if (length(unique_values) > 1) {
           varying_columns <- c(varying_columns, col)
         }
-      }
+      #}
     }
     
     return(varying_columns)
@@ -5794,7 +5794,7 @@ server <- function(input, output, session) {
   
   diff_allele <- reactive({
     if (!is.null(DB$data) & !is.null(input$compare_select) & !is.null(DB$cust_var)) {
-      var_alleles(select(DB$data, input$compare_select)) + (12 + nrow(DB$cust_var))
+      var_alleles(select(DB$data, input$compare_select)) + (13 + nrow(DB$cust_var))
     }
   })
   
@@ -7896,7 +7896,7 @@ server <- function(input, output, session) {
                               hot_col(3, readOnly = TRUE) %>%
                               hot_col(c(1, 5, 10, 11, 12, 13),
                                       readOnly = TRUE) %>%
-                              hot_col(3:(12 + nrow(DB$cust_var)), 
+                              hot_col(3:(13 + nrow(DB$cust_var)), 
                                       valign = "htMiddle",
                                       halign = "htLeft") %>%
                               hot_col(3, validator = "
@@ -7995,7 +7995,7 @@ server <- function(input, output, session) {
                                 highlightRow = TRUE,
                                 contextMenu = FALSE
                               )  %>%
-                                hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
+                                hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
                                         valign = "htMiddle",
                                         halign = "htCenter",
                                         readOnly = TRUE) %>%
@@ -8039,7 +8039,7 @@ server <- function(input, output, session) {
                                     }
                                   }
                                 ") %>%
-                                hot_col(3:(12 + nrow(DB$cust_var)), 
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
                                         valign = "htMiddle",
                                         halign = "htLeft") %>%
                                 hot_col(8, type = "dropdown", source = country_names) %>%
@@ -8162,7 +8162,7 @@ server <- function(input, output, session) {
                                 hot_col(3, readOnly = TRUE) %>%
                                 hot_col(c(1, 5, 10, 11, 12, 13),
                                         readOnly = TRUE) %>%
-                                hot_col(3:(12 + nrow(DB$cust_var)), 
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
                                         valign = "htMiddle",
                                         halign = "htLeft") %>%
                                 hot_col(3, validator = "
@@ -8302,11 +8302,11 @@ server <- function(input, output, session) {
                                 highlightCol = TRUE, 
                                 highlightRow = TRUE
                               ) %>%
-                                hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
+                                hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
                                         readOnly = TRUE, 
                                         valign = "htMiddle",
                                         halign = "htCenter") %>%
-                                hot_col(3:(12 + nrow(DB$cust_var)), 
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
                                         valign = "htMiddle",
                                         halign = "htLeft") %>%
                                 hot_col(3, readOnly = TRUE) %>%
@@ -8522,7 +8522,7 @@ server <- function(input, output, session) {
                                     Shiny.setInputValue('invalid_date', true);
                                   }
                                 }") %>%
-                                hot_col(3:(12 + nrow(DB$cust_var)), 
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
                                         valign = "htMiddle",
                                         halign = "htLeft") %>%
                                 hot_rows(fixedRowsTop = 0) %>%
@@ -9929,6 +9929,11 @@ server <- function(input, output, session) {
   observeEvent(input$reload_db, {
     log_print("Input reload_db")
     
+    dataa <<- DB$data
+    comp_sel <<- input$compare_select
+    cust_var <<- DB$cust_var
+    all_prof <<- DB$allelic_profile
+    
     if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
       show_toast(
         title = "Pending Multi Typing",
@@ -10038,7 +10043,7 @@ server <- function(input, output, session) {
                 hot_col(3, readOnly = TRUE) %>%
                 hot_col(c(1, 5, 10, 11, 12, 13),
                         readOnly = TRUE) %>%
-                hot_col(3:(12 + nrow(DB$cust_var)), 
+                hot_col(3:(13 + nrow(DB$cust_var)), 
                         valign = "htMiddle",
                         halign = "htLeft") %>%
                 hot_col(3, validator = "
@@ -10137,7 +10142,7 @@ server <- function(input, output, session) {
                   highlightRow = TRUE,
                   contextMenu = FALSE
                 )  %>%
-                  hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
+                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
                           valign = "htMiddle",
                           halign = "htCenter",
                           readOnly = TRUE) %>%
@@ -10147,7 +10152,7 @@ server <- function(input, output, session) {
                   hot_col(3, readOnly = TRUE) %>%
                   hot_col(c(1, 5, 10, 11, 12, 13),
                           readOnly = TRUE) %>%
-                  hot_col(3:(12 + nrow(DB$cust_var)), 
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
                           valign = "htMiddle",
                           halign = "htLeft") %>%
                   hot_col(3, validator = "
@@ -10304,7 +10309,7 @@ server <- function(input, output, session) {
                   hot_col(3, readOnly = TRUE) %>%
                   hot_col(c(1, 5, 10, 11, 12, 13),
                           readOnly = TRUE) %>%
-                  hot_col(3:(12 + nrow(DB$cust_var)), 
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
                           valign = "htMiddle",
                           halign = "htLeft") %>%
                   hot_col(3, validator = "
@@ -10444,11 +10449,11 @@ server <- function(input, output, session) {
                   highlightCol = TRUE, 
                   highlightRow = TRUE
                 ) %>%
-                  hot_col((13 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
+                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
                           readOnly = TRUE, 
                           valign = "htMiddle",
                           halign = "htCenter") %>%
-                  hot_col(3:(12 + nrow(DB$cust_var)), 
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
                           valign = "htMiddle",
                           halign = "htLeft") %>%
                   hot_col(3, readOnly = TRUE) %>%
@@ -10664,7 +10669,7 @@ server <- function(input, output, session) {
                                     Shiny.setInputValue('invalid_date', true);
                                   }
                                 }") %>%
-                  hot_col(3:(12 + nrow(DB$cust_var)), 
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
                           valign = "htMiddle",
                           halign = "htLeft") %>%
                   hot_rows(fixedRowsTop = 0) %>%
@@ -10983,7 +10988,7 @@ server <- function(input, output, session) {
       }
       
       if (input$download_table_loci == FALSE) {
-        download_matrix <- select(download_matrix, 1:(12 + nrow(DB$cust_var)))
+        download_matrix <- select(download_matrix, 1:(13 + nrow(DB$cust_var)))
       } 
       
       write.csv(download_matrix, file, row.names=FALSE, quote=FALSE) 
@@ -11083,19 +11088,10 @@ server <- function(input, output, session) {
     
     # Ensure correct logical data type
     Data[["Typing"]][["Include"]] <- as.logical(Data[["Typing"]][["Include"]])
-    saveRDS(Data, paste0(
-      DB$database, "/",
-      gsub(" ", "_", DB$scheme),
-      "/Typing.rds"
-    ))
+    saveRDS(Data, file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
     
     # Load database from files  
-    Database <-
-      readRDS(paste0(
-        DB$database, "/",
-        gsub(" ", "_", DB$scheme),
-        "/Typing.rds"
-      ))
+    Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
     
     DB$data <- Database[["Typing"]]
     
diff --git a/www/body.css b/www/body.css
index 96c94e3..96b963f 100644
--- a/www/body.css
+++ b/www/body.css
@@ -34,10 +34,17 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
   background-color: #282F38 !important;
 }
 
-.handsontable .wtBorder .area .corner {
+.handsontable .wtBorder.area.corner {
   background-color: #20e6e5 !important;
 }
 
+/*.handsontable td.area:before,
+.handsontable .htBottom.fill.area.highlight
+.handsontable .wtBorder.area,
+.handsontable .wtBorder.corner {
+  background: #20e6e5 !important;
+}*/
+
 .tooltip-inner {
   white-space: normal;
   max-width: 800px; /* Adjust the width as needed */

From 0a03a715528021503e602bd2f9bd82f489f1b70b Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Mon, 19 Aug 2024 15:52:18 +0200
Subject: [PATCH 62/75] Minor corrections for last commit

---
 App.R | 17 +++++------------
 1 file changed, 5 insertions(+), 12 deletions(-)

diff --git a/App.R b/App.R
index 05028db..d2803dc 100644
--- a/App.R
+++ b/App.R
@@ -5563,13 +5563,11 @@ server <- function(input, output, session) {
     varying_columns <- c()
     
     for (col in 1:ncol(dataframe)) {
-      #if(class(dataframe[, col]) == "integer") {
-        unique_values <- unique(dataframe[, col])
-        
-        if (length(unique_values) > 1) {
-          varying_columns <- c(varying_columns, col)
-        }
-      #}
+      unique_values <- unique(dataframe[, col])
+      
+      if (length(unique_values) > 1) {
+        varying_columns <- c(varying_columns, col)
+      }
     }
     
     return(varying_columns)
@@ -9929,11 +9927,6 @@ server <- function(input, output, session) {
   observeEvent(input$reload_db, {
     log_print("Input reload_db")
     
-    dataa <<- DB$data
-    comp_sel <<- input$compare_select
-    cust_var <<- DB$cust_var
-    all_prof <<- DB$allelic_profile
-    
     if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
       show_toast(
         title = "Pending Multi Typing",

From 556c1a46014b1e11d84d3fea7147c776771bf20d Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Tue, 20 Aug 2024 13:49:17 +0200
Subject: [PATCH 63/75] Added hash truncation to entry table download; Minor
 Entry Browser UI changes

---
 App.R        | 170 ++++++++++++++++++++++++++++++++-------------------
 www/body.css |  11 +++-
 www/head.css |  22 +++----
 3 files changed, 128 insertions(+), 75 deletions(-)

diff --git a/App.R b/App.R
index d2803dc..e77a663 100644
--- a/App.R
+++ b/App.R
@@ -282,7 +282,93 @@ ui <- dashboardPage(
           column(1),
           column(
             width = 8,
-            uiOutput("db_entries_table")
+            uiOutput("db_entries_table"),
+            fluidRow(
+              column(
+                width = 3,
+                fluidRow(
+                  column(
+                    width = 3,
+                    div(
+                      class = "rectangle-blue" 
+                    )
+                  ),
+                  column(
+                    width = 7,
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px", " = included for analyses")
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 3,
+                fluidRow(
+                  column(
+                    width = 3,
+                    div(
+                      class = "rectangle-orange" 
+                    )
+                  ),
+                  column(
+                    width = 7,
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -45px", " =  duplicated assembly name")
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 3,
+                fluidRow(
+                  column(
+                    width = 3,
+                    div(
+                      class = "rectangle-red" 
+                    )
+                  ),
+                  column(
+                    width = 7,
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -75px", " =  ≥ 5% of loci missing")
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 3,
+                fluidRow(
+                  column(
+                    width = 3,
+                    div(
+                      class = "rectangle-green" 
+                    )
+                  ),
+                  column(
+                    width = 9,
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -105px", " =  locus contains multiple variants")
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            )
           ),
           column(
             width = 3,
@@ -8930,9 +9016,8 @@ server <- function(input, output, session) {
                         ),
                         hr(),
                         fluidRow(
-                          column(2),
                           column(
-                            width = 10,
+                            width = 8,
                             align = "left",
                             br(),
                             div(
@@ -8953,12 +9038,19 @@ server <- function(input, output, session) {
                                 right = TRUE
                               )
                             ),
+                            div(
+                              class = "mat-switch-db",
+                              materialSwitch(
+                                "download_table_hashes",
+                                h5(p("Truncate Hashes"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            ),
                             br(),
-                          )
-                        ),
-                        fluidRow(
+                          ),
                           column(
-                            width = 12,
+                            width = 4,
                             align = "center",
                             downloadBttn(
                               "download_entry_table",
@@ -8969,59 +9061,6 @@ server <- function(input, output, session) {
                               color = "primary"
                             )
                           )
-                        ),
-                        br()
-                      )
-                    ),
-                    column(
-                      width = 12,
-                      fluidRow(
-                        column(
-                          width = 2,
-                          div(
-                            class = "rectangle-blue" 
-                          ),
-                          div(
-                            class = "rectangle-orange" 
-                          ),
-                          div(
-                            class = "rectangle-red" 
-                          ),
-                          div(
-                            class = "rectangle-green" 
-                          )
-                        ),
-                        column(
-                          width = 10,
-                          align = "left",
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -12px", " = included for analyses")
-                              )
-                            )
-                          ),
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -13px", " =  duplicated name/ID")
-                              )
-                            )
-                          ),
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -14px", " =  ≥ 5% of loci missing")
-                              )
-                            )
-                          ),
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -15px", " =  locus contains multiple variants")
-                              )
-                            )
-                          ),
                         )
                       )
                     )
@@ -10974,7 +11013,13 @@ server <- function(input, output, session) {
       paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")
     },
     content = function(file) {
-      download_matrix <- hot_to_r(input$db_entries)
+      download_matrix <<- hot_to_r(input$db_entries)
+      
+      if(input$download_table_hashes == TRUE) {
+        included_loci <<- colnames(select(download_matrix, -(1:(13 + nrow(DB$cust_var)))))
+        full_hashes <<- DB$allelic_profile[included_loci]
+        download_matrix[included_loci] <- full_hashes
+      }
       
       if (input$download_table_include == TRUE) {
         download_matrix <- download_matrix[which(download_matrix$Include == TRUE),]
@@ -11066,7 +11111,8 @@ server <- function(input, output, session) {
     
     Data[["Typing"]] <- select(Data[["Typing"]], -(1:(13 + length(cust_vars_pre))))
     
-    meta_hot <- hot_to_r(input$db_entries)
+    meta_hot <- hot_to_r(input$db_entries) %>%
+      select(1:(13 + nrow(DB$cust_var))) 
     
     if(length(DB$deleted_entries > 0)) {
       
diff --git a/www/body.css b/www/body.css
index 96b963f..976d7a3 100644
--- a/www/body.css
+++ b/www/body.css
@@ -776,7 +776,7 @@ button#download_distmatrix_bttn {
   border: 1px solid white;
   position: absolute;
   top: -50px;
-  transition: border-color 0.3s ease; /* Smooth transition for border color */
+  transition: border-color 0.3s ease; 
 }
 
 button#download_entry_table_bttn {
@@ -785,6 +785,13 @@ button#download_entry_table_bttn {
   color: #ffffff;
   border: 1px solid white;
   transition: border-color 0.3s ease; 
+  margin-top: 55px;
+}
+
+#download_entry_table_bttn .fas .fa-download,
+#download_entry_table_bttn > i {
+  position: relative;
+  top: 1px;
 }
 
 button#download_schemeinfo_bttn {
@@ -857,7 +864,7 @@ button#edit_button.btn.btn-default.action-button.shiny-bound-input {
 }
 
 #multi_typing_results .mult_res_sel .selectize-input.items.full.has-options.has-items {
-  width: auto;
+  width: -webkit-fill-available;
 }
 
 body > div.htDatepickerHolder > div > div > table > tbody > tr > td.is-today.is-selected > button{
diff --git a/www/head.css b/www/head.css
index 2359336..64d296b 100644
--- a/www/head.css
+++ b/www/head.css
@@ -1,27 +1,27 @@
 /* Entry table legend */
 .rectangle-orange {
-  width: 75px;
-  height: 23px;
+  width: 50px;
+  height: 20px;
   margin-top: 10px;
-  margin-left: 10px;
+  margin-left: -40px;
   border: 1px solid #BCBCBC;
   background-color: #DEB200;
 }
 
 .rectangle-green {
-  width: 75px;
-  height: 23px;
+  width: 50px;
+  height: 20px;
   margin-top: 10px;
-  margin-left: 10px;
+  margin-left: -100px;
   border: 1px solid #BCBCBC;
   background-color: #74BC8B;
 }
 
 .rectangle-red {
-  width: 75px;
-  height: 23px;
+  width: 50px;
+  height: 20px;
   margin-top: 10px;
-  margin-left: 10px;
+  margin-left: -70px;
   border: 1px solid #BCBCBC;
   background-color: #FF7334;
 }
@@ -36,8 +36,8 @@
 }
 
 .rectangle-blue {
-  width: 75px;
-  height: 23px;
+  width: 50px;
+  height: 20px;
   margin-top: 10px;
   margin-left: 10px;
   border: 1px solid #BCBCBC;

From d418e37fe70249ba7018ef52ab8de5843183b660 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Tue, 20 Aug 2024 14:16:15 +0200
Subject: [PATCH 64/75] Minor changes in MST Cluster scale default value;
 Deleting entries button UI

---
 App.R        | 44 +++++++++++++++++++++++++++++++++++---------
 www/body.css | 15 +++++----------
 2 files changed, 40 insertions(+), 19 deletions(-)

diff --git a/App.R b/App.R
index e77a663..1de9ff7 100644
--- a/App.R
+++ b/App.R
@@ -283,6 +283,7 @@ ui <- dashboardPage(
           column(
             width = 8,
             uiOutput("db_entries_table"),
+            br(),
             fluidRow(
               column(
                 width = 3,
@@ -1511,7 +1512,7 @@ ui <- dashboardPage(
                           selectInput(
                             "mst_cluster_col_scale",
                             label = h5("Color Scale", style = "color:white; margin-bottom: 0px;"),
-                            choices = c("Viridis", "Rainbow"),
+                            choices = c("Rainbow", "Viridis"),
                             width = "150px"
                           )
                         )
@@ -11189,12 +11190,25 @@ server <- function(input, output, session) {
       if( (length(input$select_delete) - nrow(DB$data) ) == 0) {
         showModal(
           modalDialog(
-            paste0("Deleting will lead to removal of all entries and assemblies from local ", DB$scheme, " database. The data can not be recovered afterwards. Continue?"),
+            HTML(paste0("Deleting will lead to removal of <strong>ALL entries</strong> and assemblies from local ", DB$scheme, " database. The data can not be recovered afterwards. Continue?")),
             easyClose = TRUE,
             title = "Deleting Entries",
             footer = tagList(
-              modalButton("Cancel"),
-              actionButton("conf_delete_all", "Delete", class = "btn btn-danger")
+              fluidRow(
+                column(6),
+                column(
+                  width = 4,
+                  modalButton("Cancel"),
+                ),
+                column(
+                  width = 2,
+                  div(
+                    class = "danger-button",
+                    actionButton("conf_delete_all", "Delete")
+                  )
+                )
+              )
+             
             )
           )
         )
@@ -11208,11 +11222,23 @@ server <- function(input, output, session) {
             fade = TRUE,
             easyClose = TRUE,
             footer = tagList(
-              modalButton("Cancel"),
-              actionButton(
-                "conf_delete", 
-                "Delete", 
-                class = "btn btn-danger")
+              fluidRow(
+                column(6),
+                column(
+                  width = 4,
+                  modalButton("Cancel")
+                ),
+                column(
+                  width = 2,
+                  div(
+                    class = "danger-button",
+                    actionButton(
+                      "conf_delete", 
+                      "Delete"
+                    )
+                  )
+                )
+              )
             )
           )
         )
diff --git a/www/body.css b/www/body.css
index 976d7a3..ef35f62 100644
--- a/www/body.css
+++ b/www/body.css
@@ -38,12 +38,11 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
   background-color: #20e6e5 !important;
 }
 
-/*.handsontable td.area:before,
-.handsontable .htBottom.fill.area.highlight
-.handsontable .wtBorder.area,
-.handsontable .wtBorder.corner {
-  background: #20e6e5 !important;
-}*/
+.danger-button .btn-default:hover {
+  background-color: #ff5964 !important;
+  border-color: #ff5964 !important;
+  color: white !important;
+}
 
 .tooltip-inner {
   white-space: normal;
@@ -68,10 +67,6 @@ body > div.swal2-container.swal2-bottom-end.swal2-backdrop-show {
   border-color: white;  
 }
 
-#conf_delete .btn-default:hover {
-  background-color: #FF5964 !important;
-}
-
 .datepicker table tr td.active:active, .datepicker table tr td.active.active, .datepicker table tr td.active.highlighted:active, .datepicker table tr td.active.highlighted.active {
   color: #000000;
   background-color: #20E6E5;  

From 4f2f27f756103e6c97bde82d488b776e71b2dad9 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Tue, 20 Aug 2024 14:58:15 +0200
Subject: [PATCH 65/75] Changes in download status UI; Manage schemes
 functionality

---
 App.R        | 480 ++++++++++++++++++++++++++++++++++-----------------
 www/body.css |  12 +-
 2 files changed, 330 insertions(+), 162 deletions(-)

diff --git a/App.R b/App.R
index 1de9ff7..e836b2c 100644
--- a/App.R
+++ b/App.R
@@ -284,92 +284,6 @@ ui <- dashboardPage(
             width = 8,
             uiOutput("db_entries_table"),
             br(),
-            fluidRow(
-              column(
-                width = 3,
-                fluidRow(
-                  column(
-                    width = 3,
-                    div(
-                      class = "rectangle-blue" 
-                    )
-                  ),
-                  column(
-                    width = 7,
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px", " = included for analyses")
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 3,
-                fluidRow(
-                  column(
-                    width = 3,
-                    div(
-                      class = "rectangle-orange" 
-                    )
-                  ),
-                  column(
-                    width = 7,
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -45px", " =  duplicated assembly name")
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 3,
-                fluidRow(
-                  column(
-                    width = 3,
-                    div(
-                      class = "rectangle-red" 
-                    )
-                  ),
-                  column(
-                    width = 7,
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -75px", " =  ≥ 5% of loci missing")
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 3,
-                fluidRow(
-                  column(
-                    width = 3,
-                    div(
-                      class = "rectangle-green" 
-                    )
-                  ),
-                  column(
-                    width = 9,
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -105px", " =  locus contains multiple variants")
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            )
           ),
           column(
             width = 3,
@@ -551,51 +465,7 @@ ui <- dashboardPage(
             br(),
             br(),
             br(),
-            pickerInput(
-              inputId = "select_cgmlst",
-              label = NULL,
-              choices = list(
-                "Acinetobacter baumanii",
-                "Bacillus anthracis",
-                "Bordetella pertussis",
-                "Brucella melitensis",
-                "Brucella spp.",
-                "Burkholderia mallei (FLI)",
-                "Burkholderia mallei (RKI)",
-                "Burkholderia pseudomallei",
-                "Campylobacter jejuni/coli",
-                "Clostridioides difficile",
-                "Clostridium perfringens",
-                "Corynebacterium diphtheriae",
-                "Cronobacter sakazakii/malonaticus",
-                "Enterococcus faecalis",
-                "Enterococcus faecium",
-                "Escherichia coli",
-                "Francisella tularensis",
-                "Klebsiella oxytoca sensu lato",
-                "Klebsiella pneumoniae sensu lato",
-                "Legionella pneumophila",
-                "Listeria monocytogenes",
-                "Mycobacterium tuberculosis complex",
-                "Mycobacteroides abscessus",
-                "Mycoplasma gallisepticum",
-                "Paenibacillus larvae",
-                "Pseudomonas aeruginosa",
-                "Salmonella enterica",
-                "Serratia marcescens",
-                "Staphylococcus aureus",
-                "Staphylococcus capitis",
-                "Streptococcus pyogenes"
-              ),
-              width = "300px",
-              options = list(
-                `live-search` = TRUE,
-                `actions-box` = TRUE,
-                size = 10,
-                style = "background-color: white; border-radius: 5px;"
-              ),
-              multiple = FALSE
-            )
+            uiOutput("scheme_selector")
           ),
           column(
             width = 2,
@@ -615,8 +485,28 @@ ui <- dashboardPage(
               icon = icon("download")
             ),
             shinyjs::hidden(
-              div(id = "loading",
-                  HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
+              div(
+                id = "downloading",
+                HTML(
+                  paste0(
+                    "<span style='color: white; font-size: 15px; position: relative;top: -3px;'>", 
+                    "Downloading scheme",
+                    '<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white; margin-left: 15px; position: relative; top: 6px;"></i>'
+                  )
+                )
+              )
+            ),
+            shinyjs::hidden(
+              div(
+                id = "hashing",
+                HTML(
+                  paste0(
+                    "<span style='color: white; font-size: 15px; position: relative;top: -3px;'>", 
+                    "Hashing scheme",
+                    '<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white; margin-left: 15px; position: relative; top: 6px;"></i>'
+                  )
+                )
+              )
             )
           )
         ),
@@ -5951,15 +5841,15 @@ server <- function(input, output, session) {
                        block_db = FALSE, 
                        load_selected = TRUE,
                        no_na_switch = FALSE,
-                       first_look = FALSE) # reactive variables related to local database
+                       first_look = FALSE,
+                       status = "") # reactive variables related to local database
   
   Typing <- reactiveValues(table = data.frame(), 
                            single_path = data.frame(),
                            progress = 0, 
                            progress_format_start = 0, 
                            progress_format_end = 0,
-                           result_list = NULL,
-                           status = "") # reactive variables related to typing process
+                           result_list = NULL) # reactive variables related to typing process
   
   Screening <- reactiveValues(status = "idle",
                               picker_status = TRUE,
@@ -7948,12 +7838,190 @@ server <- function(input, output, session) {
                 output$db_entries_table <- renderUI({
                   if(!is.null(DB$data)) {
                     if(between(nrow(DB$data), 1, 30)) {
-                      rHandsontableOutput("db_entries")
+                      fluidRow(
+                        column(
+                          width = 12,
+                          rHandsontableOutput("db_entries")
+                        ),
+                        column(
+                          width = 3,
+                          fluidRow(
+                            column(
+                              width = 3,
+                              div(
+                                class = "rectangle-blue" 
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              p(
+                                HTML(
+                                  paste(
+                                    tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px", " = included for analyses")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        ),
+                        column(
+                          width = 3,
+                          fluidRow(
+                            column(
+                              width = 3,
+                              div(
+                                class = "rectangle-orange" 
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              p(
+                                HTML(
+                                  paste(
+                                    tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -45px", " =  duplicated assembly name")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        ),
+                        column(
+                          width = 3,
+                          fluidRow(
+                            column(
+                              width = 3,
+                              div(
+                                class = "rectangle-red" 
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              p(
+                                HTML(
+                                  paste(
+                                    tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -75px", " =  ≥ 5% of loci missing")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        ),
+                        column(
+                          width = 3,
+                          fluidRow(
+                            column(
+                              width = 3,
+                              div(
+                                class = "rectangle-green" 
+                              )
+                            ),
+                            column(
+                              width = 9,
+                              p(
+                                HTML(
+                                  paste(
+                                    tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -105px", " =  locus contains multiple variants")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
                     } else {
-                      addSpinner(
-                        rHandsontableOutput("db_entries"),
-                        spin = "dots",
-                        color = "#ffffff"
+                      fluidRow(
+                        column(
+                          width = 12,
+                          addSpinner(
+                            rHandsontableOutput("db_entries"),
+                            spin = "dots",
+                            color = "#ffffff"
+                          )
+                        ),
+                        column(
+                          width = 3,
+                          fluidRow(
+                            column(
+                              width = 3,
+                              div(
+                                class = "rectangle-blue" 
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              p(
+                                HTML(
+                                  paste(
+                                    tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px", " = included for analyses")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        ),
+                        column(
+                          width = 3,
+                          fluidRow(
+                            column(
+                              width = 3,
+                              div(
+                                class = "rectangle-orange" 
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              p(
+                                HTML(
+                                  paste(
+                                    tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -45px", " =  duplicated assembly name")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        ),
+                        column(
+                          width = 3,
+                          fluidRow(
+                            column(
+                              width = 3,
+                              div(
+                                class = "rectangle-red" 
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              p(
+                                HTML(
+                                  paste(
+                                    tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -75px", " =  ≥ 5% of loci missing")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        ),
+                        column(
+                          width = 3,
+                          fluidRow(
+                            column(
+                              width = 3,
+                              div(
+                                class = "rectangle-green" 
+                              )
+                            ),
+                            column(
+                              width = 9,
+                              p(
+                                HTML(
+                                  paste(
+                                    tags$span(style="color: white; font-size: 12px; position: relative; bottom: -10px; margin-left: -105px", " =  locus contains multiple variants")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
                       )
                     }
                   }
@@ -9565,6 +9633,106 @@ server <- function(input, output, session) {
   
   ### Conditional UI Elements rendering ----
   
+  # Scheme selector UI 
+  output$scheme_selector <- renderUI(
+    if(!is.null(DB$scheme)) {
+      pickerInput(
+        inputId = "select_cgmlst",
+        label = NULL,
+        choices = list(
+          "Acinetobacter baumanii",
+          "Bacillus anthracis",
+          "Bordetella pertussis",
+          "Brucella melitensis",
+          "Brucella spp.",
+          "Burkholderia mallei (FLI)",
+          "Burkholderia mallei (RKI)",
+          "Burkholderia pseudomallei",
+          "Campylobacter jejuni/coli",
+          "Clostridioides difficile",
+          "Clostridium perfringens",
+          "Corynebacterium diphtheriae",
+          "Cronobacter sakazakii/malonaticus",
+          "Enterococcus faecalis",
+          "Enterococcus faecium",
+          "Escherichia coli",
+          "Francisella tularensis",
+          "Klebsiella oxytoca sensu lato",
+          "Klebsiella pneumoniae sensu lato",
+          "Legionella pneumophila",
+          "Listeria monocytogenes",
+          "Mycobacterium tuberculosis complex",
+          "Mycobacteroides abscessus",
+          "Mycoplasma gallisepticum",
+          "Paenibacillus larvae",
+          "Pseudomonas aeruginosa",
+          "Salmonella enterica",
+          "Serratia marcescens",
+          "Staphylococcus aureus",
+          "Staphylococcus capitis",
+          "Streptococcus pyogenes"
+        ),
+        width = "300px",
+        selected = DB$scheme,
+        options = list(
+          `live-search` = TRUE,
+          `actions-box` = TRUE,
+          size = 10,
+          style = "background-color: white; border-radius: 5px;"
+        ),
+        multiple = FALSE
+      )
+    } else {
+      pickerInput(
+        inputId = "select_cgmlst",
+        label = NULL,
+        choices = list(
+          "Acinetobacter baumanii",
+          "Bacillus anthracis",
+          "Bordetella pertussis",
+          "Brucella melitensis",
+          "Brucella spp.",
+          "Burkholderia mallei (FLI)",
+          "Burkholderia mallei (RKI)",
+          "Burkholderia pseudomallei",
+          "Campylobacter jejuni/coli",
+          "Clostridioides difficile",
+          "Clostridium perfringens",
+          "Corynebacterium diphtheriae",
+          "Cronobacter sakazakii/malonaticus",
+          "Enterococcus faecalis",
+          "Enterococcus faecium",
+          "Escherichia coli",
+          "Francisella tularensis",
+          "Klebsiella oxytoca sensu lato",
+          "Klebsiella pneumoniae sensu lato",
+          "Legionella pneumophila",
+          "Listeria monocytogenes",
+          "Mycobacterium tuberculosis complex",
+          "Mycobacteroides abscessus",
+          "Mycoplasma gallisepticum",
+          "Paenibacillus larvae",
+          "Pseudomonas aeruginosa",
+          "Salmonella enterica",
+          "Serratia marcescens",
+          "Staphylococcus aureus",
+          "Staphylococcus capitis",
+          "Streptococcus pyogenes"
+        ),
+        width = "300px",
+        selected = NULL,
+        options = list(
+          `live-search` = TRUE,
+          `actions-box` = TRUE,
+          size = 10,
+          style = "background-color: white; border-radius: 5px;"
+        ),
+        multiple = FALSE
+      )
+    }
+  
+  )
+  
   # Contro custom variables table
   output$cust_var_select <- renderUI({
     if(nrow(DB$cust_var) > 5) {
@@ -11550,6 +11718,7 @@ server <- function(input, output, session) {
   ## Download cgMLST ----
   
   observe({
+    req(input$select_cgmlst)
     if (input$select_cgmlst == "Acinetobacter baumanii") {
       species <- "Abaumannii1907"
       Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
@@ -11743,22 +11912,10 @@ server <- function(input, output, session) {
     log_print(paste0("Started download of scheme for ", Scheme$folder_name))
     
     shinyjs::hide("download_cgMLST")
-    shinyjs::show("loading")
-    
-    output$statustext <- renderUI(
-      fluidRow(
-        tags$li(
-          class = "dropdown", 
-          tags$span(HTML(
-            paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                  "Status:&nbsp;&nbsp;&nbsp; <i>Downloading scheme...</i>")),
-            style = "color:white;")
-        )
-      )
-    )
+    shinyjs::show("downloading")
     
     show_toast(
-      title = "Download started",
+      title = paste("Downloading", input$select_cgmlst,  "scheme"),
       type = "success",
       position = "bottom-end",
       timer = 5000
@@ -11802,6 +11959,16 @@ server <- function(input, output, session) {
     )
     
     log_print("Hashing downloaded database")
+    shinyjs::show("hashing")
+    shinyjs::hide("downloading")
+    
+    show_toast(
+      title = paste("Hashing of", input$select_cgmlst,  "started"),
+      type = "success",
+      position = "bottom-end",
+      timer = 5000
+    )
+    
     # Hash temporary folder
     hash_database(file.path(DB$database, 
                             Scheme$folder_name, 
@@ -11913,7 +12080,7 @@ server <- function(input, output, session) {
     DB$exist <- length(dir_ls(DB$database)) == 0
     
     shinyjs::show("download_cgMLST")
-    shinyjs::hide("loading")
+    shinyjs::hide("hashing")
     
     output$statustext <- renderUI(
       fluidRow(
@@ -11957,6 +12124,7 @@ server <- function(input, output, session) {
   
   # Download Target Info (CSV Table)
   observe({
+    req(input$select_cgmlst)
     input$download_cgMLST
     
     scheme_overview <- read_html(Scheme$link_scheme) %>%
diff --git a/www/body.css b/www/body.css
index ef35f62..c3c3df1 100644
--- a/www/body.css
+++ b/www/body.css
@@ -606,12 +606,12 @@ i.far.fa-pen-to-square {
 
 /* Database */
   
-  #db_entries > div > div > div > div > table > tbody > tr > td,
-  #db_distancematrix > div > div > div > div > table > tbody > tr > td,
-  #table_missing_values > div > div > div > div > table > tbody > tr > td,
-  #multi_select_table > div > div > div > div > table > tbody > tr > td,
-  #multi_typing_result_table > div > div > div > div > table > tbody > tr > td,
-  #typing_result_table > div > div > div > div > table > tbody > tr > td {
+#db_entries > div > div > div > div > table > tbody > tr > td,
+#db_distancematrix > div > div > div > div > table > tbody > tr > td,
+#table_missing_values > div > div > div > div > table > tbody > tr > td,
+#multi_select_table > div > div > div > div > table > tbody > tr > td,
+#multi_typing_result_table > div > div > div > div > table > tbody > tr > td,
+#typing_result_table > div > div > div > div > table > tbody > tr > td {
   color: black !important;
 }
 

From fb822131e8433d95a3f6708037daa06a98117bc6 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Tue, 20 Aug 2024 15:27:34 +0200
Subject: [PATCH 66/75] Small fix in Gene Screening conditional UI

---
 App.R | 184 ++++++++++++++++++++++++++++++----------------------------
 1 file changed, 94 insertions(+), 90 deletions(-)

diff --git a/App.R b/App.R
index e836b2c..9f57ace 100644
--- a/App.R
+++ b/App.R
@@ -7843,6 +7843,7 @@ server <- function(input, output, session) {
                           width = 12,
                           rHandsontableOutput("db_entries")
                         ),
+                        br(),
                         column(
                           width = 3,
                           fluidRow(
@@ -7938,6 +7939,7 @@ server <- function(input, output, session) {
                             color = "#ffffff"
                           )
                         ),
+                        br(),
                         column(
                           width = 3,
                           fluidRow(
@@ -22866,110 +22868,114 @@ server <- function(input, output, session) {
   
   # Conditionally render table selectiom interface
   output$gs_table_selection <- renderUI({
-    req(DB$data, input$gs_view)
-    if(input$gs_view == "Table") {
-      fluidRow(
-        column(1),
-        column(
-          width = 10,
-          div(class = "loci_table",
-              dataTableOutput("gs_isolate_table"))
+    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
+      req(DB$data, input$gs_view)
+      if(input$gs_view == "Table") {
+        fluidRow(
+          column(1),
+          column(
+            width = 10,
+            div(class = "loci_table",
+                dataTableOutput("gs_isolate_table"))
+          )
         )
-      )
+      } else {NULL}
     } else {NULL}
   })
   
   # Resistance profile table output display
   output$gs_profile_display <- renderUI({
     req(DB$data)
-    if(!is.null(DB$meta_gs) & !is.null(input$gs_view)) {
-      if(input$gs_view == "Table") {
-        column(
-          width = 10,
-          hr(), 
-          fluidRow(
-            column(
-              width = 4,
-              p(
-                HTML(
-                  paste0("<span style='color: white; font-size: 18px'>", 
-                         "Gene Screening Results</br>",
-                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
-                         "Comprising genes for resistance, virulence, stress, etc.")
+    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
+      if(!is.null(DB$meta_gs) & !is.null(input$gs_view)) {
+        if(input$gs_view == "Table") {
+          column(
+            width = 10,
+            hr(), 
+            fluidRow(
+              column(
+                width = 4,
+                p(
+                  HTML(
+                    paste0("<span style='color: white; font-size: 18px'>", 
+                           "Gene Screening Results</br>",
+                           "<span style='color: white; font-size: 12px; font-style:italic'>", 
+                           "Comprising genes for resistance, virulence, stress, etc.")
+                  )
                 )
+              ),
+              column(
+                width = 4,
+                uiOutput("gs_download")
               )
             ),
-            column(
-              width = 4,
-              uiOutput("gs_download")
-            )
-          ),
-          br(),
-          uiOutput("gs_results_table")
-        )
-      } else {
-        column(
-          width = 10,
-          fluidRow(
-            column(
-              width = 4,
-              p(
-                HTML(
-                  paste0("<span style='color: white; font-size: 18px'>", 
-                         "Gene Screening Results</br>",
-                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
-                         "Comprising genes for resistance, virulence, stress, etc.")
+            br(),
+            uiOutput("gs_results_table")
+          )
+        } else {
+          column(
+            width = 10,
+            fluidRow(
+              column(
+                width = 4,
+                p(
+                  HTML(
+                    paste0("<span style='color: white; font-size: 18px'>", 
+                           "Gene Screening Results</br>",
+                           "<span style='color: white; font-size: 12px; font-style:italic'>", 
+                           "Comprising genes for resistance, virulence, stress, etc.")
+                  )
                 )
-              )
-            ),
-            column(
-              width = 4,
-              div(
-                class = "gs-picker",
-                pickerInput(
-                  "gs_profile_select",
-                  "",
-                  choices = list(
-                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
-                    },
-                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
-                    },
-                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
-                    }
-                  ),
-                  choicesOpt = list(
-                    disabled = c(
-                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
-                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
-                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
+              ),
+              column(
+                width = 4,
+                div(
+                  class = "gs-picker",
+                  pickerInput(
+                    "gs_profile_select",
+                    "",
+                    choices = list(
+                      Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
+                        as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
+                      } else {
+                        DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+                      },
+                      Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
+                        as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
+                      } else {
+                        DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
+                      },
+                      `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
+                        as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
+                      } else {
+                        DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
+                      }
+                    ),
+                    choicesOpt = list(
+                      disabled = c(
+                        rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
+                        rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
+                        rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
+                      )
+                    ),
+                    options = list(
+                      `live-search` = TRUE,
+                      size = 10,
+                      style = "background-color: white; border-radius: 5px;"
                     )
-                  ),
-                  options = list(
-                    `live-search` = TRUE,
-                    size = 10,
-                    style = "background-color: white; border-radius: 5px;"
                   )
                 )
+              ),
+              column(
+                width = 3,
+                uiOutput("gs_download")
               )
             ),
-            column(
-              width = 3,
-              uiOutput("gs_download")
-            )
-          ),
-          br(),
-          uiOutput("gs_results_table")
-        )
-      }
+            br(),
+            uiOutput("gs_results_table")
+          )
+        }
+      } else {NULL}
     } else {NULL}
   })
   
@@ -23128,7 +23134,6 @@ server <- function(input, output, session) {
   
   # Availablity feedback
   output$gene_screening_info <- renderUI({
-    req(DB$data)
     if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
       p(
         HTML(
@@ -23153,7 +23158,6 @@ server <- function(input, output, session) {
   })
   
   output$gene_resistance_info <- renderUI({
-    req(DB$data)
     if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
       p(
         HTML(

From f07f12ed7dc675a652bebf6f606069178ef154ff Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Tue, 20 Aug 2024 15:47:45 +0200
Subject: [PATCH 67/75] Type 2 clustering initial implementation

---
 App.R | 51731 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 25896 insertions(+), 25835 deletions(-)

diff --git a/App.R b/App.R
index d2803dc..0cd1d6b 100644
--- a/App.R
+++ b/App.R
@@ -1,25835 +1,25896 @@
-######## PhyloTrace #########
-
-# _______________________ ####
-# CRAN Packages
-library(shiny)
-library(R.utils)
-library(igraph)
-library(shinyWidgets)
-library(shinydashboard)
-library(dashboardthemes)
-library(ggplot2)
-library(ggnewscale)
-library(ggplotify) 
-library(ape)
-library(tidyverse)
-library(rlang)
-library(tidytree)
-library(shinyFiles)
-library(dplyr)
-library(downloader)
-library(rvest)
-library(rmarkdown)
-library(knitr)
-library(kableExtra)
-library(fs)
-library(data.table)
-library(zoo)
-library(ggnetwork)
-library(rhandsontable)
-library(visNetwork)
-library(proxy)
-library(phangorn)
-library(cowplot)
-library(viridis)
-library(RColorBrewer)
-library(bslib)
-library(bsicons)
-library(DT)
-library(shinyBS)
-library(openssl)
-library(logr)
-# Bioconductor Packages
-library(treeio)
-library(ggtree)
-library(ggtreeExtra)
-
-source(paste0(getwd(), "/www/resources.R"))
-
-options(ignore.negative.edge=TRUE)
-
-# User Interface ----
-
-ui <- dashboardPage(
-  
-  title = "PhyloTrace 1.5.0",
-  
-  # Title
-  dashboardHeader(
-    
-    title = span(
-      div(
-        class = "img_logo",
-        img(
-          src = "PhyloTrace.jpg", width = 190
-        )
-      )
-    ),
-    uiOutput("loaded_scheme"),
-    uiOutput("databasetext"),
-    uiOutput("statustext"),
-    tags$li(class = "dropdown", 
-            tags$span(id = "currentTime", style = "color:white; font-weight:bold;")),
-    disable = FALSE
-  ),
-  
-  ## Sidebar ----
-  dashboardSidebar(
-    tags$head(includeCSS("www/head.css")),
-    tags$style(includeCSS("www/body.css")),
-    tags$style(HTML(
-      "@keyframes pulsate {
-          0% { transform: scale(1); }
-          50% { transform: scale(1.1); }
-          100% { transform: scale(1); }
-        }
-        .pulsating-button {
-          animation: pulsate 1s ease infinite;
-        }
-        .pulsating-button:hover {
-          animation: none;
-        }")),
-    br(), br(),
-    sidebarMenu(
-      id = "tabs",
-      sidebarMenuOutput("menu"),
-      uiOutput("menu_sep2"),
-      conditionalPanel(
-        "input.tabs==='db_browse_entries'",
-        uiOutput("entrytable_sidebar")
-      ),
-      conditionalPanel(
-        "input.tabs==='db_distmatrix'",
-        uiOutput("distmatrix_sidebar")
-      ),
-      conditionalPanel(
-        "input.tabs==='db_missing_values'",
-        uiOutput("missing_values_sidebar")
-      ),
-      conditionalPanel(
-        "input.tabs==='typing'",
-        uiOutput("typing_sidebar")
-      ),
-      conditionalPanel(
-        "input.tabs==='visualization'",
-        uiOutput("visualization_sidebar")
-      ),
-      conditionalPanel(
-        "input.tabs==='gs_profile'",
-        uiOutput("screening_sidebar")
-      )
-    )
-  ),
-  
-  dashboardBody(
-    tags$head(tags$link(rel = "shortcut icon", href = "favicon.ico")),
-    shinyjs::useShinyjs(),
-    
-    shinyDashboardThemeDIY(
-      ### general
-      appFontFamily = "Liberation Sans",
-      appFontColor = "#000000",
-      primaryFontColor = "#ffffff",
-      infoFontColor = "rgb(0,0,0)",
-      successFontColor = "rgb(0,0,0)",
-      warningFontColor = "rgb(0,0,0)",
-      dangerFontColor = "rgb(0,0,0)",
-      bodyBackColor = cssGradientThreeColors(
-        direction = "down",
-        colorStart = "#282f38",
-        colorMiddle = "#384454",
-        colorEnd = "#495d78",
-        colorStartPos = 0,
-        colorMiddlePos = 50,
-        colorEndPos = 100
-      ),
-      
-      ### header
-      logoBackColor = "#282f38",
-      headerButtonBackColor = "#282f38",
-      headerButtonIconColor = "#18ece1",
-      headerButtonBackColorHover = "#282f38",
-      headerButtonIconColorHover = "#ffffff",
-      headerBackColor = "#282f38",
-      headerBoxShadowColor = "#aaaaaa",
-      headerBoxShadowSize = "0px 0px 0px",
-      
-      ### sidebar
-      sidebarBackColor = cssGradientThreeColors(
-        direction = "down",
-        colorStart = "#282f38",
-        colorMiddle = "#384454",
-        colorEnd = "#495d78",
-        colorStartPos = 0,
-        colorMiddlePos = 50,
-        colorEndPos = 100),
-      
-      sidebarPadding = 0,
-      sidebarMenuBackColor = "transparent",
-      sidebarMenuPadding = 0,
-      sidebarMenuBorderRadius = 0,
-      sidebarShadowRadius = "5px 5px 5px",
-      sidebarShadowColor = "#282f38",
-      sidebarUserTextColor = "#ffffff",
-      sidebarSearchBackColor = "rgb(55,72,80)",
-      sidebarSearchIconColor = "rgb(153,153,153)",
-      sidebarSearchBorderColor = "rgb(55,72,80)",
-      sidebarTabTextColor = "rgb(255,255,255)",
-      sidebarTabTextSize = 15,
-      sidebarTabBorderStyle = "none none solid none",
-      sidebarTabBorderColor = "rgb(35,106,135)",
-      sidebarTabBorderWidth = 0,
-      sidebarTabBackColorSelected = cssGradientThreeColors(
-        direction = "right",
-        colorStart = "rgba(44,222,235,1)",
-        colorMiddle = "rgba(44,222,235,1)",
-        colorEnd = "rgba(0,255,213,1)",
-        colorStartPos = 0,
-        colorMiddlePos = 30,
-        colorEndPos = 100
-      ),
-      sidebarTabTextColorSelected = "rgb(0,0,0)",
-      sidebarTabRadiusSelected = "0px 0px 0px 0px",
-      sidebarTabBackColorHover = cssGradientThreeColors(
-        direction = "right",
-        colorStart = "rgba(44,222,235,1)",
-        colorMiddle = "rgba(44,222,235,1)",
-        colorEnd = "rgba(0,255,213,1)",
-        colorStartPos = 0,
-        colorMiddlePos = 30,
-        colorEndPos = 100
-      ),
-      sidebarTabTextColorHover = "rgb(50,50,50)",
-      sidebarTabBorderStyleHover = "none none solid none",
-      sidebarTabBorderColorHover = "rgb(75,126,151)",
-      sidebarTabBorderWidthHover = 0,
-      sidebarTabRadiusHover = "0px 0px 0px 0px",
-      
-      ### boxes
-      boxBackColor = "#ffffff",
-      boxBorderRadius = 7,
-      boxShadowSize = "0px 0px 0px",
-      boxShadowColor = "#ffffff",
-      boxTitleSize = 20,
-      boxDefaultColor = "#00a65a",
-      boxPrimaryColor = "#ffffff",
-      boxInfoColor = "#00a65a",
-      boxSuccessColor = "#00a65a",
-      boxWarningColor = "#ffffff",
-      boxDangerColor = "#ffffff",
-      tabBoxTabColor = "#ffffff",
-      tabBoxTabTextSize = 14,
-      tabBoxTabTextColor = "rgb(0,0,0)",
-      tabBoxTabTextColorSelected = "rgb(0,0,0)",
-      tabBoxBackColor = "#ffffff",
-      tabBoxHighlightColor = "#ffffff",
-      tabBoxBorderRadius = 5,
-      
-      ### inputs
-      buttonBackColor = "#282F38",
-      buttonTextColor = "#ffffff",
-      buttonBorderColor = "#282F38",
-      buttonBorderRadius = 5,
-      buttonBackColorHover = cssGradientThreeColors(
-        direction = "right",
-        colorStart = "rgba(44,222,235,1)",
-        colorMiddle = "rgba(44,222,235,1)",
-        colorEnd = "rgba(0,255,213,1)",
-        colorStartPos = 0,
-        colorMiddlePos = 30,
-        colorEndPos = 100
-      ),
-      buttonTextColorHover = "#000000",
-      buttonBorderColorHover = "transparent",
-      textboxBackColor = "#ffffff",
-      textboxBorderColor = "#ffffff",
-      textboxBorderRadius = 5,
-      textboxBackColorSelect = "#ffffff",
-      textboxBorderColorSelect = "#000000",
-      
-      ### tables
-      tableBackColor = "rgb(255,255,255)",
-      tableBorderColor = "rgb(240,240,240)",
-      tableBorderTopSize = 1,
-      tableBorderRowSize = 1
-    ),
-    
-    uiOutput("start_message"),
-    
-    tabItems(
-      
-      ## Tab Database ----
-      
-      ### Tab Browse Entries ----
-      
-      tabItem(
-        tabName = "db_browse_entries",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Browse Local Database"), style = "color:white")
-          )
-        ),
-        hr(), br(),
-        br(),
-        br(),
-        uiOutput("no_scheme_entries"),
-        uiOutput("db_no_entries"),
-        uiOutput("entry_table_controls"),
-        br(), br(),
-        fluidRow(
-          column(1),
-          column(
-            width = 8,
-            uiOutput("db_entries_table")
-          ),
-          column(
-            width = 3,
-            align = "left",
-            uiOutput("delete_box"),
-            uiOutput("compare_allele_box"),
-            uiOutput("download_entries"),
-            br(), br(), br(), br(), br(), br(), br(), br(),
-            br(), br(), br(), br(), br(), br(), br()
-          )
-        ),
-        br()
-      ),
-      
-      ### Tab Scheme Info  ----  
-      
-      tabItem(
-        tabName = "db_schemeinfo",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Scheme Info"), style = "color:white")
-          )
-        ),
-        hr(), br(), br(), br(),
-        uiOutput("no_scheme_info"),
-        fluidRow(
-          column(2),
-          column(
-            width = 7,
-            align = "center",
-            fluidRow(
-              column(
-                width = 7,
-                align = "right",
-                uiOutput("scheme_header")
-              ),
-              column(
-                width = 2,
-                align = "left",
-                uiOutput("download_scheme_info")
-              )
-            ),
-            br(),
-            br(),
-            uiOutput("scheme_info")
-          )
-        )
-      ),
-      
-      ### Tab Loci Info  ----  
-      
-      tabItem(
-        tabName = "db_loci_info",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Loci Info"), style = "color:white")
-          )
-        ),
-        hr(), br(), br(), br(),
-        fluidRow(
-          column(1),
-          column(
-            width = 10,
-            align = "center",
-            fluidRow(
-              column(
-                width = 6,
-                align = "right",
-                uiOutput("loci_header")
-              ),
-              column(
-                width = 2,
-                align = "left",
-                uiOutput("download_loci")
-              )
-            ),
-            br(),
-            div(class = "loci_table",
-                dataTableOutput("db_loci"))
-          )
-        ),
-        br(), br(),
-        fluidRow(
-          column(1),
-          uiOutput("sequence_selector"), 
-          column(1),
-          column(
-            width = 7,
-            br(),
-            uiOutput("loci_sequences")
-          )
-        )
-      ),
-      
-      ### Tab Distance Matrix  ----  
-      
-      tabItem(
-        tabName = "db_distmatrix",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Distance Matrix"), style = "color:white")
-          )
-        ),
-        hr(), br(), br(), br(),
-        uiOutput("no_scheme_distancematrix"),
-        uiOutput("distancematrix_no_entries"),
-        fluidRow(
-          column(1),
-          uiOutput("distmatrix_show")
-        ),
-        br(), br()
-      ),
-      
-      ### Tab Missing Values ----
-      
-      tabItem(
-        tabName = "db_missing_values",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Missing Values"), style = "color:white")
-          )
-        ),
-        hr(), br(), br(), br(),
-        fluidRow(
-          column(
-            width = 3,
-            uiOutput("missing_values"),
-            fluidRow(
-              column(
-                width = 2,
-                div(
-                  class = "rectangle-red-space" 
-                )
-              ),
-              column(
-                width = 10,
-                align = "left",
-                p(
-                  HTML(
-                    paste(
-                      tags$span(style="color: white; font-size: 15px; margin-left: 75px; position: relative; bottom: -12px", " =  ≥ 5% of loci missing")
-                    )
-                  )
-                )
-              )
-            )
-          ),
-          column(
-            width = 8,
-            rHandsontableOutput("table_missing_values")
-          )
-        )
-      ),
-      
-      ## Tab Manage Schemes  ----  
-      
-      tabItem(
-        tabName = "init",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Select cgMLST Scheme"), style = "color:white")
-          )
-        ),
-        hr(),
-        fluidRow(
-          column(1),
-          column(
-            width = 3,
-            br(),
-            br(),
-            br(),
-            pickerInput(
-              inputId = "select_cgmlst",
-              label = NULL,
-              choices = list(
-                "Acinetobacter baumanii",
-                "Bacillus anthracis",
-                "Bordetella pertussis",
-                "Brucella melitensis",
-                "Brucella spp.",
-                "Burkholderia mallei (FLI)",
-                "Burkholderia mallei (RKI)",
-                "Burkholderia pseudomallei",
-                "Campylobacter jejuni/coli",
-                "Clostridioides difficile",
-                "Clostridium perfringens",
-                "Corynebacterium diphtheriae",
-                "Cronobacter sakazakii/malonaticus",
-                "Enterococcus faecalis",
-                "Enterococcus faecium",
-                "Escherichia coli",
-                "Francisella tularensis",
-                "Klebsiella oxytoca sensu lato",
-                "Klebsiella pneumoniae sensu lato",
-                "Legionella pneumophila",
-                "Listeria monocytogenes",
-                "Mycobacterium tuberculosis complex",
-                "Mycobacteroides abscessus",
-                "Mycoplasma gallisepticum",
-                "Paenibacillus larvae",
-                "Pseudomonas aeruginosa",
-                "Salmonella enterica",
-                "Serratia marcescens",
-                "Staphylococcus aureus",
-                "Staphylococcus capitis",
-                "Streptococcus pyogenes"
-              ),
-              width = "300px",
-              options = list(
-                `live-search` = TRUE,
-                `actions-box` = TRUE,
-                size = 10,
-                style = "background-color: white; border-radius: 5px;"
-              ),
-              multiple = FALSE
-            )
-          ),
-          column(
-            width = 2,
-            br(),
-            br(),
-            br(),
-            h5(textOutput("scheme_update_info"), style = "color: white")
-          ),
-          column(
-            width = 2,
-            br(),
-            br(),
-            br(),
-            actionButton(
-              "download_cgMLST",
-              label = "Download",
-              icon = icon("download")
-            ),
-            shinyjs::hidden(
-              div(id = "loading",
-                  HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
-            )
-          )
-        ),
-        fluidRow(
-          column(1),
-          column(
-            width = 6,
-            align = "center",
-            br(),
-            br(),
-            br(),
-            addSpinner(
-              tableOutput("cgmlst_scheme"),
-              spin = "dots",
-              color = "#ffffff"
-            )
-          )
-        )
-      ),
-      
-      
-      
-      ## Tab Allelic Typing ----------------------------------------------
-      
-      
-      tabItem(
-        tabName = "typing",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Generate Allelic Profile"), style = "color:white")
-          )
-        ),
-        hr(),
-        uiOutput("typing_no_db"),
-        conditionalPanel(
-          "input.typing_mode == 'Single'",
-          fluidRow(
-            uiOutput("initiate_typing_ui"),
-            uiOutput("single_typing_progress"),
-            column(1),
-            uiOutput("metadata_single_box"),
-            column(1),
-            uiOutput("start_typing_ui")
-          )
-        ),
-        conditionalPanel(
-          "input.typing_mode == 'Multi'",
-          fluidRow(
-            uiOutput("initiate_multi_typing_ui"),
-            uiOutput("multi_stop"),
-            column(1),
-            uiOutput("metadata_multi_box"),
-            column(1),
-            uiOutput("start_multi_typing_ui")
-          ),
-          fluidRow(
-            column(
-              width = 6,
-              uiOutput("pending_typing")
-            ),
-            column(
-              width = 6,
-              uiOutput("multi_typing_results")
-            )
-          )
-        )
-      ),
-      
-      
-      ## Tab Visualization -------------------------------------------------------
-      
-      
-      tabItem(
-        tabName = "visualization",
-        fluidRow(
-          tags$script(src = "javascript_functions.js"),
-          column(
-            width = 12,
-            align = "center",
-            br(),
-            conditionalPanel(
-              "input.tree_algo=='Minimum-Spanning'",
-              uiOutput("mst_field")
-            ),
-            conditionalPanel(
-              "input.tree_algo=='Neighbour-Joining'",
-              uiOutput("nj_field")
-            ),
-            conditionalPanel(
-              "input.tree_algo=='UPGMA'",
-              uiOutput("upgma_field")
-            )
-          )
-        ),
-        br(),
-        hr(),
-        
-        ### Control panels MST ----
-        conditionalPanel(
-          "input.tree_algo=='Minimum-Spanning'",
-          fluidRow(
-            column(
-              width = 4,
-              box(
-                solidHeader = TRUE,
-                status = "primary",
-                width = "100%",
-                height = "500px",
-                h3(p("Layout"), style = "color:white; position:relative; right:-15px"),
-                hr(),
-                fluidRow(
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Title"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          textInput(
-                            "mst_title",
-                            label = "",
-                            width = "100%",
-                            placeholder = "Plot Title"
-                          ),
-                          fluidRow(
-                            column(
-                              width = 7,
-                              colorPickr(
-                                inputId = "mst_title_color",
-                                selected = "#000000",
-                                label = "",
-                                update = "changestop",
-                                interaction = list(clear = FALSE,
-                                                   save = FALSE),
-                                position = "right-start",
-                                width = "100%"
-                              )
-                            ),
-                            column(
-                              width = 5,
-                              dropMenu(
-                                actionBttn(
-                                  "mst_title_menu",
-                                  label = "",
-                                  color = "default",
-                                  size = "sm",
-                                  style = "material-flat",
-                                  icon = icon("sliders")
-                                ),
-                                placement = "top-start",
-                                theme = "translucent",
-                                numericInput(
-                                  "mst_title_size",
-                                  label = h5("Size", style = "color:white; margin-bottom: 0px;"),
-                                  value = 40,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Subtitle"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          textInput(
-                            "mst_subtitle",
-                            label = "",
-                            width = "100%",
-                            placeholder = "Plot Subtitle"
-                          ),
-                          fluidRow(
-                            column(
-                              width = 7,
-                              colorPickr(
-                                inputId = "mst_subtitle_color",
-                                selected = "#000000",
-                                label = "",
-                                update = "changestop",
-                                interaction = list(clear = FALSE,
-                                                   save = FALSE),
-                                position = "right-start",
-                                width = "100%"
-                              )
-                            ),
-                            column(
-                              width = 5,
-                              dropMenu(
-                                actionBttn(
-                                  "mst_subtitle_menu",
-                                  label = "",
-                                  color = "default",
-                                  size = "sm",
-                                  style = "material-flat",
-                                  icon = icon("sliders")
-                                ),
-                                placement = "top-start",
-                                theme = "translucent",
-                                numericInput(
-                                  "mst_subtitle_size",
-                                  label = h5("Size", style = "color:white; margin-bottom: 0px;"),
-                                  value = 20,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                ),
-                hr(),
-                fluidRow(
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Legend"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 7,
-                              colorPickr(
-                                inputId = "mst_legend_color",
-                                selected = "#000000",
-                                label = "",
-                                update = "changestop",
-                                interaction = list(clear = FALSE,
-                                                   save = FALSE),
-                                position = "right-start",
-                                width = "100%"
-                              )
-                            ),
-                            column(
-                              width = 5,
-                              dropMenu(
-                                actionBttn(
-                                  "mst_legend_menu",
-                                  label = "",
-                                  color = "default",
-                                  size = "sm",
-                                  style = "material-flat",
-                                  icon = icon("sliders")
-                                ),
-                                placement = "top-start",
-                                theme = "translucent",
-                                fluidRow(
-                                  column(
-                                    width = 11,
-                                    sliderInput(
-                                      "mst_font_size",
-                                      label = h5("Font Size", style = "color:white; margin-bottom: 0px;"),
-                                      value = 18,
-                                      min = 15,
-                                      max = 30,
-                                      step = 1,
-                                      ticks = FALSE,
-                                      width = "180px"
-                                    )
-                                  ),
-                                  column(1)
-                                ),
-                                br(),
-                                fluidRow(
-                                  column(
-                                    width = 11,
-                                    sliderInput(
-                                      "mst_symbol_size",
-                                      label = h5("Key Size", style = "color:white; margin-bottom: 0px;"),
-                                      value = 20,
-                                      min = 10,
-                                      max = 30,
-                                      step = 1,
-                                      ticks = FALSE,
-                                      width = "180px"
-                                    )
-                                  ),
-                                  column(1)
-                                )
-                              )
-                            )
-                          ),
-                          fluidRow(
-                            column(
-                              width = 7,
-                              selectInput(
-                                "mst_legend_ori",
-                                label = "",
-                                width = "100%",
-                                choices = c("Left" = "left", "Right" = "right")
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Background"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "left",
-                              div(
-                                class = "mat-switch-mst-nodes",
-                                materialSwitch(
-                                  "mst_background_transparent",
-                                  h5(p("Transparent"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            )
-                          ),
-                          fluidRow(
-                            column(
-                              width = 7,
-                              colorPickr(
-                                inputId = "mst_background_color",
-                                width = "100%",
-                                selected = "#ffffff",
-                                label = "",
-                                update = "changestop",
-                                interaction = list(clear = FALSE,
-                                                   save = FALSE),
-                                position = "right-start"
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            column(
-              width = 4,
-              box(
-                solidHeader = TRUE,
-                status = "primary",
-                width = "100%",
-                height = "500px",
-                h3(p("Nodes"), style = "color:white; position:relative; right:-15px"),
-                hr(),
-                fluidRow(
-                  column(
-                    width = 6,
-                    column(
-                      width = 12,
-                      align = "left",
-                      h4(p("Label"), style = "color:white;")
-                    ),
-                    column(
-                      width = 12,
-                      align = "center",
-                      div(
-                        class = "label_sel",
-                        uiOutput("mst_node_label")
-                      ),
-                      fluidRow(
-                        column(
-                          width = 7,
-                          colorPickr(
-                            inputId = "node_font_color",
-                            width = "100%",
-                            selected = "#000000",
-                            label = "",
-                            update = "changestop",
-                            interaction = list(clear = FALSE,
-                                               save = FALSE),
-                            position = "right-start"
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          dropMenu(
-                            actionBttn(
-                              "mst_label_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            numericInput(
-                              "node_label_fontsize",
-                              label = h5("Size", style = "color:white; margin-bottom: 0px;"),
-                              value = 14,
-                              min = 8,
-                              max = 30,
-                              step = 1,
-                              width = "80px"
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Color"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 10,
-                              align = "left",
-                              div(
-                                class = "mat-switch-mst-nodes",
-                                materialSwitch(
-                                  "mst_color_var",
-                                  h5(p("Add Variable"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            column(
-                              width = 2,
-                              bslib::tooltip(
-                                bsicons::bs_icon("info-circle", title = "Only categorical variables can \nbe mapped to the node color", color = "white", 
-                                                 height = "12px", width = "12px", position = "relative", top = "27px", right = "56px"),
-                                "Text shown in the tooltip.",
-                                show = FALSE,
-                                id = "mst_node_col_info"
-                              )
-                            )
-                          ),
-                          uiOutput("mst_color_mapping")
-                        )
-                      )
-                    ), br()
-                  )
-                ),
-                hr(),
-                fluidRow(
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Size"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "left",
-                              div(
-                                class = "mat-switch-mst-nodes",
-                                materialSwitch(
-                                  "scale_nodes",
-                                  h5(p("Scale by Duplicates"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                  value = TRUE,
-                                  right = TRUE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    column(
-                      width = 12,
-                      align = "left",
-                      fluidRow(
-                        column(
-                          width = 3,
-                          align = "left",
-                          conditionalPanel(
-                            "input.scale_nodes==true",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Range')
-                              )
-                            )
-                          ),
-                          conditionalPanel(
-                            "input.scale_nodes==false",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Size')
-                              )
-                            )
-                          )
-                        ),
-                        column(
-                          width = 9,
-                          align = "center",
-                          conditionalPanel(
-                            "input.scale_nodes==true",
-                            div(
-                              class = "mst_scale_slider",
-                              sliderInput(
-                                "mst_node_scale",
-                                label = "",
-                                min = 1,
-                                max = 80,
-                                value = c(20, 40),
-                                ticks = FALSE
-                              )
-                            )
-                          ),
-                          conditionalPanel(
-                            "input.scale_nodes==false",
-                            div(
-                              class = "mst_scale_slider",
-                              sliderInput(
-                                inputId = "mst_node_size",
-                                label = "",
-                                min = 1,
-                                max = 100,
-                                value = 30,
-                                ticks = FALSE
-                              ) 
-                            )
-                          )
-                        )
-                      ),
-                      br()
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Other Elements"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "left",
-                              div(
-                                class = "mat-switch-mst-nodes",
-                                materialSwitch(
-                                  "mst_shadow",
-                                  h5(p("Show Shadow"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                  value = TRUE,
-                                  right = TRUE
-                                )
-                              ),
-                              fluidRow(
-                                column(
-                                  width = 3,
-                                  align = "left",
-                                  HTML(
-                                    paste(
-                                      tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Shape')
-                                    )
-                                  )
-                                ),
-                                column(
-                                  width = 9,
-                                  align = "center",
-                                  div(
-                                    class = "mst_shape_sel",
-                                    selectInput(
-                                      "mst_node_shape",
-                                      "",
-                                      choices = list(`Label inside` = c("Circle" = "circle", "Box" = "box", "Text" = "text"),
-                                                     `Label outside` = c("Diamond" = "diamond", "Hexagon" = "hexagon","Dot" = "dot", "Square" = "square")),
-                                      selected = c("Dot" = "dot"),
-                                      width = "85%"
-                                    )
-                                  )
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            column(
-              width = 4,
-              box(
-                solidHeader = TRUE,
-                status = "primary",
-                width = "100%",
-                height = "500px",
-                h3(p("Edges"), style = "color:white; position:relative; right:-15px"),
-                hr(),
-                fluidRow(
-                  column(
-                    width = 6,
-                    column(
-                      width = 12,
-                      align = "left",
-                      h4(p("Label"), style = "color:white;")
-                    ),
-                    column(
-                      width = 12,
-                      align = "center",
-                      div(
-                        class = "label_sel",
-                        selectInput(
-                          "mst_edge_label",
-                          label = "",
-                          choices = c(
-                            `Allelic Distance` = "weight",
-                            Index = "index",
-                            `Assembly ID` = "assembly_id",
-                            `Assembly Name` = "assembly_name",
-                            `Isolation Date` = "isolation_date",
-                            Host = "host",
-                            Country = "country",
-                            City = "city"
-                          ),
-                          selected = c(`Allelic Distance` = "weight"),
-                          width = "100%"
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 7,
-                          colorPickr(
-                            inputId = "mst_edge_font_color",
-                            width = "100%",
-                            selected = "#000000",
-                            label = "",
-                            update = "changestop",
-                            interaction = list(clear = FALSE,
-                                               save = FALSE),
-                            position = "right-start"
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          dropMenu(
-                            actionBttn(
-                              "mst_edgelabel_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            width = 5,
-                            numericInput(
-                              "mst_edge_font_size",
-                              label = h5("Size", style = "color:white; margin-bottom: 0px;"),
-                              value = 18,
-                              step = 1,
-                              min = 8,
-                              max = 30,
-                              width = "80px"
-                            )
-                          )
-                        )
-                      ),
-                      br()
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Color"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 7,
-                              div(
-                                class = "node_color",
-                                colorPickr(
-                                  inputId = "mst_color_edge",
-                                  width = "100%",
-                                  selected = "#000000",
-                                  label = "",
-                                  update = "changestop",
-                                  interaction = list(clear = FALSE,
-                                                     save = FALSE),
-                                  position = "right-start"
-                                )
-                              )
-                            ),
-                            column(
-                              width = 5,
-                              dropMenu(
-                                actionBttn(
-                                  "mst_edgecolor_menu",
-                                  label = "",
-                                  color = "default",
-                                  size = "sm",
-                                  style = "material-flat",
-                                  icon = icon("sliders")
-                                ),
-                                placement = "top-start",
-                                theme = "translucent",
-                                width = 5,
-                                sliderInput(
-                                  "mst_edge_opacity",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px;"),
-                                  value = 0.7,
-                                  step = 0.1,
-                                  min = 0,
-                                  max = 1,
-                                  ticks = FALSE,
-                                  width = "150px"
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                ),
-                hr(style = "margin-top: 3px !important"),
-                fluidRow(
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Length multiplier"), style = "color:white; position: relative; right: -15px; margin-bottom: -5px")
-                      )
-                    ),
-                    column(
-                      width = 12,
-                      align = "left",
-                      br(),
-                      div(
-                        class = "switch-mst-edges",
-                        materialSwitch(
-                          "mst_scale_edges",
-                          h5(p("Scale Allelic Distance"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                          value = FALSE,
-                          right = TRUE
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          align = "left",
-                          conditionalPanel(
-                            "input.mst_scale_edges==true",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Multiplier')
-                              )
-                            )
-                          ),
-                          conditionalPanel(
-                            "input.mst_scale_edges==false",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Length')
-                              )
-                            )
-                          )
-                        ),
-                        column(
-                          width = 9,
-                          align = "center",
-                          conditionalPanel(
-                            "input.mst_scale_edges==true",
-                            div(
-                              class = "slider_edge",
-                              sliderInput(
-                                inputId = "mst_edge_length_scale",
-                                label = NULL,
-                                min = 1,
-                                max = 40,
-                                value = 15,
-                                ticks = FALSE
-                              ) 
-                            )
-                          ),
-                          conditionalPanel(
-                            "input.mst_scale_edges==false",
-                            div(
-                              class = "slider_edge",
-                              sliderTextInput(
-                                inputId = "mst_edge_length",
-                                label = NULL,
-                                choices = append(seq(0.1, 1, 0.1), 2:100),
-                                selected = 35,
-                                hide_min_max = FALSE
-                              ) 
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 6,
-                        align = "left",
-                        h4(p("Clustering"), style = "color:white; text-align: left; position: relative; right: -15px")
-                      ),
-                      column(
-                        width = 2,
-                        bslib::tooltip(
-                          bsicons::bs_icon("info-circle", 
-                                           title = "Cluster threshold according to species-specific\nComplex Type Distance (cgMLST.org)", 
-                                           color = "white", height = "14px", width = "14px", 
-                                           position = "relative", top = "9px", right = "28px"),
-                          "Text shown in the tooltip.",
-                          show = FALSE,
-                          id = "mst_cluster_info"
-                        )
-                      )
-                    ),
-                    br(),
-                    fluidRow(
-                      column(
-                        width = 9,
-                        div(
-                          class = "mst-cluster-switch",
-                          materialSwitch(
-                            "mst_show_clusters",
-                            h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        dropMenu(
-                          actionBttn(
-                            "mst_cluster_col_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          width = 5,
-                          selectInput(
-                            "mst_cluster_col_scale",
-                            label = h5("Color Scale", style = "color:white; margin-bottom: 0px;"),
-                            choices = c("Viridis", "Rainbow"),
-                            width = "150px"
-                          )
-                        )
-                      )
-                    ),
-                    br(),
-                    fluidRow(
-                      column(
-                        width = 4,
-                        HTML(
-                          paste(
-                            tags$span(style='color: white; text-align: left; font-size: 14px; margin-left: 15px', 'Threshold')
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        uiOutput("mst_cluster")
-                      ),
-                      column(
-                        width = 4,
-                        actionButton(
-                          "mst_cluster_reset",
-                          label = "",
-                          icon = icon("rotate")
-                        ),
-                        bsTooltip("mst_cluster_reset", 
-                                  HTML("Reset to default Complex Type Distance"), 
-                                  placement = "top", trigger = "hover")
-                      )
-                    )
-                  ),
-                  br(),
-                )
-              ), br(), br(), br(), br(), br(), br()
-            )
-          )
-        ),
-        
-        ### Control Panels NJ ----
-        
-        conditionalPanel(
-          "input.tree_algo=='Neighbour-Joining'",
-          fluidRow(
-            column(
-              width = 1,
-              radioGroupButtons(
-                inputId = "nj_controls",
-                label = "",
-                choices = c("Layout", "Label", "Elements", "Variables"),
-                direction = "vertical"
-              )
-            ),
-            conditionalPanel(
-              "input.nj_controls=='Layout'",
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Theme"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "center",
-                        selectInput(
-                          inputId = "nj_layout",
-                          label = "",
-                          choices = list(
-                            Linear = list(
-                              "Rectangular" = "rectangular",
-                              "Roundrect" = "roundrect",
-                              "Slanted" = "slanted",
-                              "Ellipse" = "ellipse"
-                            ),
-                            Circular = list("Circular" = "circular",
-                                            "Inward" = "inward")
-                          ),
-                          selected = "rectangular",
-                          width = "90%"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch-layout",
-                          materialSwitch(
-                            "nj_rootedge_show",
-                            h5(p("Rootedge"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "nj_rootedge_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("nj_rootedge_length"),
-                              br(),
-                              selectInput(
-                                "nj_rootedge_line",
-                                label = h5("Rootedge Line", style = "color:white"),
-                                choices = c(Solid = "solid", Dashed = "dashed", Dotted = "dotted"),
-                                selected = c(Dotted = "solid"),
-                                width = "100px"
-                              ),
-                              br(),
-                              conditionalPanel(
-                                "input.nj_layout=='circular'",
-                                sliderInput(
-                                  "nj_xlim",
-                                  label = h5("Adjust Circular", style = "color:white"),
-                                  min = -50,
-                                  max = 0,
-                                  value = -10,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.nj_layout=='inward'",
-                                sliderInput(
-                                  "nj_inward_xlim",
-                                  label = h5("Adjust Circular", style = "color:white"),
-                                  min = 30,
-                                  max = 120,
-                                  value = 50,
-                                  ticks = FALSE,
-                                  width = "150px",
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch-re",
-                          materialSwitch(
-                            "nj_ladder",
-                            h5(p("Ladderize"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                            value = TRUE,
-                            right = TRUE
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Color"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Lines/Text"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
-                      ),
-                      column(
-                        width = 7,
-                        colorPickr(
-                          inputId = "nj_color",
-                          width = "90%",
-                          selected = "#000000",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    br(),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Background"), style = "color:white; position: relative; right: -15px; margin-top: 7px; margin-bottom: 38px")
-                      ),
-                      column(
-                        width = 7,
-                        colorPickr(
-                          inputId = "nj_bg",
-                          width = "90%",
-                          selected = "#ffffff",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ), 
-                    br()
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Title"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      textInput(
-                        "nj_title",
-                        label = "",
-                        width = "100%",
-                        placeholder = "Plot Title"
-                      ),
-                      textInput(
-                        "nj_subtitle",
-                        label = "",
-                        width = "100%",
-                        placeholder = "Plot Subtitle"
-                      ),
-                      br(),
-                      fluidRow(
-                        column(
-                          width = 7,
-                          colorPickr(
-                            inputId = "nj_title_color",
-                            selected = "#000000",
-                            label = "",
-                            update = "changestop",
-                            interaction = list(clear = FALSE,
-                                               save = FALSE),
-                            position = "right-start",
-                            width = "100%"
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "nj_title_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                numericInput(
-                                  "nj_title_size",
-                                  label = h5("Title Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 30,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                ),
-                                br(),
-                                numericInput(
-                                  "nj_subtitle_size",
-                                  label = h5("Subtitle Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 20,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      br()
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Sizing"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      br(),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Ratio", style = "color: white; font-size: 14px;")
-                        ),
-                        column(
-                          width = 6,
-                          align = "left",
-                          div(
-                            class = "ratio-sel",
-                            selectInput(
-                              "nj_ratio",
-                              "",
-                              choices = c("16:10" = (16/10), "16:9" = (16/9), "4:3" = (4/3))
-                            )
-                          )
-                        ),
-                        column(
-                          width = 3,
-                          dropMenu(
-                            actionBttn(
-                              "nj_size_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                sliderInput(
-                                  "nj_v",
-                                  label = h5("Vertical Position", style = "color:white; margin-bottom: 0px"),
-                                  min = -0.5,
-                                  max = 0.5,
-                                  step = 0.01,
-                                  value = 0,
-                                  width = "150px",
-                                  ticks = FALSE
-                                ),
-                                br(),
-                                sliderInput(
-                                  "nj_h",
-                                  label = h5("Horizontal Position", style = "color:white; margin-bottom: 0px"),
-                                  min = -0.5,
-                                  max = 0.5,
-                                  step = 0.01,
-                                  value = 0,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Size", style = "color: white; font-size: 14px; margin-top: 30px")
-                        ),
-                        column(
-                          width = 9,
-                          sliderInput(
-                            "nj_scale",
-                            "",
-                            min = 500,
-                            max = 1200,
-                            value = 800,
-                            step = 5,
-                            width = "95%",
-                            ticks = FALSE
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Zoom", style = "color: white; font-size: 14px; margin-top: 30px")
-                        ),
-                        column(
-                          width = 9,
-                          div(
-                            class = "zoom-slider",
-                            sliderInput(
-                              "nj_zoom",
-                              label = NULL,
-                              min = 0.5,
-                              max = 1.5,
-                              step = 0.05,
-                              value = 0.95,
-                              ticks = FALSE
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Tree Scale"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      fluidRow(
-                        column(
-                          width = 8,
-                          align = "left",
-                          div(
-                            class = "mat-switch-layout",
-                            materialSwitch(
-                              "nj_treescale_show",
-                              h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                              value = TRUE,
-                              right = TRUE
-                            )
-                          ),
-                          br()
-                        ),
-                        column(
-                          width = 4,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "nj_treescale_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                uiOutput("nj_treescale_width"),
-                                br(),
-                                uiOutput("nj_treescale_x"),
-                                br(),
-                                uiOutput("nj_treescale_y")
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Legend"), style = "color:white; position: relative; right: -15px; margin-top: 10px; margin-bottom: -2px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      fluidRow(
-                        column(
-                          width = 7,
-                          align = "left",
-                          prettyRadioButtons(
-                            "nj_legend_orientation",
-                            "",
-                            choices = c(Horizontal = "horizontal",
-                                        Vertical = "vertical"),
-                            selected = c(Vertical = "vertical"),
-                            inline = FALSE
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "nj_legend_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                numericInput(
-                                  "nj_legend_size",
-                                  label = h5("Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 10,
-                                  min = 5,
-                                  max = 25,
-                                  step = 1,
-                                  width = "80px"
-                                ),
-                                br(),
-                                sliderInput(
-                                  "nj_legend_x",
-                                  label = h5("Horizontal Position", style = "color:white; margin-bottom: 0px"),
-                                  value = 0.9,
-                                  min = -0.9,
-                                  max = 1.9,
-                                  step = 0.2,
-                                  width = "150px",
-                                  ticks = FALSE
-                                ),
-                                br(),
-                                sliderInput(
-                                  "nj_legend_y",
-                                  label = h5("Vertical Position", style = "color:white; margin-bottom: 0px"),
-                                  value = 0.2,
-                                  min = -1.5,
-                                  max = 1.5,
-                                  step = 0.1,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.nj_controls=='Label'",
-              column(
-                width = 4,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Tips"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 4,
-                            align = "left",
-                            div(
-                              class = "mat-switch-lab",
-                              materialSwitch(
-                                "nj_tiplab_show",
-                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                                value = TRUE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 4,
-                            align = "center",
-                            uiOutput("nj_tiplab")
-                          ),
-                          column(
-                            width = 3,
-                            div(
-                              class = "mat-switch-align",
-                              materialSwitch(
-                                "nj_align",
-                                h5(p("Align"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 1,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "nj_labeltext_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-start",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  sliderInput(
-                                    "nj_tiplab_alpha",
-                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                    min = 0.1,
-                                    max = 1,
-                                    value = 1,
-                                    width = "150px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  conditionalPanel(
-                                    "!(input.nj_layout=='inward'|input.nj_layout=='circular')",
-                                    sliderInput(
-                                      inputId = "nj_tiplab_nudge_x",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = 0,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  conditionalPanel(
-                                    "input.nj_layout=='circular'",
-                                    sliderInput(
-                                      inputId = "nj_tiplab_position",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = -0.05,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  conditionalPanel(
-                                    "input.nj_layout=='inward'",
-                                    sliderInput(
-                                      inputId = "nj_tiplab_position_inw",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = 1.1,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "nj_tiplab_angle",
-                                    label = h5("Angle", style = "color:white; margin-bottom: 0px"),
-                                    min = -90,
-                                    max = 90,
-                                    value = 0,
-                                    ticks = FALSE,
-                                    width = "150px",
-                                  )      
-                                ),
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  uiOutput("nj_tiplab_size"),
-                                  br(),
-                                  selectInput(
-                                    "nj_tiplab_fontface",
-                                    label = h5("Fontface", style = "color:white; margin-bottom: 5px; margin-top: 16px"),
-                                    width = "250px",
-                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
-                                  )
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 4,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px")
-                      ),
-                      column(
-                        width = 4,
-                        align = "center",
-                        colorPickr(
-                          inputId = "nj_tiplab_color",
-                          width = "100%",
-                          selected = "#000000",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 4,
-                        align = "left",
-                        br(),
-                        div(
-                          class = "mat-switch-geom",
-                          materialSwitch(
-                            "nj_geom",
-                            h5(p("Panels"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        colorPickr(
-                          inputId = "nj_tiplab_fill",
-                          width = "100%",
-                          selected = "#84D9A0",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "left",
-                        dropMenu(
-                          actionBttn(
-                            "nj_labelformat_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("nj_tiplab_padding"),
-                              br(),
-                              sliderInput(
-                                inputId = "nj_tiplab_labelradius",
-                                label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
-                                min = 0,
-                                max = 0.5,
-                                value = 0.2,
-                                width = "150px",
-                                ticks = FALSE
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 3,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Branches"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 5,
-                            align = "left",
-                            div(
-                              class = "mat-switch-lab",
-                              materialSwitch(
-                                "nj_show_branch_label",
-                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 5,
-                            align = "center",
-                            uiOutput("nj_branch_label")
-                          ),
-                          column(
-                            width = 2,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "nj_branch_label_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-start",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  sliderInput(
-                                    "nj_branchlab_alpha",
-                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                    min = 0.1,
-                                    max = 1,
-                                    value = 0.65,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "nj_branch_x",
-                                    label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-                                    min = -3,
-                                    max = 3,
-                                    value = 0,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "nj_branch_y",
-                                    label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-                                    min = -3,
-                                    max = 3,
-                                    value = 0,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  )
-                                ),
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  uiOutput("nj_branch_size"),
-                                  selectInput(
-                                    "nj_branchlab_fontface",
-                                    label = h5("Fontface", style = "color:white; margin-bottom: 0px;"),
-                                    width = "250px",
-                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    "nj_branch_labelradius",
-                                    label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
-                                    min = 0,
-                                    max = 0.5,
-                                    value = 0.5,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  )
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px; margin-bottom: 109px")
-                      ),
-                      column(
-                        width = 5,
-                        colorPickr(
-                          inputId = "nj_branch_label_color",
-                          width = "100%",
-                          selected = "#FFB7B7",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 3,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Custom Labels"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 6,
-                            textInput(
-                              "nj_new_label_name",
-                              "",
-                              placeholder = "New Label"
-                            )
-                          ),
-                          column(
-                            width = 3,
-                            actionButton(
-                              "nj_add_new_label",
-                              "",
-                              icon = icon("plus")
-                            )
-                          ),
-                          column(
-                            width = 2,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "nj_custom_label_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-end",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 12,
-                                  align = "center",
-                                  uiOutput("nj_custom_labelsize"),
-                                  br(),
-                                  uiOutput("nj_sliderInput_y"),
-                                  br(),
-                                  uiOutput("nj_sliderInput_x")
-                                )
-                              )
-                            )
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 6,
-                            uiOutput("nj_custom_label_select")
-                          ),
-                          column(
-                            width = 4,
-                            uiOutput("nj_del_label"),
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 12,
-                            align = "center",
-                            uiOutput("nj_cust_label_save")
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.nj_controls=='Elements'",
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Tip Points"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "nj_tippoint_show",
-                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "nj_tippoint_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              sliderInput(
-                                "nj_tippoint_alpha",
-                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                value = 0.5,
-                                min = 0.1,
-                                max = 1,
-                                width = "150px",
-                                ticks = FALSE
-                              ), 
-                              br(),
-                              uiOutput("nj_tippoint_size")
-                            )
-                          )
-                        )  
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        colorPickr(
-                          inputId = "nj_tippoint_color",
-                          width = "100%",
-                          selected = "#3A4657",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        conditionalPanel(
-                          "input.nj_tipshape_mapping_show==false",
-                          selectInput(
-                            "nj_tippoint_shape",
-                            "",
-                            width = "100%",
-                            choices = c(
-                              Circle = "circle", 
-                              Square = "square", 
-                              Diamond = "diamond", 
-                              Triangle = "triangle",
-                              Cross = "cross", 
-                              Asterisk = "asterisk"
-                            )
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.nj_tipshape_mapping_show==true",
-                          h5(p("Variable assigned"), style = "color:white; position: relative; right: -15px; margin-top: 30px; font-style: italic")
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Node Points"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "nj_nodepoint_show",
-                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "nj_nodepoint_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              sliderInput(
-                                "nj_nodepoint_alpha",
-                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                value = 1,
-                                min = 0.1,
-                                max = 1,
-                                width = "150px",
-                                ticks = FALSE
-                              ), 
-                              br(),
-                              uiOutput("nj_nodepoint_size")
-                            )
-                          )
-                        )  
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        colorPickr(
-                          inputId = "nj_nodepoint_color",
-                          width = "100%",
-                          selected = "#3A4657",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        selectInput(
-                          "nj_nodepoint_shape",
-                          "",
-                          choices = c(
-                            Circle = "circle", 
-                            Square = "square", 
-                            Diamond = "diamond", 
-                            Triangle = "triangle",
-                            Cross = "cross", 
-                            Asterisk = "asterisk"
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 6,
-                        h4(p("Tiles"), style = "color:white; position: relative; right: -15px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        div(
-                          class = "sel-tile-number",
-                          selectInput(
-                            "nj_tile_number",
-                            "",
-                            choices = 1:5,
-                            width = "70px"
-                          )
-                        )
-                      ),
-                      column(
-                        width = 7,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "nj_tile_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              conditionalPanel(
-                                "input.nj_tile_num == 1",
-                                sliderInput(
-                                  "nj_fruit_alpha",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.nj_tile_num == 2",
-                                sliderInput(
-                                  "nj_fruit_alpha_2",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.nj_tile_num == 3",
-                                sliderInput(
-                                  "nj_fruit_alpha_3",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.nj_tile_num == 4",
-                                sliderInput(
-                                  "nj_fruit_alpha_4",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.nj_tile_num == 5",
-                                sliderInput(
-                                  "nj_fruit_alpha_5",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.nj_tile_num == 1",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_width"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 68px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_offset_circ"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.nj_tile_num == 2",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_width2"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_offset_circ_2"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.nj_tile_num == 3",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_width3"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_offset_circ_3"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.nj_tile_num == 4",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_width4"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_offset_circ_4"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.nj_tile_num == 5",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_width5"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_offset_circ_5"),
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 6,
-                        h4(p("Heatmap"), style = "color:white; position: relative; right: -15px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        h5("Title", style = "color:white; margin-left: 15px; margin-top: 32px;")
-                      ),
-                      column(
-                        width = 6,
-                        align = "center",
-                        textInput(
-                          "nj_heatmap_title",
-                          label = "",
-                          value = "Heatmap",
-                          placeholder = "Heatmap" 
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "nj_heatmap_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("nj_colnames_angle"),
-                              br(),
-                              uiOutput("nj_colnames_y")
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5("Width", style = "color: white; margin-left: 15px; margin-top: 40px;")
-                      ),
-                      column(
-                        width = 7,
-                        uiOutput("nj_heatmap_width")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5("Position", style = "color:white; margin-left: 15px; margin-top: 36px;")
-                      ),
-                      column(
-                        width = 7,
-                        uiOutput("nj_heatmap_offset")
-                      )
-                    ),
-                    br(), br()
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Clade Highlight"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 12,
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "nj_nodelabel_show",
-                            h5(p("Toggle Node View"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        h5(p("Nodes"), style = "color:white; position: relative; right: -15px; margin-top: 20px")
-                      ),
-                      column(
-                        width = 9,
-                        uiOutput("nj_parentnode")
-                      )
-                    ),
-                    uiOutput("nj_clade_scale"),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Form"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
-                      ),
-                      column(
-                        width = 7,
-                        div(
-                          class = "sel-clade",
-                          selectInput(
-                            "nj_clade_type",
-                            "",
-                            choices = c("Rect" = "rect",
-                                        "Round" = "roundrect"),
-                            selected = c("Round" = "roundrect")
-                          ) 
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.nj_controls=='Variables'",
-              column(
-                width = 7,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 3,
-                        align = "center",
-                        h4(p("Element"), style = "color:white; margin-bottom: 20px")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        h4(p("Variable"), style = "color:white; margin-bottom: 20px; margin-right: 30px;")
-                      ),
-                      column(
-                        width = 6,
-                        align = "center",
-                        h4(p("Color Scale"), style = "color:white; margin-bottom: 20px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "nj_mapping_show",
-                            h5(p("Tip Label Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_color_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_tiplab_scale")
-                      ),
-                      uiOutput("nj_tiplab_mapping_info"),
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "nj_tipcolor_mapping_show",
-                            h5(p("Tip Point Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_tipcolor_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_tippoint_scale")
-                      ),
-                      uiOutput("nj_tipcolor_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "nj_tipshape_mapping_show",
-                            h5(p("Tip Point Shape"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_tipshape_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        HTML(
-                          paste(
-                            tags$span(style='color: white; font-size: 14px; font-style: italic; position: relative; bottom: -16px; right: -40px;', 'No scale for shapes')
-                          )
-                        )
-                      ),
-                      uiOutput("nj_tipshape_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        fluidRow(
-                          column(
-                            width = 8,
-                            conditionalPanel(
-                              "input.nj_tile_num == 1",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "nj_tiles_show_1",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px; margin-right: 10px"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.nj_tile_num == 2",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "nj_tiles_show_2",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.nj_tile_num == 3",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "nj_tiles_show_3",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.nj_tile_num == 4",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "nj_tiles_show_4",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.nj_tile_num == 5",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "nj_tiles_show_5",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            )
-                          ), 
-                          column(
-                            width = 4,
-                            align = "left",
-                            div(
-                              class = "tile-sel",
-                              selectInput(
-                                "nj_tile_num",
-                                "",
-                                choices = 1:5,
-                                width = "50px"
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        conditionalPanel(
-                          "input.nj_tile_num == 1",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_fruit_variable")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.nj_tile_num == 2",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_fruit_variable2")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.nj_tile_num == 3",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_fruit_variable3")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.nj_tile_num == 4",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_fruit_variable4")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.nj_tile_num == 5",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_fruit_variable5")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.nj_tile_num == 1",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_tiles_scale_1")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.nj_tile_num == 2",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_tiles_scale_2")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.nj_tile_num == 3",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_tiles_scale_3")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.nj_tile_num == 4",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_tiles_scale_4")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.nj_tile_num == 5",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_tiles_scale_5")
-                          )
-                        )
-                      ),
-                      uiOutput("nj_fruit_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "nj_heatmap_show",
-                            h5(p("Heatmap"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_heatmap_sel")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        div(
-                          class = "heatmap-scale",
-                          uiOutput("nj_heatmap_scale")
-                        )
-                      ),
-                      uiOutput("nj_heatmap_mapping_info")
-                    )
-                  )
-                )
-              )
-            )
-          ),
-          br(), br(), br(), br(), br(), br()
-        ),
-        
-        ### Control Panels UPGMA ----
-        
-        conditionalPanel(
-          "input.tree_algo=='UPGMA'",
-          fluidRow(
-            column(
-              width = 1,
-              radioGroupButtons(
-                inputId = "upgma_controls",
-                label = "",
-                choices = c("Layout", "Label", "Elements", "Variables"),
-                direction = "vertical"
-              )
-            ),
-            conditionalPanel(
-              "input.upgma_controls=='Layout'",
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Theme"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "center",
-                        selectInput(
-                          inputId = "upgma_layout",
-                          label = "",
-                          choices = list(
-                            Linear = list(
-                              "Rectangular" = "rectangular",
-                              "Roundrect" = "roundrect",
-                              "Slanted" = "slanted",
-                              "Ellipse" = "ellipse"
-                            ),
-                            Circular = list("Circular" = "circular",
-                                            "Inward" = "inward")
-                          ),
-                          selected = "rectangular",
-                          width = "90%"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch-layout",
-                          materialSwitch(
-                            "upgma_rootedge_show",
-                            h5(p("Rootedge"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_rootedge_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("upgma_rootedge_length"),
-                              br(),
-                              selectInput(
-                                "upgma_rootedge_line",
-                                label = h5("Rootedge Line", style = "color:white"),
-                                choices = c(Solid = "solid", Dashed = "dashed", Dotted = "dotted"),
-                                selected = c(Dotted = "solid"),
-                                width = "100px"
-                              ),
-                              br(),
-                              conditionalPanel(
-                                "input.upgma_layout=='circular'",
-                                sliderInput(
-                                  "upgma_xlim",
-                                  label = h5("Adjust Circular", style = "color:white"),
-                                  min = -50,
-                                  max = 0,
-                                  value = -10,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.upgma_layout=='inward'",
-                                sliderInput(
-                                  "upgma_inward_xlim",
-                                  label = h5("Adjust Circular", style = "color:white"),
-                                  min = 30,
-                                  max = 120,
-                                  value = 50,
-                                  ticks = FALSE,
-                                  width = "150px",
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch-re",
-                          materialSwitch(
-                            "upgma_ladder",
-                            h5(p("Ladderize"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                            value = TRUE,
-                            right = TRUE
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Color"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Lines/Text"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
-                      ),
-                      column(
-                        width = 7,
-                        colorPickr(
-                          inputId = "upgma_color",
-                          width = "90%",
-                          selected = "#000000",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    br(),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Background"), style = "color:white; position: relative; right: -15px; margin-top: 7px; margin-bottom: 38px")
-                      ),
-                      column(
-                        width = 7,
-                        colorPickr(
-                          inputId = "upgma_bg",
-                          width = "90%",
-                          selected = "#ffffff",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Title"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      textInput(
-                        "upgma_title",
-                        label = "",
-                        width = "100%",
-                        placeholder = "Plot Title"
-                      ),
-                      textInput(
-                        "upgma_subtitle",
-                        label = "",
-                        width = "100%",
-                        placeholder = "Plot Subtitle"
-                      ),
-                      br(),
-                      fluidRow(
-                        column(
-                          width = 7,
-                          colorPickr(
-                            inputId = "upgma_title_color",
-                            selected = "#000000",
-                            label = "",
-                            update = "changestop",
-                            interaction = list(clear = FALSE,
-                                               save = FALSE),
-                            position = "right-start",
-                            width = "100%"
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "upgma_title_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                numericInput(
-                                  "upgma_title_size",
-                                  label = h5("Title Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 30,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                ),
-                                br(),
-                                numericInput(
-                                  "upgma_subtitle_size",
-                                  label = h5("Subtitle Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 20,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Sizing"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      br(),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Ratio", style = "color: white; font-size: 14px;")
-                        ),
-                        column(
-                          width = 6,
-                          align = "left",
-                          div(
-                            class = "ratio-sel",
-                            selectInput(
-                              "upgma_ratio",
-                              "",
-                              choices = c("16:10" = (16/10), "16:9" = (16/9), "4:3" = (4/3))
-                            )
-                          )
-                        ),
-                        column(
-                          width = 3,
-                          dropMenu(
-                            actionBttn(
-                              "upgma_size_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                sliderInput(
-                                  "upgma_v",
-                                  label = "Vertical Position",
-                                  min = -0.5,
-                                  max = 0.5,
-                                  step = 0.01,
-                                  value = 0,
-                                  width = "150px",
-                                  ticks = FALSE
-                                ),
-                                br(),
-                                sliderInput(
-                                  "upgma_h",
-                                  label = "Horizontal Position",
-                                  min = -0.5,
-                                  max = 0.5,
-                                  step = 0.01,
-                                  value = 0,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Size", style = "color: white; font-size: 14px; margin-top: 30px")
-                        ),
-                        column(
-                          width = 9,
-                          sliderInput(
-                            "upgma_scale",
-                            "",
-                            min = 500,
-                            max = 1200,
-                            value = 800,
-                            step = 5,
-                            width = "95%",
-                            ticks = FALSE
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Zoom", style = "color: white; font-size: 14px; margin-top: 30px")
-                        ),
-                        column(
-                          width = 9,
-                          div(
-                            class = "zoom-slider",
-                            sliderInput(
-                              "upgma_zoom",
-                              label = NULL,
-                              min = 0.5,
-                              max = 1.5,
-                              step = 0.05,
-                              value = 0.95,
-                              ticks = FALSE
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Tree Scale"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      fluidRow(
-                        column(
-                          width = 8,
-                          align = "left",
-                          div(
-                            class = "mat-switch-layout",
-                            materialSwitch(
-                              "upgma_treescale_show",
-                              h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                              value = TRUE,
-                              right = TRUE
-                            )
-                          ),
-                          br()
-                        ),
-                        column(
-                          width = 4,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "upgma_treescale_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                uiOutput("upgma_treescale_width"),
-                                br(),
-                                uiOutput("upgma_treescale_x"),
-                                br(),
-                                uiOutput("upgma_treescale_y")
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Legend"), style = "color:white; position: relative; right: -15px; margin-top: 10px; margin-bottom: -2px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      fluidRow(
-                        column(
-                          width = 7,
-                          align = "left",
-                          prettyRadioButtons(
-                            "upgma_legend_orientation",
-                            "",
-                            choices = c(Horizontal = "horizontal",
-                                        Vertical = "vertical"),
-                            selected = c(Vertical = "vertical"),
-                            inline = FALSE
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "upgma_legend_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                numericInput(
-                                  "upgma_legend_size",
-                                  label = h5("Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 10,
-                                  min = 5,
-                                  max = 25,
-                                  step = 1,
-                                  width = "80px"
-                                ),
-                                br(),
-                                sliderInput(
-                                  "upgma_legend_x",
-                                  label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-                                  value = 0.9,
-                                  min = -0.9,
-                                  max = 1.9,
-                                  step = 0.2,
-                                  width = "150px",
-                                  ticks = FALSE
-                                ),
-                                br(),
-                                sliderInput(
-                                  "upgma_legend_y",
-                                  label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-                                  value = 0.2,
-                                  min = -1.5,
-                                  max = 1.5,
-                                  step = 0.1,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.upgma_controls=='Label'",
-              column(
-                width = 4,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Tips"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 4,
-                            align = "left",
-                            div(
-                              class = "mat-switch-lab",
-                              materialSwitch(
-                                "upgma_tiplab_show",
-                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                                value = TRUE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 4,
-                            align = "center",
-                            uiOutput("upgma_tiplab")
-                          ),
-                          column(
-                            width = 3,
-                            div(
-                              class = "mat-switch-align",
-                              materialSwitch(
-                                "upgma_align",
-                                h5(p("Align"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 1,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "upgma_labeltext_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-start",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  sliderInput(
-                                    "upgma_tiplab_alpha",
-                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                    min = 0.1,
-                                    max = 1,
-                                    value = 1,
-                                    width = "150px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  conditionalPanel(
-                                    "!(input.upgma_layout=='inward'|input.upgma_layout=='circular')",
-                                    sliderInput(
-                                      inputId = "upgma_tiplab_nudge_x",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = 0,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  conditionalPanel(
-                                    "input.upgma_layout=='circular'",
-                                    sliderInput(
-                                      inputId = "upgma_tiplab_position",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = -0.05,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  conditionalPanel(
-                                    "input.upgma_layout=='inward'",
-                                    sliderInput(
-                                      inputId = "upgma_tiplab_position_inw",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = 1.1,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "upgma_tiplab_angle",
-                                    label = h5("Angle", style = "color:white; margin-bottom: 0px"),
-                                    min = -90,
-                                    max = 90,
-                                    value = 0,
-                                    ticks = FALSE,
-                                    width = "150px",
-                                  )      
-                                ),
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  uiOutput("upgma_tiplab_size"),
-                                  br(),
-                                  selectInput(
-                                    "upgma_tiplab_fontface",
-                                    label = h5("Fontface", style = "color:white; margin-bottom: 5px; margin-top: 16px"),
-                                    width = "250px",
-                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
-                                  )
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 4,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px")
-                      ),
-                      column(
-                        width = 4,
-                        align = "center",
-                        colorPickr(
-                          inputId = "upgma_tiplab_color",
-                          width = "100%",
-                          selected = "#000000",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 4,
-                        align = "left",
-                        br(),
-                        div(
-                          class = "mat-switch-geom",
-                          materialSwitch(
-                            "upgma_geom",
-                            h5(p("Panels"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        colorPickr(
-                          inputId = "upgma_tiplab_fill",
-                          width = "100%",
-                          selected = "#84D9A0",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "left",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_labelformat_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("upgma_tiplab_padding"),
-                              br(),
-                              sliderInput(
-                                inputId = "upgma_tiplab_labelradius",
-                                label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
-                                min = 0,
-                                max = 0.5,
-                                value = 0.2,
-                                width = "150px",
-                                ticks = FALSE
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 3,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Branches"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 5,
-                            align = "left",
-                            div(
-                              class = "mat-switch-lab",
-                              materialSwitch(
-                                "upgma_show_branch_label",
-                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 5,
-                            align = "center",
-                            uiOutput("upgma_branch_label")
-                          ),
-                          column(
-                            width = 2,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "upgma_branch_label_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-start",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  sliderInput(
-                                    "upgma_branchlab_alpha",
-                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                    min = 0.1,
-                                    max = 1,
-                                    value = 0.65,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "upgma_branch_x",
-                                    label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-                                    min = -3,
-                                    max = 3,
-                                    value = 0,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "upgma_branch_y",
-                                    label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-                                    min = -3,
-                                    max = 3,
-                                    value = 0,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  )
-                                ),
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  uiOutput("upgma_branch_size"),
-                                  selectInput(
-                                    "upgma_branchlab_fontface",
-                                    label = h5("Fontface", style = "color:white; margin-bottom: 0px;"),
-                                    width = "250px",
-                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    "upgma_branch_labelradius",
-                                    label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
-                                    min = 0,
-                                    max = 0.5,
-                                    value = 0.5,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  )
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px; margin-bottom: 109px")
-                      ),
-                      column(
-                        width = 5,
-                        colorPickr(
-                          inputId = "upgma_branch_label_color",
-                          width = "100%",
-                          selected = "#FFB7B7",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        ),
-                        br(), br()
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 3,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Custom Labels"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 6,
-                            textInput(
-                              "upgma_new_label_name",
-                              "",
-                              placeholder = "New Label"
-                            )
-                          ),
-                          column(
-                            width = 3,
-                            actionButton(
-                              "upgma_add_new_label",
-                              "",
-                              icon = icon("plus")
-                            )
-                          ),
-                          column(
-                            width = 2,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "upgma_custom_label_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-end",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 12,
-                                  align = "center",
-                                  uiOutput("upgma_custom_labelsize"),
-                                  br(),
-                                  uiOutput("upgma_sliderInput_y"),
-                                  br(),
-                                  uiOutput("upgma_sliderInput_x")
-                                )
-                              )
-                            )
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 6,
-                            uiOutput("upgma_custom_label_select")
-                          ),
-                          column(
-                            width = 4,
-                            uiOutput("upgma_del_label"),
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 12,
-                            align = "center",
-                            uiOutput("upgma_cust_label_save")
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.upgma_controls=='Elements'",
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Tip Points"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "upgma_tippoint_show",
-                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_tippoint_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              sliderInput(
-                                "upgma_tippoint_alpha",
-                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                value = 0.5,
-                                min = 0.1,
-                                max = 1,
-                                width = "150px",
-                                ticks = FALSE
-                              ), 
-                              br(),
-                              uiOutput("upgma_tippoint_size")
-                            )
-                          )
-                        )  
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        colorPickr(
-                          inputId = "upgma_tippoint_color",
-                          width = "100%",
-                          selected = "#3A4657",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        conditionalPanel(
-                          "input.upgma_tipshape_mapping_show==false",
-                          selectInput(
-                            "upgma_tippoint_shape",
-                            "",
-                            width = "100%",
-                            choices = c(
-                              Circle = "circle", 
-                              Square = "square", 
-                              Diamond = "diamond", 
-                              Triangle = "triangle",
-                              Cross = "cross", 
-                              Asterisk = "asterisk"
-                            )
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.upgma_tipshape_mapping_show==true",
-                          h5(p("Variable assigned"), style = "color:white; position: relative; right: -15px; margin-top: 30px; font-style: italic")
-                        ),
-                        br()
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Node Points"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "upgma_nodepoint_show",
-                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_nodepoint_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              sliderInput(
-                                "upgma_nodepoint_alpha",
-                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                value = 1,
-                                min = 0.1,
-                                max = 1,
-                                width = "150px",
-                                ticks = FALSE
-                              ), 
-                              br(),
-                              uiOutput("upgma_nodepoint_size")
-                            )
-                          )
-                        )  
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        colorPickr(
-                          inputId = "upgma_nodepoint_color",
-                          width = "100%",
-                          selected = "#3A4657",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        selectInput(
-                          "upgma_nodepoint_shape",
-                          "",
-                          choices = c(
-                            Circle = "circle", 
-                            Square = "square", 
-                            Diamond = "diamond", 
-                            Triangle = "triangle",
-                            Cross = "cross", 
-                            Asterisk = "asterisk"
-                          )
-                        ),
-                        br()
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 6,
-                        h4(p("Tiles"), style = "color:white; position: relative; right: -15px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        div(
-                          class = "sel-tile-number",
-                          selectInput(
-                            "upgma_tile_number",
-                            "",
-                            choices = 1:5,
-                            width = "70px"
-                          )
-                        )
-                      ),
-                      column(
-                        width = 7,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_tile_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              conditionalPanel(
-                                "input.upgma_tile_num == 1",
-                                sliderInput(
-                                  "upgma_fruit_alpha",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.upgma_tile_num == 2",
-                                sliderInput(
-                                  "upgma_fruit_alpha_2",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.upgma_tile_num == 3",
-                                sliderInput(
-                                  "upgma_fruit_alpha_3",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.upgma_tile_num == 4",
-                                sliderInput(
-                                  "upgma_fruit_alpha_4",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.upgma_tile_num == 5",
-                                sliderInput(
-                                  "upgma_fruit_alpha_5",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.upgma_tile_num == 1",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_width"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 68px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_offset_circ"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.upgma_tile_num == 2",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_width2"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_offset_circ_2"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.upgma_tile_num == 3",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_width3"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_offset_circ_3"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.upgma_tile_num == 4",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_width4"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_offset_circ_4"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.upgma_tile_num == 5",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_width5"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_offset_circ_5"),
-                          br()
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 6,
-                        h4(p("Heatmap"), style = "color:white; position: relative; right: -15px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        h5("Title", style = "color:white; margin-left: 15px; margin-top: 32px;")
-                      ),
-                      column(
-                        width = 6,
-                        align = "center",
-                        textInput(
-                          "upgma_heatmap_title",
-                          label = "",
-                          value = "Heatmap",
-                          placeholder = "Heatmap" 
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_heatmap_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("upgma_colnames_angle"),
-                              br(),
-                              uiOutput("upgma_colnames_y")
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5("Width", style = "color: white; margin-left: 15px; margin-top: 40px;")
-                      ),
-                      column(
-                        width = 7,
-                        uiOutput("upgma_heatmap_width")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5("Position", style = "color:white; margin-left: 15px; margin-top: 36px;")
-                      ),
-                      column(
-                        width = 7,
-                        uiOutput("upgma_heatmap_offset")
-                      )
-                    ),
-                    br(), br()
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Clade Highlight"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 12,
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "upgma_nodelabel_show",
-                            h5(p("Toggle Node View"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        h5(p("Nodes"), style = "color:white; position: relative; right: -15px; margin-top: 20px")
-                      ),
-                      column(
-                        width = 9,
-                        uiOutput("upgma_parentnode")
-                      )
-                    ),
-                    uiOutput("upgma_clade_scale"),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Form"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
-                      ),
-                      column(
-                        width = 7,
-                        div(
-                          class = "sel-clade",
-                          selectInput(
-                            "upgma_clade_type",
-                            "",
-                            choices = c("Rect" = "rect",
-                                        "Round" = "roundrect"),
-                            selected = c("Round" = "roundrect")
-                          ) 
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.upgma_controls=='Variables'",
-              column(
-                width = 7,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 3,
-                        align = "center",
-                        h4(p("Element"), style = "color:white; margin-bottom: 20px")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        h4(p("Variable"), style = "color:white; margin-bottom: 20px; margin-right: 30px;")
-                      ),
-                      column(
-                        width = 6,
-                        align = "center",
-                        h4(p("Color Scale"), style = "color:white; margin-bottom: 20px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "upgma_mapping_show",
-                            h5(p("Tip Label Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_color_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_tiplab_scale")
-                      ),
-                      uiOutput("upgma_tiplab_mapping_info"),
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "upgma_tipcolor_mapping_show",
-                            h5(p("Tip Point Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_tipcolor_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_tippoint_scale")
-                      ),
-                      uiOutput("upgma_tipcolor_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "upgma_tipshape_mapping_show",
-                            h5(p("Tip Point Shape"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_tipshape_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        HTML(
-                          paste(
-                            tags$span(style='color: white; font-size: 14px; font-style: italic; position: relative; bottom: -16px; right: -40px;', 'No scale for shapes')
-                          )
-                        )
-                      ),
-                      uiOutput("upgma_tipshape_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        fluidRow(
-                          column(
-                            width = 8,
-                            conditionalPanel(
-                              "input.upgma_tile_num == 1",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "upgma_tiles_show_1",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px; margin-right: 10px"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.upgma_tile_num == 2",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "upgma_tiles_show_2",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.upgma_tile_num == 3",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "upgma_tiles_show_3",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.upgma_tile_num == 4",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "upgma_tiles_show_4",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.upgma_tile_num == 5",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "upgma_tiles_show_5",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            )
-                          ), 
-                          column(
-                            width = 4,
-                            align = "left",
-                            div(
-                              class = "tile-sel",
-                              selectInput(
-                                "upgma_tile_num",
-                                "",
-                                choices = 1:5,
-                                width = "50px"
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        conditionalPanel(
-                          "input.upgma_tile_num == 1",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_fruit_variable")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.upgma_tile_num == 2",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_fruit_variable2")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.upgma_tile_num == 3",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_fruit_variable3")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.upgma_tile_num == 4",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_fruit_variable4")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.upgma_tile_num == 5",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_fruit_variable5")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.upgma_tile_num == 1",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_tiles_scale_1")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.upgma_tile_num == 2",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_tiles_scale_2")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.upgma_tile_num == 3",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_tiles_scale_3")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.upgma_tile_num == 4",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_tiles_scale_4")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.upgma_tile_num == 5",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_tiles_scale_5")
-                          )
-                        )
-                      ),
-                      uiOutput("upgma_fruit_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "upgma_heatmap_show",
-                            h5(p("Heatmap"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_heatmap_sel")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        div(
-                          class = "heatmap-scale",
-                          uiOutput("upgma_heatmap_scale")
-                        )
-                      ),
-                      uiOutput("upgma_heatmap_mapping_info")
-                    )
-                  )
-                )
-              )
-            )
-          ),
-          br(), br(), br(), br(), br(), br()
-        )
-      ),
-      
-      ## Tab Utilities -------------------------------------------------------
-      
-      tabItem(
-        tabName = "utilities",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Utilities"), style = "color:white")
-          )
-        ),
-        br(),
-        hr(),
-        column(
-          width = 5,
-          align = "left",
-          shinyDirButton(
-            "hash_dir",
-            "Choose folder with .fasta files",
-            title = "Locate folder with loci",
-            buttonType = "default",
-            style = "border-color: white; margin: 10px; min-width: 200px; text-align: center"
-          ),
-          actionButton("hash_start", "Start Hashing", icon = icon("circle-play")),
-          shinyjs::hidden(
-            div(id = "hash_loading",
-                HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
-          )
-        )
-          # br(),
-          # actionButton(
-          #   "backup_database",
-          #   "Create backup",
-          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
-          # ),
-          # br(),
-          # actionButton(
-          #   "import_db_backup",
-          #   "Restore backup",
-          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
-          # )
-      ),
-      
-      
-      ## Tab Screening -------------------------------------------------------
-      
-      tabItem(
-        tabName = "gs_screening",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Screening"), style = "color:white; margin-bottom: -20px;")
-          ),
-          column(
-            width = 7,
-            align = "left",
-            uiOutput("gene_screening_info")
-          )
-        ),
-        br(),
-        hr(),
-        fluidRow(
-          uiOutput("screening_interface")
-        )
-      ),
-      
-      ## Tab Resistance Profile -------------------------------------------------------
-      
-      tabItem(
-        tabName = "gs_profile",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Browse Entries"), style = "color:white; margin-bottom: -20px")
-          ),
-          column(
-            width = 7,
-            align = "left",
-            uiOutput("gene_resistance_info")
-          )
-        ),
-        br(),
-        hr(),
-        br(), br(),
-        uiOutput("gs_table_selection"),
-        fluidRow(
-          column(1),
-          uiOutput("gs_profile_display")
-        )
-      )
-    ) # End tabItems
-  ) # End dashboardPage
-) # end UI
-
-# _______________________ ####
-
-# Server ----
-
-server <- function(input, output, session) {
-  
-  phylotraceVersion <- paste("1.5.0")
-  
-  #TODO Enable this, or leave disabled
-  # Kill server on session end
-  session$onSessionEnded( function() {
-    stopApp()
-  })
-  
-  # Disable various user inputs (visualization control)
-  shinyjs::disable('mst_edge_label') 
-  
-  ## Functions ----
-  
-  # Function to read and format FASTA sequences
-  format_fasta <- function(filepath) {
-    fasta <- readLines(filepath)
-    formatted_fasta <- list()
-    current_sequence <- ""
-    
-    for (line in fasta) {
-      if (startsWith(line, ">")) {
-        if (current_sequence != "") {
-          formatted_fasta <- append(formatted_fasta, list(current_sequence))
-          current_sequence <- ""
-        }
-        formatted_fasta <- append(formatted_fasta, list(line))
-      } else {
-        current_sequence <- paste0(current_sequence, line)
-      }
-    }
-    if (current_sequence != "") {
-      formatted_fasta <- append(formatted_fasta, list(current_sequence))
-    }
-    
-    formatted_fasta
-  }
-  
-  # Function to color-code the bases in a sequence
-  color_sequence <- function(sequence) {
-    sequence <- gsub("A", "<span class='base-a'>A</span>", sequence)
-    sequence <- gsub("T", "<span class='base-t'>T</span>", sequence)
-    sequence <- gsub("G", "<span class='base-g'>G</span>", sequence)
-    sequence <- gsub("C", "<span class='base-c'>C</span>", sequence)
-    sequence
-  }
-  
-  # Function to log messages to logfile
-  log_message <- function(log_file, message, append = TRUE) {
-    cat(format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "-", message, "\n", file = log_file, append = append)
-  }
-  
-  # Modified gheatmap function
-  gheatmap.mod <- function(p, data, offset=0, width=1, low="green", high="red", color="white",
-                           colnames=TRUE, colnames_position="bottom", colnames_angle=0, colnames_level=NULL,
-                           colnames_offset_x = 0, colnames_offset_y = 0, font.size=4, family="", hjust=0.5, legend_title = "value",
-                           colnames_color = "black") {
-    
-    colnames_position %<>% match.arg(c("bottom", "top"))
-    variable <- value <- lab <- y <- NULL
-    
-    ## if (is.null(width)) {
-    ##     width <- (p$data$x %>% range %>% diff)/30
-    ## }
-    
-    ## convert width to width of each cell
-    width <- width * (p$data$x %>% range(na.rm=TRUE) %>% diff) / ncol(data)
-    
-    isTip <- x <- y <- variable <- value <- from <- to <- NULL
-    
-    ## handle the display of heatmap on collapsed nodes
-    ## https://github.com/GuangchuangYu/ggtree/issues/242
-    ## extract data on leaves (& on collapsed internal nodes) 
-    ## (the latter is extracted only when the input data has data on collapsed
-    ## internal nodes)
-    df <- p$data
-    nodeCo <- intersect(df %>% filter(is.na(x)) %>% 
-                          select(.data$parent, .data$node) %>% unlist(), 
-                        df %>% filter(!is.na(x)) %>% 
-                          select(.data$parent, .data$node) %>% unlist())
-    labCo <- df %>% filter(.data$node %in% nodeCo) %>% 
-      select(.data$label) %>% unlist()
-    selCo <- intersect(labCo, rownames(data))
-    isSel <- df$label %in% selCo
-    
-    df <- df[df$isTip | isSel, ]
-    start <- max(df$x, na.rm=TRUE) + offset
-    
-    dd <- as.data.frame(data)
-    ## dd$lab <- rownames(dd)
-    i <- order(df$y)
-    
-    ## handle collapsed tree
-    ## https://github.com/GuangchuangYu/ggtree/issues/137
-    i <- i[!is.na(df$y[i])]
-    
-    lab <- df$label[i]
-    ## dd <- dd[lab, , drop=FALSE]
-    ## https://github.com/GuangchuangYu/ggtree/issues/182
-    dd <- dd[match(lab, rownames(dd)), , drop = FALSE]
-    
-    
-    dd$y <- sort(df$y)
-    dd$lab <- lab
-    ## dd <- melt(dd, id=c("lab", "y"))
-    dd <- gather(dd, variable, value, -c(lab, y))
-    
-    i <- which(dd$value == "")
-    if (length(i) > 0) {
-      dd$value[i] <- NA
-    }
-    if (is.null(colnames_level)) {
-      dd$variable <- factor(dd$variable, levels=colnames(data))
-    } else {
-      dd$variable <- factor(dd$variable, levels=colnames_level)
-    }
-    V2 <- start + as.numeric(dd$variable) * width
-    mapping <- data.frame(from=dd$variable, to=V2)
-    mapping <- unique(mapping)
-    
-    dd$x <- V2
-    dd$width <- width
-    dd[[".panel"]] <- factor("Tree")
-    if (is.null(color)) {
-      p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, inherit.aes=FALSE)
-    } else {
-      p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, color=color, inherit.aes=FALSE)
-    }
-    if (is(dd$value,"numeric")) {
-      p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value=NA, name = legend_title) # "white")
-    } else {
-      p2 <- p2 + scale_fill_discrete(na.value=NA, name = legend_title) #"white")
-    }
-    
-    if (colnames) {
-      if (colnames_position == "bottom") {
-        y <- 0
-      } else {
-        y <- max(p$data$y) + 1
-      }
-      mapping$y <- y
-      mapping[[".panel"]] <- factor("Tree")
-      p2 <- p2 + geom_text(data=mapping, aes(x=to, y = y, label=from), color = colnames_color, size=font.size, family=family, inherit.aes = FALSE,
-                           angle=colnames_angle, nudge_x=colnames_offset_x, nudge_y = colnames_offset_y, hjust=hjust)
-    }
-    
-    p2 <- p2 + theme(legend.position="right")
-    ## p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))
-    
-    if (!colnames) {
-      ## https://github.com/GuangchuangYu/ggtree/issues/204
-      p2 <- p2 + scale_y_continuous(expand = c(0,0))
-    }
-    
-    attr(p2, "mapping") <- mapping
-    return(p2)
-  }
-  
-  # Get rhandsontable
-  get.entry.table.meta <- reactive({
-    if(!is.null(hot_to_r(input$db_entries))){
-      table <- hot_to_r(input$db_entries)
-      select(select(table, -13), 1:(12 + nrow(DB$cust_var)))
-    }
-  })
-  
-  # Function to find columns with varying values
-  var_alleles <- function(dataframe) {
-    
-    varying_columns <- c()
-    
-    for (col in 1:ncol(dataframe)) {
-      unique_values <- unique(dataframe[, col])
-      
-      if (length(unique_values) > 1) {
-        varying_columns <- c(varying_columns, col)
-      }
-    }
-    
-    return(varying_columns)
-  }
-  
-  # Functions to compute hamming distances dependent on missing value handling
-  hamming.dist <- function(x, y) {
-    sum(x != y)
-  }
-  
-  hamming.distIgnore <- function(x, y) {
-    sum( (x != y) & !is.na(x) & !is.na(y) )
-  }
-  
-  hamming.distCategory <- function(x, y) {
-    sum((x != y | xor(is.na(x), is.na(y))) & !(is.na(x) & is.na(y)))
-  }
-  
-  compute.distMatrix <- function(profile, hamming.method) {
-    mat <- as.matrix(profile)
-    n <- nrow(mat)
-    dist_mat <- matrix(0, n, n)
-    for (i in 1:(n-1)) {
-      for (j in (i+1):n) {
-        dist_mat[i, j] <- hamming.method(x = mat[i, ], y = mat[j, ])
-        dist_mat[j, i] <- dist_mat[i, j]
-      }
-    }
-    return(dist_mat)
-  }
-  
-  # Function to determine entry table height
-  table_height <- reactive({
-    if (input$table_height == TRUE) {
-      NULL
-    } else {900}
-  })
-  
-  # Function to determine distance matrix height
-  distancematrix_height <- reactive({
-    if(DB$distancematrix_nrow > 33) {
-      800
-    } else {NULL}
-  })
-  
-  # Function to missing value table height
-  miss.val.height <- reactive({
-    if(input$miss_val_height == TRUE) {
-      NULL
-    } else {800}
-  })
-  
-  #Function to check custom variable classes
-  column_classes <- function(df) {
-    sapply(df, function(x) {
-      if (class(x) == "numeric") {
-        return("cont")
-      } else if (class(x) == "character") {
-        return("categ")
-      } else {
-        return(class(x))
-      }
-    })
-  }
-  
-  # Function to hash database
-  hash_database <- function(folder) {
-    loci_files <- list.files(folder)
-    loci_names <- sapply(strsplit(loci_files, "[.]"), function(x) x[1])
-    loci_paths <- file.path(folder, loci_files)
-    
-    hashes <- sapply(loci_paths, hash_locus)
-    names(hashes) <- loci_names
-    hashes
-  }
-  
-  # Function to hash a locus
-  hash_locus <- function(locus_path) {
-    locus_file <- readLines(locus_path)
-    seq_list <- locus_file[seq(2, length(locus_file), 3)]
-    seq_hash <- sha256(seq_list)
-    seq_idx <- paste0(">", seq_hash)
-    
-    locus_file[seq(1, length(locus_file), 3)] <- seq_idx
-    writeLines(locus_file, locus_path)
-    
-    seq_hash
-  }
-  
-  # Get locus hashes
-  get_locus_hashes <- function(locus_path) {
-    locus_file <- readLines(locus_path)
-    hash_list <- locus_file[seq(1, length(locus_file), 3)]
-    hash_list <- sapply(strsplit(hash_list, "[>]"), function(x) x[2])
-  }
-  
-  extract_seq <- function(locus_path, hashes) {
-    locus_file <- readLines(locus_path)
-    hash_list <- sapply(strsplit(locus_file[seq(1, length(locus_file), 3)], "[>]"), function(x) x[2])
-    seq_list <- locus_file[seq(2, length(locus_file), 3)]
-    seq_idx <- hash_list %in% hashes
-    
-    list(
-      idx = hash_list[seq_idx],
-      seq = seq_list[seq_idx]
-    )
-  }
-  
-  add_new_sequences <- function(locus_path, sequences) {
-    locus_file <- file(locus_path, open = "a+")
-    for (i in seq_along(sequences$idx)) {
-      writeLines(c("", paste0(">", sequences$idx[i]), sequences$seq[i]), locus_file)
-    }
-    close(locus_file)
-  }
-  
-  # Compute clusters to use in visNetwork
-  compute_clusters <- function(nodes, edges, threshold) {
-    groups <- rep(0, length(nodes$id))
-    
-    edges_table <- data.frame(
-      from = edges$from,
-      to = edges$to,
-      weight = edges$weight
-    )
-    
-    count <- 0
-    while (any(groups == 0)) {
-      group_na <- groups == 0
-      labels <- nodes$id[group_na]
-      
-      cluster <- nodes$id[group_na][1] # Initialize with 1 label
-      while (!is_empty(labels)) {
-        sub_tb <- edges_table[(edges_table$from %in% cluster | edges_table$to %in% cluster) & edges_table$weight <= threshold,]
-        
-        if (nrow(sub_tb) == 0 | length(unique(c(sub_tb$from, sub_tb$to))) == length(cluster)) {
-          count <- count + 1
-          groups[nodes$id %in% cluster] <- paste("Group", count)
-          break
-        } else {
-          cluster <- unique(c(sub_tb$from, sub_tb$to))
-        }
-      }
-    }
-    groups
-  }
-  
-  # Check gene screening status
-  check_status <- function(isolate) {
-    iso_name <- gsub(".zip", "", basename(isolate))
-    if(file.exists(file.path(DB$database, gsub(" ", "_", DB$scheme),
-                             "Isolates", iso_name, "status.txt"))) {
-      if(str_detect(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
-                                        "Isolates", iso_name, "status.txt"))[1], 
-                    "successfully")) {
-        return("success")
-      } else {
-        return("fail")
-      }
-    } else {return("unfinished")}
-  }
-  
-  # Reset gene screening status
-  remove.screening.status <- function(isolate) {
-    if(file.exists(file.path(DB$database, 
-                             gsub(" ", "_", DB$scheme),
-                             "Isolates",
-                             isolate,
-                             "status.txt"))) {
-      file.remove(
-        file.path(DB$database, 
-                  gsub(" ", "_", DB$scheme),
-                  "Isolates",
-                  isolate,
-                  "status.txt")
-      )
-    }
-  }
-  
-  # Truncate hashes
-  truncHash <- function(hash) {
-    if(!is.na(hash)) {
-      paste0(str_sub(hash, 1, 4), "...", str_sub(hash, nchar(hash) - 3, nchar(hash))) 
-    } else {NA}
-  }
-  
-  # Function to check for duplicate isolate IDs for multi typing start
-  dupl_mult_id <- reactive({
-    req(Typing$multi_sel_table)
-    if(!is.null(DB$data)) {
-      selection <- Typing$multi_sel_table[which(unlist(Typing$multi_sel_table$Files) %in% unlist(DB$data["Assembly ID"])),]
-      selection$Files
-    } else {""}
-  })
-  
-  # Function to check single typing log file
-  check_new_entry <- reactive({
-    
-    invalidateLater(5000, session)
-    
-    if(!is.null(DB$database)) {
-      if(file_exists(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))) {
-        
-        Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
-        
-        if(is.null(DB$data)) {
-          if(nrow(Database[["Typing"]]) >= 1) {
-            TRUE
-          } else {FALSE}
-        } else {
-          if(nrow(DB$data) < nrow(Database[["Typing"]])) {
-            TRUE
-          } else {
-            FALSE
-          }
-        }
-      } else {FALSE}
-    }
-  })
-  
-  # Render Entry Table Highlights 
-  
-  diff_allele <- reactive({
-    if (!is.null(DB$data) & !is.null(input$compare_select) & !is.null(DB$cust_var)) {
-      var_alleles(select(DB$data, input$compare_select)) + (13 + nrow(DB$cust_var))
-    }
-  })
-  
-  err_thresh <- reactive({
-    if (!is.null(DB$data) & !is.null(DB$number_loci)) {
-      which(as.numeric(DB$data[["Errors"]]) >= (DB$number_loci * 0.05)) 
-    }
-  })
-  
-  err_thresh_na <- reactive({
-    if (!is.null(DB$na_table) & !is.null(DB$number_loci)) {
-      which(as.numeric(DB$na_table[["Errors"]]) >= (DB$number_loci * 0.05)) 
-    }
-  })
-  
-  true_rows <- reactive({
-    if (!is.null(DB$data)) {
-      which(DB$data$Include == TRUE)
-    }
-  })
-  
-  duplicated_names <- reactive({
-    if (!is.null(DB$meta)) {
-      which(duplicated(DB$meta$`Assembly Name`) | duplicated(DB$meta$`Assembly Name`, fromLast = TRUE))
-    }
-  })
-  
-  duplicated_ids <- reactive({
-    if (!is.null(DB$meta)) {
-      which(duplicated(DB$meta$`Assembly ID`) | duplicated(DB$meta$`Assembly ID`, fromLast = TRUE))
-    }
-  })
-  
-  # _______________________ ####
-  
-  ## Startup ----
-  shinyjs::addClass(selector = "body", class = "sidebar-collapse")
-  shinyjs::removeClass(selector = "body", class = "sidebar-toggle")
-  
-  output$messageMenu <- renderText({
-    HTML(format(Sys.time(), "%Y-%m-%d %H:%M:%S %Z"))
-  })
-  
-  # Initiate logging
-  if(!dir_exists(paste0(getwd(), "/logs"))) {
-    dir_create(paste0(getwd(), "/logs"))
-  }
-  
-  logfile <- file.path(paste0(getwd(), "/logs/phylotrace.log"))
-  
-  log <- log_open(logfile, logdir = FALSE)
-  
-  log_print("Session started")
-  
-  # Clear screening file
-  if(file.exists(paste0(getwd(), "/execute/screening/output_file.tsv"))) {
-    file.remove(paste0(getwd(), "/execute/screening/output_file.tsv"))
-  }
-  
-  if(file.exists(paste0(getwd(), "/execute/screening/error.txt"))) {
-    file.remove(paste0(getwd(), "/execute/screening/error.txt"))
-  }
-  
-  # Declare reactive variables
-  Startup <- reactiveValues(sidebar = TRUE, 
-                            header = TRUE) # reactive variables related to startup process
-  
-  DB <- reactiveValues(data = NULL, 
-                       block_db = FALSE, 
-                       load_selected = TRUE,
-                       no_na_switch = FALSE,
-                       first_look = FALSE) # reactive variables related to local database
-  
-  Typing <- reactiveValues(table = data.frame(), 
-                           single_path = data.frame(),
-                           progress = 0, 
-                           progress_format_start = 0, 
-                           progress_format_end = 0,
-                           result_list = NULL,
-                           status = "") # reactive variables related to typing process
-  
-  Screening <- reactiveValues(status = "idle",
-                              picker_status = TRUE,
-                              first_result = NULL) # reactive variables related to gene screening
-  
-  Vis <- reactiveValues(cluster = NULL, 
-                        metadata = list(),
-                        custom_label_nj = data.frame(),
-                        nj_label_pos_y = list(),
-                        nj_label_pos_x = list(),
-                        nj_label_size = list(),
-                        custom_label_upgma = data.frame(),
-                        upgma_label_pos_y = list(),
-                        upgma_label_pos_x = list(),
-                        upgma_label_size = list()) # reactive variables related to visualization
-  
-  Report <- reactiveValues() # reactive variables related to report functions
-  
-  Scheme <- reactiveValues() # reactive variables related to scheme  functions
-  
-  # Load last used database if possible
-  if(paste0(getwd(), "/execute/last_db.rds") %in% dir_ls(paste0(getwd(), "/execute"))) {
-    DB$last_db <- TRUE
-  }
-  
-  # Locate local Database
-  observe({
-    shinyDirChoose(input,
-                   "db_location",
-                   roots = c(Home = path_home(), Root = "/"),
-                   defaultRoot = "Home",
-                   session = session)
-    
-    if(!is.null(DB$select_new)) {
-      if(DB$select_new == FALSE) {
-        if(DB$block_db == FALSE) {
-          DB$database <- as.character(
-            parseDirPath(
-              roots = c(Home = path_home(), Root = "/"),
-              input$db_location
-            )
-          )
-          
-          DB$exist <- (length(dir_ls(DB$database)) == 0)  # Logical any local database present
-          
-          DB$available <- gsub("_", " ", basename(dir_ls(DB$database))) # List of local schemes available
-        }
-        
-      } else if (DB$select_new ==  TRUE) {
-        DB$database <- paste0(DB$new_database, "/Database")
-        
-      }
-    } else {
-      if(!is.null(DB$last_db) & file.exists(paste0(getwd(), "/execute/last_db.rds"))) {
-        
-        DB$database <- readRDS(paste0(getwd(), "/execute/last_db.rds"))
-        
-        if(dir_exists(DB$database)) {
-          DB$exist <- (length(dir_ls(DB$database)) == 0)  # Logical any local database present
-          
-          DB$available <- gsub("_", " ", basename(dir_ls(DB$database))) # List of local schemes available
-        }
-      }
-    }
-  })
-  
-  ### Set up typing environment ----
-  
-  # Null typing progress trackers
-  writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
-  writeLines("0\n", paste0(getwd(), "/logs/progress.txt"))
-  
-  if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
-    unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
-  }
-  
-  # Reset typing feedback values
-  Typing$pending <- FALSE
-  Typing$multi_started <- FALSE
-  Typing$multi_help <- FALSE
-  saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
-  Typing$last_success <- "0" # Null last multi typing success name
-  Typing$last_failure <- "0" # Null last multi typing failure name
-  
-  ### Landing page UI ----
-  observe({
-    if (Startup$sidebar == FALSE) {
-      shinyjs::removeClass(selector = "body", class = "sidebar-collapse")
-      shinyjs::addClass(selector = "body", class = "sidebar-toggle")
-    }
-  })
-  
-  output$start_message <- renderUI({
-    column(
-      width = 12, 
-      align = "center",
-      br(), br(), br(), br(), br(), br(),
-      div( 
-        class = "image",
-        imageOutput("imageOutput")
-      ),
-      br(), br(), br(),
-      p(
-        HTML(
-          paste(
-            tags$span(style='color: white; font-size: 16px;', 'Proceed by loading a compatible local database or create a new one.')
-          )
-        )
-      ),
-      br(), 
-      fluidRow(
-        column(
-          width = 6,
-          align = "right",
-          shinyDirButton(
-            "db_location",
-            "Browse",
-            icon = icon("folder-open"),
-            title = "Locate the database folder",
-            buttonType = "default",
-            root = path_home()
-          )
-        ),
-        column(
-          width = 6,
-          align = "left",
-          shinyDirButton(
-            "create_new_db",
-            "Create New",
-            icon = icon("plus"),
-            title = "Choose location for new PhyloTrace database",
-            buttonType = "default",
-            root = path_home()
-          )
-        )
-      ),
-      br(), br(),
-      fluidRow(
-        column(
-          width = 12,
-          align = "center",
-          uiOutput("load_db"),
-          br(), br(), br(), br(), br(), br(), br()
-        )
-      )
-    )
-  })
-  
-  # User selection new db or load db
-  observeEvent(input$create_new_db, {
-    log_print("Input create_new_db")
-    DB$select_new <- TRUE
-  })
-  
-  observeEvent(input$db_location, {
-    log_print("Input db_location")
-    DB$select_new <- FALSE
-  })
-  
-  # Load db & scheme selection UI
-  output$load_db <- renderUI({
-    if(!is.null(DB$select_new)) {
-      if(length(DB$new_database) > 0 & DB$select_new) {
-        column(
-          width = 12,
-          p(
-            tags$span(
-              style='color: white; font-size: 15px;',
-              HTML(
-                paste(
-                  'New database will be created in',
-                  DB$new_database
-                )
-              )
-            )
-          ),
-          br(),
-          actionButton(
-            "load",
-            "Create",
-            class = "load-start"
-          )
-        )
-      } else if(length(DB$available) > 0 & !(DB$select_new)) {
-        if(any(!(gsub(" ", "_", DB$available) %in% schemes))) {
-          column(
-            width = 12,
-            p(
-              tags$span(
-                style='color: white; font-size: 15px; font-style: italic;',
-                HTML(
-                  paste('Selected:', DB$database)
-                )
-              )
-            ),
-            uiOutput("scheme_db"),
-            br(), 
-            p(
-              HTML(
-                paste(
-                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
-                            'Warning: Folder contains invalid elements.')
-                )
-              )
-            ),
-            br(),
-            actionButton(
-              "load",
-              "Load",
-              class = "load-start"
-            )
-          )
-        } else {
-          column(
-            width = 12,
-            p(
-              tags$span(
-                style='color: white; font-size: 15px; font-style: italic;',
-                HTML(
-                  paste('Selected:', DB$database)
-                )
-              )
-            ),
-            uiOutput("scheme_db"),
-            br(), br(),
-            actionButton(
-              "load",
-              "Load",
-              class = "load-start"
-            )
-          )
-        }
-      } 
-    } else if((!is.null(DB$last_db)) & (!is.null(DB$available))) {
-      if (DB$last_db == TRUE & (length(DB$available) > 0)) {
-        if(any(!(gsub(" ", "_", DB$available) %in% schemes))) {
-          column(
-            width = 12,
-            p(
-              tags$span(
-                style='color: white; font-size: 15px; font-style: italic;',
-                HTML(
-                  paste('Last used:', DB$database)
-                )
-              )
-            ),
-            uiOutput("scheme_db"),
-            br(), 
-            p(
-              HTML(
-                paste(
-                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
-                            'Warning: Folder contains invalid elements.')
-                )
-              )
-            ),
-            br(),
-            actionButton(
-              "load",
-              "Load",
-              class = "load-start"
-            )
-          )
-        } else {
-          column(
-            width = 12,
-            p(
-              tags$span(
-                style='color: white; font-size: 15px; font-style: italic;',
-                HTML(
-                  paste('Last used:', DB$database)
-                )
-              )
-            ),
-            uiOutput("scheme_db"),
-            br(), br(),
-            actionButton(
-              "load",
-              "Load",
-              class = "load-start"
-            )
-          )
-        }
-      } else if (DB$last_db == TRUE & (length(DB$available) == 0)) {
-        column(
-          width = 12,
-          p(
-            tags$span(
-              style='color: white; font-size: 15px; font-style: italic;',
-              HTML(
-                paste('Last used:', DB$database)
-              )
-            )
-          ),
-          br(),
-          actionButton(
-            "load",
-            "Load",
-            class = "load-start"
-          )
-        )
-      }
-    }
-  })
-  
-  output$imageOutput <- renderImage({
-    # Path to your PNG image with a transparent background
-    image_path <- paste0(getwd(), "/www/PhyloTrace.png")
-    
-    # Use HTML to display the image with the <img> tag
-    list(src = image_path,
-         height = 180)
-  }, deleteFile = FALSE)
-  
-  ### Load app event ----
-  
-  observeEvent(input$load, {
-    
-    # Reset reactive screening variables 
-    output$screening_start <- NULL
-    output$screening_result_sel <- NULL
-    output$screening_result <- NULL
-    output$screening_fail <- NULL
-    Screening$status_df <- NULL
-    Screening$choices <- NULL
-    Screening$picker_status <- TRUE
-    Screening$status <- "idle"
-    Screening$first_result <- NULL
-    if(!is.null(input$screening_select)) {
-      if(!is.null(DB$data)) {
-        updatePickerInput(session, "screening_select", selected = character(0))
-      }
-    }
-    
-    log_print("Input load")
-    
-    # set typing start control variable
-    Typing$reload <- TRUE
-    
-    # reset typing status on start(
-    if(Typing$status == "Finalized") {Typing$status <- "Inactive"}
-    if(!is.null(Typing$single_path)) {Typing$single_path <- data.frame()}
-    
-    #### Render status bar ----
-    observe({
-      req(DB$scheme)
-      
-      if(is.null(input$scheme_position)) {
-        output$loaded_scheme <- renderUI({
-          fluidRow(
-            tags$li(
-              class = "dropdown", 
-              tags$span(HTML(
-                paste('<i class="fa-solid fa-layer-group"></i>', 
-                      "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
-                      DB$scheme,
-                      "</i>")), 
-                style = "color:white;")
-            )
-          )
-        })
-      } 
-      
-      if(!is.null(input$scheme_position)) {
-        output$loaded_scheme <- renderUI({
-          fluidRow(
-            tags$li(
-              class = "dropdown", 
-              tags$span(HTML(
-                paste('<i class="fa-solid fa-layer-group"></i>', 
-                      "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
-                      DB$scheme,
-                      "</i>")), 
-                style = "color:white;"),
-              div(
-                class = "reload-bttn",
-                style = paste0("margin-left:", 30 + input$scheme_position, "px; position: relative; top: -24px;"),
-                actionButton(
-                  "reload_db",
-                  label = "",
-                  icon = icon("rotate")
-                )
-              )
-            )
-          )
-        })
-      }
-    })
-    
-    observe({
-      if(!is.null(DB$database)){
-        if(nchar(DB$database) > 60) {
-          database <- paste0(substring(DB$database, first = 1, last = 60), "...")
-        } else {
-          database <- DB$database
-        }
-        output$databasetext <- renderUI({
-          fluidRow(
-            tags$li(
-              class = "dropdown", 
-              tags$span(HTML(
-                paste('<i class="fa-solid fa-folder-open"></i>', 
-                      "Database:&nbsp;&nbsp;&nbsp;<i>",
-                      database,
-                      "</i>")), 
-                style = "color:white;")
-            ),
-            if(nchar(database) > 60) {bsTooltip("databasetext", 
-                                                HTML(DB$database), 
-                                                placement = "bottom", 
-                                                trigger = "hover")}
-          )
-        })
-      }
-    })
-    
-    observe({
-      if(!is.null(DB$database)) {
-        if(Typing$status == "Finalized"){
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp; <i>typing finalized</i>")),
-                  style = "color:white;")
-              )
-            )
-          )
-        } else if(Typing$status == "Attaching"){
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp; <i>evaluating typing results</i>")),
-                  style = "color:white;")
-              )
-            )
-          )
-        } else if(Typing$status == "Processing") {
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp;<i> pending typing</i>")), 
-                  style = "color:white;")
-              )
-            )
-          )
-        } else if(Screening$status == "started") {
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp;<i> pending gene screening</i>")), 
-                  style = "color:white;")
-              )
-            )
-          )
-        } else if(Screening$status == "finished") {
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp;<i> gene screening finalized</i>")), 
-                  style = "color:white;")
-              )
-            )
-          )
-        } else {
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
-                  style = "color:white;")
-              )
-            )
-          )
-        }    
-      }
-    })
-    
-    # Null single typing status
-    if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
-      Typing$progress <- 0
-      
-      Typing$progress_format <- 900000
-      
-      output$single_typing_progress <- NULL
-      
-      output$typing_fin <- NULL
-      
-      output$single_typing_results <- NULL
-      
-      output$typing_formatting <- NULL
-      
-      Typing$single_path <- data.frame()
-      
-      # reset results file 
-      if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
-        unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
-        # Resetting single typing progress logfile bar 
-        con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
-        
-        cat("0\n", file = con)   
-        
-        close(con)
-      }
-    }
-    
-    shinyjs::runjs(
-      'if(document.querySelector("#loaded_scheme > div > li > span") !== null) {
-          // Select the span element
-          let spanElement = document.querySelector("#loaded_scheme > div > li > span");
-                    
-          // Get the bounding rectangle of the span element
-          let rect = spanElement.getBoundingClientRect();
-          
-          // Extract the width
-          let width = rect.width;
-          
-          Shiny.setInputValue("scheme_position", width);            
-        }'
-    )
-    
-    # Load app elements based on database availability and missing value presence
-    if(!is.null(DB$select_new)) {
-      if(DB$select_new & (paste0(DB$new_database, "/Database") %in% dir_ls(DB$new_database))) {
-        
-        log_print("Directory already contains a database")
-        
-        show_toast(
-          title = "Directory already contains a database",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-        DB$load_selected <- FALSE
-        
-      } else if(DB$select_new | (DB$select_new == FALSE & is.null(input$scheme_db))) {
-        
-        log_print(paste0("New database created in ", DB$new_database))
-        
-        DB$check_new_entries <- TRUE
-        DB$data <- NULL
-        DB$meta_gs <- NULL
-        DB$meta <- NULL
-        DB$meta_true <- NULL
-        DB$allelic_profile <- NULL
-        DB$allelic_profile_trunc <- NULL
-        DB$allelic_profile_true <- NULL
-        
-        # null Distance matrix, entry table and plots
-        output$db_distancematrix <- NULL 
-        output$db_entries_table <- NULL
-        output$tree_mst <- NULL
-        output$tree_nj <- NULL
-        output$tree_upgma <- NULL
-        
-        # null report values
-        Report$report_list_mst <- list()
-        Report$report_list_nj <- list()
-        Report$report_list_upgma <- list()
-        
-        # null plots
-        Vis$nj <- NULL
-        Vis$upgma <- NULL
-        Vis$ggraph_1 <- NULL
-        
-        removeModal()
-        
-        #### Render Menu Items ----
-        
-        Startup$sidebar <- FALSE
-        Startup$header <- FALSE
-        
-        output$menu_sep2 <- renderUI(hr())
-        
-        # Hide start message
-        output$start_message <- NULL
-        
-        DB$load_selected <- FALSE
-        
-        # Declare database path
-        DB$database <- file.path(DB$new_database, "Database")
-        
-        # Set database availability screening variables to present database
-        DB$block_db <- TRUE
-        DB$select_new <- FALSE
-        
-        # Render menu with Manage Schemes as start tab and no Missing values tab
-        output$menu <- renderMenu(
-          sidebarMenu(
-            menuItem(
-              text = "Database Browser",
-              tabName = "database",
-              icon = icon("hard-drive"),
-              startExpanded = TRUE,
-              menuSubItem(
-                text = "Browse Entries",
-                tabName = "db_browse_entries"
-              ),
-              menuSubItem(
-                text = "Scheme Info",
-                tabName = "db_schemeinfo"
-              ),
-              menuSubItem(
-                text = "Loci Info",
-                tabName = "db_loci_info"
-              ),
-              menuSubItem(
-                text = "Distance Matrix",
-                tabName = "db_distmatrix"
-              )
-            ),
-            menuItem(
-              text = "Manage Schemes",
-              tabName = "init",
-              icon = icon("layer-group"),
-              selected = TRUE
-            ),
-            menuItem(
-              text = "Allelic Typing",
-              tabName = "typing",
-              icon = icon("gears")
-            ),
-            menuItem(
-              text = "Resistance Profile",
-              tabName = "gene_screening",
-              icon = icon("dna"),
-              startExpanded = TRUE,
-              menuSubItem(
-                text = "Browse Entries",
-                tabName = "gs_profile"
-              ),
-              menuSubItem(
-                text = "Screening",
-                tabName = "gs_screening"
-              )
-            ),
-            menuItem(
-              text = "Visualization",
-              tabName = "visualization",
-              icon = icon("circle-nodes")
-            ),
-            menuItem(
-              text = "Utilities",
-              tabName = "utilities",
-              icon = icon("screwdriver-wrench")
-            )
-          )
-        )
-        
-        # Dont render these elements
-        output$db_no_entries <- NULL
-        output$distancematrix_no_entries <- NULL
-        output$db_entries <- NULL
-        output$edit_index <- NULL
-        output$edit_scheme_d <- NULL
-        output$edit_entries <- NULL
-        output$compare_select <- NULL
-        output$delete_select <- NULL
-        output$del_bttn <- NULL
-        output$compare_allele_box <- NULL
-        output$download_entries <- NULL
-        output$missing_values <- NULL
-        output$delete_box <- NULL
-        output$missing_values_sidebar <- NULL
-        output$distmatrix_sidebar <- NULL
-        output$download_scheme_info <- NULL
-        output$download_loci <- NULL
-        output$entry_table_controls <- NULL
-        output$multi_stop <- NULL
-        output$metadata_multi_box <- NULL
-        output$start_multi_typing_ui <- NULL
-        output$pending_typing <- NULL
-        output$multi_typing_results <- NULL
-        output$single_typing_progress <- NULL
-        output$metadata_single_box <- NULL
-        output$start_typing_ui <- NULL
-        
-      }
-    } else {
-      log_print(paste0("Loading existing ", input$scheme_db, " database from ", DB$database))
-    }
-    
-    if(DB$load_selected == TRUE) {
-      
-      if(gsub(" ", "_", input$scheme_db) %in% schemes) { #Check if selected scheme valid
-        
-        # Save database path for next start
-        saveRDS(DB$database, paste0(getwd(), "/execute/last_db.rds"))
-        
-        DB$check_new_entries <- TRUE
-        DB$data <- NULL
-        DB$meta_gs <- NULL
-        DB$meta <- NULL
-        DB$meta_true <- NULL
-        DB$allelic_profile <- NULL
-        DB$allelic_profile_trunc <- NULL
-        DB$allelic_profile_true <- NULL
-        DB$scheme <- input$scheme_db
-        
-        # null Distance matrix, entry table and plots
-        output$db_distancematrix <- NULL 
-        output$db_entries_table <- NULL
-        output$tree_mst <- NULL
-        output$tree_nj <- NULL
-        output$tree_upgma <- NULL
-        
-        # null typing initiation UI
-        output$multi_stop <- NULL
-        output$metadata_multi_box <- NULL
-        output$start_multi_typing_ui <- NULL
-        output$pending_typing <- NULL
-        output$multi_typing_results <- NULL
-        output$single_typing_progress <- NULL
-        output$metadata_single_box <- NULL
-        output$start_typing_ui <- NULL
-        
-        # null report values
-        Report$report_list_mst <- list()
-        Report$report_list_nj <- list()
-        Report$report_list_upgma <- list()
-        
-        # null plots
-        Vis$nj <- NULL
-        Vis$upgma <- NULL
-        Vis$ggraph_1 <- NULL
-        
-        removeModal()
-        
-        #### Render Menu Items ----
-        
-        Startup$sidebar <- FALSE
-        Startup$header <- FALSE
-        
-        output$menu_sep2 <- renderUI(hr())
-        
-        # Hide start message
-        output$start_message <- NULL
-        
-        if(any(grepl(gsub(" ", "_", DB$scheme), dir_ls(DB$database)))) {
-          
-          if(!any(grepl("alleles", dir_ls(paste0(
-            DB$database, "/", 
-            gsub(" ", "_", DB$scheme)))))) {
-            
-            log_print("Missing loci files")
-            
-            # Show message that loci files are missing
-            showModal(
-              modalDialog(
-                paste0("Whoops! No loci files are present in the local ", 
-                       DB$scheme, 
-                       " folder. Download the scheme again (no influence on already typed assemblies)."),
-                title = "Local Database Error",
-                fade = TRUE,
-                easyClose = TRUE,
-                footer = tagList(
-                  modalButton("Okay")
-                )
-              )
-            )
-            
-            # Render menu with Manage Schemes as start tab
-            output$menu <- renderMenu(
-              sidebarMenu(
-                menuItem(
-                  text = "Database Browser",
-                  tabName = "database",
-                  icon = icon("hard-drive"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "db_browse_entries"
-                  ),
-                  menuSubItem(
-                    text = "Scheme Info",
-                    tabName = "db_schemeinfo"
-                  ),
-                  menuSubItem(
-                    text = "Loci Info",
-                    tabName = "db_loci_info"
-                  ),
-                  menuSubItem(
-                    text = "Distance Matrix",
-                    tabName = "db_distmatrix"
-                  ),
-                  menuSubItem(
-                    text = "Missing Values",
-                    tabName = "db_missing_values",
-                    icon = icon("triangle-exclamation")
-                  )
-                ),
-                menuItem(
-                  text = "Manage Schemes",
-                  tabName = "init",
-                  icon = icon("layer-group"),
-                  selected = TRUE
-                ),
-                menuItem(
-                  text = "Allelic Typing",
-                  tabName = "typing",
-                  icon = icon("gears")
-                ),
-                menuItem(
-                  text = "Resistance Profile",
-                  tabName = "gene_screening",
-                  icon = icon("dna"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "gs_profile"
-                  ),
-                  menuSubItem(
-                    text = "Screening",
-                    tabName = "gs_screening"
-                  )
-                ),
-                menuItem(
-                  text = "Visualization",
-                  tabName = "visualization",
-                  icon = icon("circle-nodes")
-                ),
-                menuItem(
-                  text = "Utilities",
-                  tabName = "utilities",
-                  icon = icon("screwdriver-wrench")
-                )
-              )
-            )
-          } else if (!any(grepl("scheme_info.html", dir_ls(paste0(
-            DB$database, "/", 
-            gsub(" ", "_", DB$scheme)))))) {
-            
-            output$download_scheme_info <- NULL
-            
-            log_print("Scheme info file missing")
-            
-            # Show message that scheme info is missing
-            showModal(
-              modalDialog(
-                paste0("Whoops! Scheme info of the local ", 
-                       DB$scheme, 
-                       " database is missing. Download the scheme again (no influence on already typed assemblies)."),
-                title = "Local Database Error",
-                fade = TRUE,
-                easyClose = TRUE,
-                footer = tagList(
-                  modalButton("Okay")
-                )
-              )
-            )
-            
-            # Render menu with Manage Schemes as start tab
-            output$menu <- renderMenu(
-              sidebarMenu(
-                menuItem(
-                  text = "Database Browser",
-                  tabName = "database",
-                  icon = icon("hard-drive"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "db_browse_entries"
-                  ),
-                  menuSubItem(
-                    text = "Scheme Info",
-                    tabName = "db_schemeinfo"
-                  ),
-                  menuSubItem(
-                    text = "Loci Info",
-                    tabName = "db_loci_info"
-                  ),
-                  menuSubItem(
-                    text = "Distance Matrix",
-                    tabName = "db_distmatrix"
-                  ),
-                  menuSubItem(
-                    text = "Missing Values",
-                    tabName = "db_missing_values",
-                    icon = icon("triangle-exclamation")
-                  )
-                ),
-                menuItem(
-                  text = "Manage Schemes",
-                  tabName = "init",
-                  icon = icon("layer-group"),
-                  selected = TRUE
-                ),
-                menuItem(
-                  text = "Allelic Typing",
-                  tabName = "typing",
-                  icon = icon("gears")
-                ),
-                menuItem(
-                  text = "Resistance Profile",
-                  tabName = "gene_screening",
-                  icon = icon("dna"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "gs_profile"
-                  ),
-                  menuSubItem(
-                    text = "Screening",
-                    tabName = "gs_screening"
-                  )
-                ),
-                menuItem(
-                  text = "Visualization",
-                  tabName = "visualization",
-                  icon = icon("circle-nodes")
-                ),
-                menuItem(
-                  text = "Utilities",
-                  tabName = "utilities",
-                  icon = icon("screwdriver-wrench")
-                )
-              )
-            )
-            
-          } else if (!any(grepl("targets.csv", dir_ls(paste0(
-            DB$database, "/", 
-            gsub(" ", "_", DB$scheme)))))) {
-            
-            # Dont render target download button
-            output$download_loci <- NULL
-            
-            log_print("Missing loci info (targets.csv)")
-            
-            # Show message that scheme info is missing
-            showModal(
-              modalDialog(
-                paste0("Whoops! Loci info of the local ", 
-                       DB$scheme, 
-                       " database is missing. Download the scheme again (no influence on already typed assemblies)."),
-                title = "Local Database Error",
-                fade = TRUE,
-                easyClose = TRUE,
-                footer = tagList(
-                  modalButton("Okay")
-                )
-              )
-            )
-            
-            # Render menu with Manage Schemes as start tab
-            output$menu <- renderMenu(
-              sidebarMenu(
-                menuItem(
-                  text = "Database Browser",
-                  tabName = "database",
-                  icon = icon("hard-drive"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "db_browse_entries"
-                  ),
-                  menuSubItem(
-                    text = "Scheme Info",
-                    tabName = "db_schemeinfo"
-                  ),
-                  menuSubItem(
-                    text = "Loci Info",
-                    tabName = "db_loci_info"
-                  ),
-                  menuSubItem(
-                    text = "Distance Matrix",
-                    tabName = "db_distmatrix"
-                  ),
-                  menuSubItem(
-                    text = "Missing Values",
-                    tabName = "db_missing_values",
-                    icon = icon("triangle-exclamation")
-                  )
-                ),
-                menuItem(
-                  text = "Manage Schemes",
-                  tabName = "init",
-                  icon = icon("layer-group"),
-                  selected = TRUE
-                ),
-                menuItem(
-                  text = "Allelic Typing",
-                  tabName = "typing",
-                  icon = icon("gears")
-                ),
-                menuItem(
-                  text = "Resistance Profile",
-                  tabName = "gene_screening",
-                  icon = icon("dna"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "gs_profile"
-                  ),
-                  menuSubItem(
-                    text = "Screening",
-                    tabName = "gs_screening"
-                  )
-                ),
-                menuItem(
-                  text = "Visualization",
-                  tabName = "visualization",
-                  icon = icon("circle-nodes")
-                ),
-                menuItem(
-                  text = "Utilities",
-                  tabName = "utilities",
-                  icon = icon("screwdriver-wrench")
-                )
-              )
-            )
-            
-          } else {
-            # Produce Scheme Info Table
-            schemeinfo <-
-              read_html(paste0(
-                DB$database, "/",
-                gsub(" ", "_", DB$scheme),
-                "/scheme_info.html"
-              )) %>%
-              html_table(header = FALSE) %>%
-              as.data.frame(stringsAsFactors = FALSE)
-            names(schemeinfo) <- NULL
-            DB$schemeinfo <- schemeinfo
-            number_loci <- as.vector(DB$schemeinfo[6, 2])
-            DB$number_loci <- as.numeric(gsub(",", "", number_loci))
-            
-            # Produce Loci Info table
-            DB$loci_info <- read.csv(
-              file.path(DB$database, gsub(" ", "_", DB$scheme), "targets.csv"),
-              header = TRUE,
-              sep = "\t",
-              row.names = NULL,
-              colClasses = c(
-                "NULL",
-                "character",
-                "character",
-                "integer",
-                "integer",
-                "character",
-                "integer",
-                "NULL"
-              )
-            )
-            
-            # Check if number of loci/fastq-files of alleles is coherent with number of targets in scheme
-            if(DB$number_loci > length(dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")))) {
-              
-              log_print(paste0("Loci files are missing in the local ", DB$scheme, " folder"))
-              
-              # Show message that loci files are missing
-              showModal(
-                modalDialog(
-                  paste0("Whoops! Some loci files are missing in the local ", 
-                         DB$scheme, 
-                         " folder. Download the scheme again (no influence on already typed assemblies)."),
-                  title = "Local Database Error",
-                  fade = TRUE,
-                  easyClose = TRUE,
-                  footer = tagList(
-                    modalButton("Okay")
-                  )
-                )
-              )
-              
-              # Render menu with Manage Schemes as start tab
-              output$menu <- renderMenu(
-                sidebarMenu(
-                  menuItem(
-                    text = "Database Browser",
-                    tabName = "database",
-                    icon = icon("hard-drive"),
-                    startExpanded = TRUE,
-                    menuSubItem(
-                      text = "Browse Entries",
-                      tabName = "db_browse_entries"
-                    ),
-                    menuSubItem(
-                      text = "Scheme Info",
-                      tabName = "db_schemeinfo"
-                    ),
-                    menuSubItem(
-                      text = "Loci Info",
-                      tabName = "db_loci_info"
-                    ),
-                    menuSubItem(
-                      text = "Distance Matrix",
-                      tabName = "db_distmatrix"
-                    ),
-                    menuSubItem(
-                      text = "Missing Values",
-                      tabName = "db_missing_values",
-                      icon = icon("triangle-exclamation")
-                    )
-                  ),
-                  menuItem(
-                    text = "Manage Schemes",
-                    tabName = "init",
-                    icon = icon("layer-group"),
-                    selected = TRUE
-                  ),
-                  menuItem(
-                    text = "Allelic Typing",
-                    tabName = "typing",
-                    icon = icon("gears")
-                  ),
-                  menuItem(
-                    text = "Resistance Profile",
-                    tabName = "gene_screening",
-                    icon = icon("dna"),
-                    startExpanded = TRUE,
-                    menuSubItem(
-                      text = "Browse Entries",
-                      tabName = "gs_profile"
-                    ),
-                    menuSubItem(
-                      text = "Screening",
-                      tabName = "gs_screening"
-                    )
-                  ),
-                  menuItem(
-                    text = "Visualization",
-                    tabName = "visualization",
-                    icon = icon("circle-nodes")
-                  ),
-                  menuItem(
-                    text = "Utilities",
-                    tabName = "utilities",
-                    icon = icon("screwdriver-wrench")
-                  )
-                )
-              )
-              
-            } else {
-              ###### Alle checks bestanden -> Laden der DTB
-              # If typed entries present
-              if (any(grepl("Typing.rds", dir_ls(paste0(
-                DB$database, "/", gsub(" ", "_", DB$scheme)
-              ))))) {
-                
-                # Load database from files  
-                Database <- readRDS(file.path(DB$database, 
-                                              gsub(" ", "_", DB$scheme), 
-                                              "Typing.rds"))
-                
-                DB$data <- Database[["Typing"]]
-                
-                if(!is.null(DB$data)){
-                  if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-                    cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-                    DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
-                  } else {
-                    DB$cust_var <- data.frame()
-                  }
-                }
-                
-                DB$change <- FALSE
-                DB$meta_gs <- select(DB$data, c(1, 3:13))
-                DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-                DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-                DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-                DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
-                DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-                
-                # Null pipe 
-                con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
-                
-                cat("0\n", file = con)
-                
-                # Close the file connection
-                close(con)
-                
-                # Reset other reactive typing variables
-                Typing$progress_format_end <- 0 
-                Typing$progress_format_start <- 0
-                Typing$pending_format <- 0
-                Typing$entry_added <- 0
-                Typing$progress <- 0
-                Typing$progress_format <- 900000
-                output$single_typing_progress <- NULL
-                output$typing_fin <- NULL
-                output$single_typing_results <- NULL
-                output$typing_formatting <- NULL
-                Typing$single_path <- data.frame()
-                
-                # Null multi typing feedback variable
-                Typing$reset <- TRUE
-                
-                # Check need for new missing vlaue display
-                if(DB$first_look == TRUE) {
-                  if(sum(apply(DB$data, 1, anyNA)) >= 1) {
-                    DB$no_na_switch <- TRUE
-                  } else {
-                    DB$no_na_switch <- FALSE
-                  }
-                }
-                
-                DB$first_look <- TRUE
-                
-                output$initiate_typing_ui <- renderUI({
-                  column(
-                    width = 4,
-                    align = "center",
-                    br(),
-                    br(),
-                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-                    br(),
-                    br(),
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "center",
-                        shinyFilesButton(
-                          "genome_file",
-                          "Browse" ,
-                          icon = icon("file"),
-                          title = "Select the assembly in .fasta/.fna/.fa format:",
-                          multiple = FALSE,
-                          buttonType = "default",
-                          class = NULL,
-                          root = path_home()
-                        ),
-                        br(),
-                        br(),
-                        uiOutput("genome_path"),
-                        br()
-                      )
-                    )
-                  )
-                })
-                
-                output$initiate_multi_typing_ui <- renderUI({
-                  column(
-                    width = 4,
-                    align = "center",
-                    br(),
-                    br(),
-                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-                    br(), br(),
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "center",
-                        shinyDirButton(
-                          "genome_file_multi",
-                          "Browse",
-                          icon = icon("folder-open"),
-                          title = "Select the folder containing the genome assemblies (FASTA)",
-                          buttonType = "default",
-                          root = path_home()
-                        ),
-                        br(),
-                        br(),
-                        uiOutput("multi_select_info"),
-                        br()
-                      )
-                    ),
-                    uiOutput("multi_select_tab_ctrls"),
-                    br(),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "left",
-                        rHandsontableOutput("multi_select_table")
-                      )
-                    )
-                  )
-                })
-                
-                if(!anyNA(DB$allelic_profile)) {
-                  
-                  # no NA's -> dont render missing values sidebar elements
-                  output$missing_values_sidebar <- NULL
-                  
-                  # Render menu if no NA's present
-                  output$menu <- renderMenu(
-                    sidebarMenu(
-                      menuItem(
-                        text = "Database Browser",
-                        tabName = "database",
-                        icon = icon("hard-drive"),
-                        startExpanded = TRUE,
-                        menuSubItem(
-                          text = "Browse Entries",
-                          tabName = "db_browse_entries"
-                        ),
-                        menuSubItem(
-                          text = "Scheme Info",
-                          tabName = "db_schemeinfo"
-                        ),
-                        menuSubItem(
-                          text = "Loci Info",
-                          tabName = "db_loci_info"
-                        ),
-                        menuSubItem(
-                          text = "Distance Matrix",
-                          tabName = "db_distmatrix"
-                        )
-                      ),
-                      menuItem(
-                        text = "Manage Schemes",
-                        tabName = "init",
-                        icon = icon("layer-group")
-                      ),
-                      menuItem(
-                        text = "Allelic Typing",
-                        tabName = "typing",
-                        icon = icon("gears")
-                      ),
-                      menuItem(
-                        text = "Resistance Profile",
-                        tabName = "gene_screening",
-                        icon = icon("dna"),
-                        startExpanded = TRUE,
-                        menuSubItem(
-                          text = "Browse Entries",
-                          tabName = "gs_profile"
-                        ),
-                        menuSubItem(
-                          text = "Screening",
-                          tabName = "gs_screening"
-                        )
-                      ),
-                      menuItem(
-                        text = "Visualization",
-                        tabName = "visualization",
-                        icon = icon("circle-nodes")
-                      ),
-                      menuItem(
-                        text = "Utilities",
-                        tabName = "utilities",
-                        icon = icon("screwdriver-wrench")
-                      )
-                    )
-                  )
-                } else {
-                  output$menu <- renderMenu(
-                    sidebarMenu(
-                      menuItem(
-                        text = "Database Browser",
-                        tabName = "database",
-                        icon = icon("hard-drive"),
-                        startExpanded = TRUE,
-                        menuSubItem(
-                          text = "Browse Entries",
-                          tabName = "db_browse_entries",
-                          selected = TRUE
-                        ),
-                        menuSubItem(
-                          text = "Scheme Info",
-                          tabName = "db_schemeinfo"
-                        ),
-                        menuSubItem(
-                          text = "Loci Info",
-                          tabName = "db_loci_info"
-                        ),
-                        menuSubItem(
-                          text = "Distance Matrix",
-                          tabName = "db_distmatrix"
-                        ),
-                        menuSubItem(
-                          text = "Missing Values",
-                          tabName = "db_missing_values",
-                          icon = icon("triangle-exclamation")
-                        )
-                      ),
-                      menuItem(
-                        text = "Manage Schemes",
-                        tabName = "init",
-                        icon = icon("layer-group")
-                      ),
-                      menuItem(
-                        text = "Allelic Typing",
-                        tabName = "typing",
-                        icon = icon("gears")
-                      ),
-                      menuItem(
-                        text = "Resistance Profile",
-                        tabName = "gene_screening",
-                        icon = icon("dna"),
-                        startExpanded = TRUE,
-                        menuSubItem(
-                          text = "Browse Entries",
-                          tabName = "gs_profile"
-                        ),
-                        menuSubItem(
-                          text = "Screening",
-                          tabName = "gs_screening"
-                        )
-                      ),
-                      menuItem(
-                        text = "Visualization",
-                        tabName = "visualization",
-                        icon = icon("circle-nodes")
-                      ),
-                      menuItem(
-                        text = "Utilities",
-                        tabName = "utilities",
-                        icon = icon("screwdriver-wrench")
-                      )
-                    )
-                  )
-                }
-                
-                # Render custom variable display
-                output$show_cust_var <- renderTable(
-                  width = "100%", 
-                  {
-                    if((!is.null(DB$cust_var)) & (!is.null(input$cust_var_select))) {
-                      if(nrow(DB$cust_var) > 5) {
-                        low <- -4
-                        high <- 0
-                        for (i in 1:input$cust_var_select) {
-                          low <- low + 5
-                          if((nrow(DB$cust_var) %% 5) != 0) {
-                            if(i == ceiling(nrow(DB$cust_var) / 5 )) {
-                              high <- high + nrow(DB$cust_var) %% 5
-                            } else {
-                              high <- high + 5
-                            }
-                          } else {
-                            high <- high + 5
-                          }
-                        }
-                        DB$cust_var[low:high,]
-                      } else {
-                        DB$cust_var
-                      }
-                    } else if (!is.null(DB$cust_var)) {
-                      DB$cust_var
-                    }
-                  })
-                
-                # render visualization sidebar elements
-                observe({
-                  Vis$tree_algo <- input$tree_algo
-                })
-                
-                output$visualization_sidebar <- renderUI({
-                  if(!is.null(DB$data)) {
-                    column(
-                      width = 12,
-                      br(),
-                      fluidRow(
-                        column(1),
-                        column(
-                          width = 11,
-                          align = "left",
-                          prettyRadioButtons(
-                            "tree_algo",
-                            choices = c("Minimum-Spanning", "Neighbour-Joining", "UPGMA"),
-                            label = "",
-                            selected = if(!is.null(Vis$tree_algo)){Vis$tree_algo} else {"Minimum-Spanning"}
-                          ),
-                        )
-                      ),
-                      br(),
-                      fluidRow(
-                        column(
-                          width = 12,
-                          align = "center",
-                          tags$div(
-                            id = "button-wrapper",
-                            actionButton(
-                              "create_tree",
-                              h5("Create Tree", style = "position: relative; left: 15px; color: white; font-size: 15px;"),
-                              width = "100%"
-                            ),
-                            tags$img(
-                              src = "phylo.png",
-                              alt = "icon",
-                              class = "icon"
-                            )
-                          )
-                        )
-                      ), 
-                      br(),
-                      hr(),
-                      conditionalPanel(
-                        "input.tree_algo=='Minimum-Spanning'",
-                        fluidRow(
-                          column(
-                            width = 12,
-                            align = "left",
-                            br(),
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 16px; margin-left: 15px', "Sizing")
-                              )
-                            )
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 12,
-                            radioGroupButtons(
-                              "mst_ratio",
-                              "",
-                              choiceNames = c("16:10", "16:9", "4:3"),
-                              choiceValues = c((16/10), (16/9), (4/3)),
-                              width = "100%"
-                            ),
-                            br(),
-                            sliderInput(
-                              "mst_scale",
-                              "",
-                              min = 500,
-                              max = 1200,
-                              step = 5,
-                              value = 800,
-                              width = "95%",
-                              ticks = FALSE
-                            )
-                          )
-                        ),
-                        br(),
-                        hr(),
-                        fluidRow(
-                          column(
-                            width = 12,
-                            column(
-                              width = 5,
-                              align = "left",
-                              conditionalPanel(
-                                "input.mst_plot_format=='jpeg'",
-                                actionBttn(
-                                  "save_plot_jpeg",
-                                  style = "simple",
-                                  label = "Save Plot",
-                                  size = "sm",
-                                  icon = NULL,
-                                  color = "primary"
-                                )  
-                              ),
-                              conditionalPanel(
-                                "input.mst_plot_format=='png'",
-                                actionBttn(
-                                  "save_plot_png",
-                                  style = "simple",
-                                  label = "Save Plot",
-                                  size = "sm",
-                                  icon = NULL,
-                                  color = "primary"
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.mst_plot_format=='bmp'",
-                                actionBttn(
-                                  "save_plot_bmp",
-                                  style = "simple",
-                                  label = "Save Plot",
-                                  size = "sm",
-                                  icon = NULL,
-                                  color = "primary"
-                                )  
-                              ),
-                              conditionalPanel(
-                                "input.mst_plot_format=='html'",
-                                downloadBttn(
-                                  "save_plot_html",
-                                  style = "simple",
-                                  label = "Save Plot",
-                                  size = "sm",
-                                  icon = NULL,
-                                  color = "primary"
-                                )
-                              )
-                            ),
-                            column(
-                              width = 7,
-                              div(
-                                style = "max-width: 150px",
-                                class = "format",
-                                selectInput(
-                                  inputId = "mst_plot_format",
-                                  label = "",
-                                  choices = c("html", "jpeg", "png", "bmp")
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.tree_algo=='Neighbour-Joining'",
-                        fluidRow(
-                          column(
-                            width = 12,
-                            column(
-                              width = 5,
-                              align = "left",
-                              downloadBttn(
-                                "download_nj",
-                                style = "simple",
-                                label = "Save Plot",
-                                size = "sm",
-                                icon = NULL,
-                                color = "primary"
-                              )
-                            ),
-                            column(
-                              width = 7,
-                              div(
-                                style = "max-width: 150px",
-                                class = "format",
-                                selectInput(
-                                  inputId = "filetype_nj",
-                                  label = "",
-                                  choices = c("png", "jpeg", "bmp", "svg")
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.tree_algo=='UPGMA'",
-                        fluidRow(
-                          column(
-                            width = 12,
-                            column(
-                              width = 5,
-                              align = "left",
-                              downloadBttn(
-                                "download_upgma",
-                                style = "simple",
-                                label = "Save Plot",
-                                size = "sm",
-                                icon = NULL,
-                                color = "primary"
-                              )
-                            ),
-                            column(
-                              width = 7,
-                              div(
-                                style = "max-width: 150px",
-                                class = "format",
-                                selectInput(
-                                  inputId = "filetype_upgma",
-                                  label = "",
-                                  choices = c("png", "jpeg", "bmp", "svg")
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 6,
-                          align = "left",
-                          br(),
-                          actionButton(
-                            "create_rep",
-                            "Print Report"
-                          )
-                        )
-                      )
-                    )
-                  }
-                })
-                
-                # Render entry table sidebar elements
-                output$entrytable_sidebar <- renderUI({
-                  if(!is.null(DB$data)) {
-                    column(
-                      width = 12,
-                      align = "center",
-                      br(), 
-                      fluidRow(
-                        column(1),
-                        column(
-                          width = 10,
-                          align = "left",
-                          if(nrow(DB$data) > 40) {
-                            div(
-                              class = "mat-switch-db-tab",
-                              materialSwitch(
-                                "table_height",
-                                h5(p("Show Full Table"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            )
-                          }
-                        )
-                      ),
-                      br(), br(), 
-                      fluidRow(
-                        column(
-                          width = 12,
-                          HTML(
-                            paste(
-                              tags$span(style='color: white; font-size: 18px; margin-bottom: 0px', 'Custom Variables')
-                            )
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 8,
-                          textInput(
-                            "new_var_name",
-                            label = "",
-                            placeholder = "New Variable"
-                          )
-                        ),
-                        column(
-                          width = 2,
-                          actionButton(
-                            "add_new_variable",
-                            "",
-                            icon = icon("plus")
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 8,
-                          align = "left",
-                          div(
-                            class = "textinput_var",
-                            selectInput(
-                              "del_which_var",
-                              "",
-                              DB$cust_var$Variable
-                            )
-                          )
-                        ),
-                        column(
-                          width = 2,
-                          align = "left",
-                          actionButton(
-                            "delete_new_variable",
-                            "",
-                            icon = icon("minus")
-                          )
-                        )
-                      ),
-                      br(), 
-                      fluidRow(
-                        column(1),
-                        column(
-                          width = 4,
-                          uiOutput("cust_var_info")
-                        )
-                      ),
-                      fluidRow(
-                        column(1),
-                        column(
-                          width = 11,
-                          align = "center",
-                          tableOutput("show_cust_var")
-                        )
-                      ),
-                      fluidRow(
-                        column(4),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("cust_var_select")
-                        )
-                      )
-                    )
-                  } 
-                })
-                
-                # Render missing values sidebar elements
-                output$missing_values_sidebar <- renderUI({
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        br(),
-                        materialSwitch(
-                          "miss_val_height",
-                          h5(p("Show Full Table"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                          value = FALSE,
-                          right = TRUE
-                        )
-                      ),
-                      br()
-                    ),
-                    fluidRow(
-                      column(
-                        width = 6,
-                        HTML(
-                          paste(
-                            tags$span(style='color: white; font-size: 14px; position: relative; bottom: -23px; right: -15px', 
-                                      'Download CSV')
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        downloadBttn(
-                          "download_na_matrix",
-                          style = "simple",
-                          label = "",
-                          size = "sm",
-                          icon = icon("download")
-                        )
-                      )
-                    )
-                  )
-                })
-                
-                # Render scheme info download button
-                output$download_loci <- renderUI({
-                  column(
-                    12,
-                    downloadBttn(
-                      "download_loci_info",
-                      style = "simple",
-                      label = "",
-                      size = "sm",
-                      icon = icon("download"),
-                      color = "primary"
-                    ),
-                    bsTooltip("download_loci_info_bttn", HTML("Save loci information <br> (without sequence)"), placement = "top", trigger = "hover")
-                  )
-                })
-                
-                # Render scheme info download button
-                output$download_scheme_info <- renderUI({
-                  downloadBttn(
-                    "download_schemeinfo",
-                    style = "simple",
-                    label = "",
-                    size = "sm",
-                    icon = icon("download"),
-                    color = "primary"
-                  )
-                })
-                
-                # Render distance matrix sidebar
-                output$distmatrix_sidebar <- renderUI({
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "center",
-                        selectInput(
-                          "distmatrix_label",
-                          label = "",
-                          choices = c("Index", "Assembly Name", "Assembly ID"),
-                          selected = c("Assembly Name"),
-                          width = "100%"
-                        ),
-                        br()
-                      )
-                    ),
-                    div(
-                      class = "mat-switch-dmatrix",
-                      materialSwitch(
-                        "distmatrix_true",
-                        h5(p("Only Included Entries"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                        value = FALSE,
-                        right = TRUE
-                      )
-                    ),
-                    div(
-                      class = "mat-switch-dmatrix",
-                      materialSwitch(
-                        "distmatrix_triangle",
-                        h5(p("Show Upper Triangle"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                        value = FALSE,
-                        right = TRUE
-                      )
-                    ),
-                    div(
-                      class = "mat-switch-dmatrix-last",
-                      materialSwitch(
-                        "distmatrix_diag",
-                        h5(p("Show Diagonal"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                        value = TRUE,
-                        right = TRUE
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 6,
-                        HTML(
-                          paste(
-                            tags$span(style='color: white; font-size: 14px; position: relative; bottom: 37px; right: -15px', 
-                                      'Download CSV')
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        downloadBttn(
-                          "download_distmatrix",
-                          style = "simple",
-                          label = "",
-                          size = "sm",
-                          icon = icon("download")
-                        )
-                      )
-                    )
-                  )
-                })
-                
-                # Render select input to choose displayed loci
-                output$compare_select <- renderUI({
-                  
-                  if(nrow(DB$data) == 1) {
-                    HTML(
-                      paste(
-                        tags$span(style='color: white; font-size: 15px;', "Type at least two assemblies to compare")
-                      )
-                    )
-                  } else {
-                    if(!is.null(input$compare_difference)) {
-                      if (input$compare_difference == FALSE) {
-                        pickerInput(
-                          inputId = "compare_select",
-                          label = "",
-                          width = "85%",
-                          choices = names(DB$allelic_profile),
-                          selected = names(DB$allelic_profile)[1:20],
-                          options = list(
-                            `live-search` = TRUE,
-                            `actions-box` = TRUE,
-                            size = 10,
-                            style = "background-color: white; border-radius: 5px;"
-                          ),
-                          multiple = TRUE
-                        )
-                      } else {
-                        pickerInput(
-                          inputId = "compare_select",
-                          label = "",
-                          width = "85%",
-                          choices = names(DB$allelic_profile),
-                          selected = names(DB$allelic_profile)[var_alleles(DB$allelic_profile)],
-                          options = list(
-                            `live-search` = TRUE,
-                            `actions-box` = TRUE,
-                            size = 10,
-                            style = "background-color: white; border-radius: 5px;"
-                          ),
-                          multiple = TRUE
-                        )
-                      }
-                    }
-                  }
-                })
-                
-                #### Render Entry Data Table ----
-                output$db_entries_table <- renderUI({
-                  if(!is.null(DB$data)) {
-                    if(between(nrow(DB$data), 1, 30)) {
-                      rHandsontableOutput("db_entries")
-                    } else {
-                      addSpinner(
-                        rHandsontableOutput("db_entries"),
-                        spin = "dots",
-                        color = "#ffffff"
-                      )
-                    }
-                  }
-                })
-                
-                if (!is.null(DB$data)) {
-                  
-                  observe({
-                    
-                    if (!is.null(DB$data)) {
-                      if (nrow(DB$data) == 1) {
-                        if(!is.null(DB$data) & !is.null(DB$cust_var)) {
-                          output$db_entries <- renderRHandsontable({
-                            rhandsontable(
-                              select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                              error_highlight = err_thresh() - 1,                              
-                              rowHeaders = NULL,
-                              contextMenu = FALSE,
-                              highlightCol = TRUE, 
-                              highlightRow = TRUE
-                            ) %>%
-                              hot_col(1, 
-                                      valign = "htMiddle",
-                                      halign = "htCenter") %>%
-                              hot_col(3, readOnly = TRUE) %>%
-                              hot_col(c(1, 5, 10, 11, 12, 13),
-                                      readOnly = TRUE) %>%
-                              hot_col(3:(13 + nrow(DB$cust_var)), 
-                                      valign = "htMiddle",
-                                      halign = "htLeft") %>%
-                              hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                              hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                              hot_col(8, type = "dropdown", source = country_names) %>%
-                              hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                                      validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                              hot_cols(fixedColumnsLeft = 1) %>%
-                              hot_col(2, type = "checkbox", width = "auto",
-                                      valign = "htTop",
-                                      halign = "htCenter") %>%
-                              hot_rows(fixedRowsTop = 0) %>%
-                              hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-                          })
-                        }
-                      } else if (between(nrow(DB$data), 2, 40)) {
-                        if (length(input$compare_select) > 0) {
-                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
-                            output$db_entries <- renderRHandsontable({
-                              
-                              entry_data <- DB$data %>%
-                                select(1:(13 + nrow(DB$cust_var))) %>%
-                                add_column(select(DB$allelic_profile_trunc, input$compare_select))
-                              
-                              rhandsontable(
-                                entry_data,
-                                col_highlight = diff_allele() - 1,
-                                dup_names_high = duplicated_names() - 1,
-                                dup_ids_high = duplicated_ids() - 1,
-                                row_highlight = true_rows() - 1,
-                                error_highlight = err_thresh() - 1,
-                                rowHeaders = NULL,
-                                highlightCol = TRUE, 
-                                highlightRow = TRUE,
-                                contextMenu = FALSE
-                              )  %>%
-                                hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
-                                        valign = "htMiddle",
-                                        halign = "htCenter",
-                                        readOnly = TRUE) %>%
-                                hot_col(1, 
-                                        valign = "htMiddle",
-                                        halign = "htCenter") %>%
-                                hot_col(3, readOnly = TRUE) %>%
-                                hot_col(c(1, 5, 10, 11, 12, 13),
-                                        readOnly = TRUE) %>%
-                                hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(3:(13 + nrow(DB$cust_var)), 
-                                        valign = "htMiddle",
-                                        halign = "htLeft") %>%
-                                hot_col(8, type = "dropdown", source = country_names) %>%
-                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                                        validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                                hot_col(2, type = "checkbox", width = "auto",
-                                        valign = "htTop",
-                                        halign = "htCenter",
-                                        strict = TRUE,
-                                        allowInvalid = FALSE,
-                                        copyable = TRUE) %>%
-                                hot_cols(fixedColumnsLeft = 1) %>%
-                                hot_rows(fixedRowsTop = 0) %>%
-                                hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-  
-                       }
-              }") %>%
-                                hot_col(diff_allele(),
-                                        renderer = "
-                  function(instance, td, row, col, prop, value, cellProperties) {
-                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
-  
-                    if (instance.params) {
-                          hcols = instance.params.col_highlight;
-                          hcols = hcols instanceof Array ? hcols : [hcols];
-                        }
-  
-                    if (instance.params && hcols.includes(col)) {
-                      td.style.background = 'rgb(116, 188, 139)';
-                    }
-                }"
-                                ) %>%
-                                hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-                            })
-                          }
-                        } else {
-                          if(!is.null(DB$data) & !is.null(DB$cust_var)) {
-                            output$db_entries <- renderRHandsontable({
-                              rhandsontable(
-                                select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                                rowHeaders = NULL,
-                                row_highlight = true_rows() - 1,
-                                dup_names_high = duplicated_names()- 1,
-                                dup_ids_high = duplicated_ids() - 1,
-                                error_highlight = err_thresh() - 1,
-                                contextMenu = FALSE,
-                                highlightCol = TRUE, 
-                                highlightRow = TRUE
-                              ) %>%
-                                hot_cols(fixedColumnsLeft = 1) %>%
-                                hot_col(1, 
-                                        valign = "htMiddle",
-                                        halign = "htCenter") %>%
-                                hot_col(3, readOnly = TRUE) %>%
-                                hot_col(c(1, 5, 10, 11, 12, 13),
-                                        readOnly = TRUE) %>%
-                                hot_col(3:(13 + nrow(DB$cust_var)), 
-                                        valign = "htMiddle",
-                                        halign = "htLeft") %>%
-                                hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(8, type = "dropdown", source = country_names) %>%
-                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                                        validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                                hot_col(2, type = "checkbox", width = "auto",
-                                        valign = "htTop",
-                                        halign = "htCenter") %>%
-                                hot_rows(fixedRowsTop = 0) %>%
-                                hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-  
-                       }
-              }") %>%
-                                hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-                            })    
-                          }
-                        }
-                      } else {
-                        if (length(input$compare_select) > 0) {
-                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
-                            output$db_entries <- renderRHandsontable({
-                              
-                              entry_data <- DB$data %>%
-                                select(1:(13 + nrow(DB$cust_var))) %>%
-                                add_column(select(DB$allelic_profile_trunc, input$compare_select))
-                              
-                              rhandsontable(
-                                entry_data,
-                                col_highlight = diff_allele() - 1,
-                                rowHeaders = NULL,
-                                height = table_height(),
-                                row_highlight = true_rows() - 1,
-                                dup_names_high = duplicated_names() - 1,
-                                dup_ids_high = duplicated_ids() - 1,
-                                error_highlight = err_thresh() - 1,
-                                contextMenu = FALSE,
-                                highlightCol = TRUE, 
-                                highlightRow = TRUE
-                              ) %>%
-                                hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
-                                        readOnly = TRUE, 
-                                        valign = "htMiddle",
-                                        halign = "htCenter") %>%
-                                hot_col(3:(13 + nrow(DB$cust_var)), 
-                                        valign = "htMiddle",
-                                        halign = "htLeft") %>%
-                                hot_col(3, readOnly = TRUE) %>%
-                                hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(c(1, 5, 10, 11, 12, 13),
-                                        readOnly = TRUE) %>%
-                                hot_col(8, type = "dropdown", source = country_names) %>%
-                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                                        validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                                hot_col(1, 
-                                        valign = "htMiddle",
-                                        halign = "htCenter") %>%
-                                hot_col(2, type = "checkbox", width = "auto",
-                                        valign = "htTop",
-                                        halign = "htCenter",
-                                        allowInvalid = FALSE,
-                                        copyable = TRUE) %>%
-                                hot_cols(fixedColumnsLeft = 1) %>%
-                                hot_rows(fixedRowsTop = 0) %>%
-                                hot_col(1, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.row_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                                                             }
-                                                           }
-                                                       }") %>%
-                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") %>%
-                                hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(diff_allele(),
-                                        renderer = "
-                  function(instance, td, row, col, prop, value, cellProperties) {
-                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
-  
-                    if (instance.params) {
-                          hcols = instance.params.col_highlight;
-                          hcols = hcols instanceof Array ? hcols : [hcols];
-                        }
-  
-                    if (instance.params && hcols.includes(col)) {
-                      td.style.background = 'rgb(116, 188, 139)';
-                    }
-                }") 
-                            })    
-                          }
-                        } else {
-                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
-                            output$db_entries <- renderRHandsontable({
-                              rhandsontable(
-                                select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                                rowHeaders = NULL,
-                                height = table_height(),
-                                dup_names_high = duplicated_names() - 1,
-                                dup_ids_high = duplicated_ids() - 1,
-                                row_highlight = true_rows() - 1,
-                                error_highlight = err_thresh() - 1,
-                                contextMenu = FALSE,
-                                highlightCol = TRUE, 
-                                highlightRow = TRUE
-                              ) %>%
-                                hot_cols(fixedColumnsLeft = 1) %>%
-                                hot_col(1, 
-                                        valign = "htMiddle",
-                                        halign = "htCenter") %>%
-                                hot_col(3, readOnly = TRUE) %>%
-                                hot_col(c(1, 5, 10, 11, 12, 13),
-                                        readOnly = TRUE) %>%
-                                hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(8, type = "dropdown", source = country_names) %>%
-                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                                        validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                                hot_col(3:(13 + nrow(DB$cust_var)), 
-                                        valign = "htMiddle",
-                                        halign = "htLeft") %>%
-                                hot_rows(fixedRowsTop = 0) %>%
-                                hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(2, type = "checkbox", width = "auto",
-                                        valign = "htTop", halign = "htCenter") %>%
-                                hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-                            })
-                          }
-                        }
-                      }
-                    }
-                    
-                    # Dynamic save button when rhandsontable changes or new entries
-                    output$edit_entry_table <- renderUI({
-                      if(check_new_entry() & DB$check_new_entries) {
-                        Typing$reload <- FALSE
-                        fluidRow(
-                          column(
-                            width = 8,
-                            align = "left",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: absolute; bottom: -30px; right: -5px', 
-                                          'New entries - reload database')
-                              )
-                            )
-                          ),
-                          column(
-                            width = 4,
-                            actionButton(
-                              "load",
-                              "",
-                              icon = icon("rotate"),
-                              class = "pulsating-button"
-                            )
-                          )
-                        )
-                      } else if(Typing$status == "Attaching") {
-                        fluidRow(
-                          column(
-                            width = 11,
-                            align = "left",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: absolute; bottom: -30px; right: -5px', 'No database changes possible - pending entry addition')
-                              )
-                            )
-                          ),
-                          column(
-                            width = 1,
-                            HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px; color:white; margin-top: 10px"></i>'))
-                          )
-                        )
-                      } else if((DB$change == TRUE) | !identical(get.entry.table.meta(), select(DB$meta, -13))) {
-                        
-                        if(!is.null(input$db_entries)) {
-                          fluidRow(
-                            column(
-                              width = 5,
-                              HTML(
-                                paste(
-                                  tags$span(style='color: white; font-size: 16px; position: absolute; bottom: -30px; right: -5px', 'Confirm changes')
-                                )
-                              )
-                            ),
-                            column(
-                              width = 3,
-                              actionButton(
-                                "edit_button",
-                                "",
-                                icon = icon("bookmark"),
-                                class = "pulsating-button"
-                              )
-                            ),
-                            column(
-                              width = 4,
-                              actionButton(
-                                "undo_changes",
-                                "Undo",
-                                icon = icon("repeat")
-                              )
-                            )
-                          )
-                        }
-                      } else {NULL}
-                    })
-                    
-                  })
-                  
-                  # Hide no entry message
-                  output$db_no_entries <- NULL
-                  output$distancematrix_no_entries <- NULL
-                  
-                } else {
-                  
-                  # If database loading not successful dont show entry table
-                  output$db_entries_table <- NULL
-                  output$entry_table_controls <- NULL
-                }
-                
-                # Render Entry table controls
-                output$entry_table_controls <- renderUI({
-                  fluidRow(
-                    column(1),
-                    column(
-                      width = 3,
-                      align = "center",
-                      fluidRow(
-                        column(
-                          width = 4,
-                          align = "center",
-                          actionButton(
-                            "sel_all_entries",
-                            "Select All",
-                            icon = icon("check")
-                          )
-                        ),
-                        column(
-                          width = 4,
-                          align = "left",
-                          actionButton(
-                            "desel_all_entries",
-                            "Deselect All",
-                            icon = icon("xmark")
-                          )
-                        )
-                      )
-                    ),
-                    column(
-                      width = 3,
-                      uiOutput("edit_entry_table")
-                    )
-                  )
-                })
-                
-                #### Render Distance Matrix ----
-                observe({
-                  if(!is.null(DB$data)) {
-                    
-                    if(any(duplicated(DB$meta$`Assembly Name`)) | any(duplicated(DB$meta$`Assembly ID`))) {
-                      output$db_distancematrix <- NULL
-                      
-                      if( (sum(duplicated(DB$meta$`Assembly Name`)) > 0) & (sum(duplicated(DB$meta$`Assembly ID`)) == 0) ) {
-                        duplicated_txt <- paste0(
-                          paste(
-                            paste0("Name  # ", which(duplicated(DB$meta$`Assembly Name`)), " - "),
-                            DB$meta$`Assembly Name`[which(duplicated(DB$meta$`Assembly Name`))]
-                          ),
-                          "<br>"
-                        )
-                      } else if ( (sum(duplicated(DB$meta$`Assembly ID`)) > 0) & (sum(duplicated(DB$meta$`Assembly Name`)) == 0) ){
-                        duplicated_txt <- paste0(
-                          paste(
-                            paste0("ID  # ", which(duplicated(DB$meta$`Assembly ID`)), " - "),
-                            DB$meta$`Assembly ID`[which(duplicated(DB$meta$`Assembly ID`))]
-                          ),
-                          "<br>"
-                        )
-                      } else {
-                        duplicated_txt <- c(
-                          paste0(
-                            paste(
-                              paste0("Name  # ", which(duplicated(DB$meta$`Assembly Name`)), " - "),
-                              DB$meta$`Assembly Name`[which(duplicated(DB$meta$`Assembly Name`))]
-                            ),
-                            "<br>"
-                          ),
-                          paste0(
-                            paste(
-                              paste0("ID  # ", which(duplicated(DB$meta$`Assembly ID`)), " - "),
-                              DB$meta$`Assembly ID`[which(duplicated(DB$meta$`Assembly ID`))]
-                            ),
-                            "<br>"
-                          )
-                        )
-                      }
-                      
-                      output$distancematrix_duplicated <- renderUI({
-                        column(
-                          width = 12,
-                          tags$span(style = "font-size: 15; color: white",
-                                    "Change duplicated entry names to display distance matrix."),
-                          br(), br(), br(),
-                          actionButton("change_entries", "Go to Entry Table", class = "btn btn-default"),
-                          br(), br(), br(),
-                          tags$span(
-                            style = "font-size: 15; color: white",
-                            HTML(
-                              append(
-                                "Duplicated:",
-                                append(
-                                  "<br>",
-                                  duplicated_txt
-                                )
-                              )
-                            )
-                          )
-                        )
-                      })
-                    } else {
-                      output$distancematrix_duplicated <- NULL
-                      if(!is.null(DB$data) & !is.null(DB$allelic_profile) & !is.null(DB$allelic_profile_true) & !is.null(DB$cust_var) & !is.null(input$distmatrix_label) & !is.null(input$distmatrix_diag) & !is.null(input$distmatrix_triangle)) {
-                        output$db_distancematrix <- renderRHandsontable({
-                          rhandsontable(hamming_df(), 
-                                        digits = 1, 
-                                        readOnly = TRUE,
-                                        contextMenu = FALSE,
-                                        highlightCol = TRUE, 
-                                        highlightRow = TRUE,
-                                        height = distancematrix_height(), rowHeaders = NULL) %>%
-                            hot_heatmap(renderer = paste0("
-                            function (instance, td, row, col, prop, value, cellProperties) {
-                              Handsontable.renderers.TextRenderer.apply(this, arguments);
-                              heatmapScale  = chroma.scale(['#17F556', '#ED6D47']);
-                            
-                              if (instance.heatmap[col]) {
-                                mn = ", DB$matrix_min, ";
-                                mx = ", DB$matrix_max, ";
-                            
-                                pt = (parseInt(value, 10) - mn) / (mx - mn);    
-                            
-                                td.style.backgroundColor = heatmapScale(pt).hex();
-                              }
-                            }")) %>%
-                            hot_rows(fixedRowsTop = 0) %>%
-                            hot_cols(fixedColumnsLeft = 1) %>%
-                            hot_col(1:(dim(DB$ham_matrix)[1]+1),
-                                    halign = "htCenter",
-                                    valign = "htMiddle") %>%
-                            hot_col(1, renderer = "
-                            function(instance, td, row, col, prop, value, cellProperties) {
-                              Handsontable.renderers.NumericRenderer.apply(this, arguments);
-                              td.style.background = '#F0F0F0'
-                            }"
-                            )
-                        })  
-                      }
-                    }
-                    
-                    # Render Distance Matrix UI
-                    
-                    output$distmatrix_show <- renderUI({
-                      if(!is.null(DB$data)) {
-                        if(nrow(DB$data) > 1) {
-                          column(
-                            width = 10,
-                            uiOutput("distancematrix_duplicated"),
-                            div(
-                              class = "distmatrix",
-                              rHandsontableOutput("db_distancematrix")
-                            )
-                          )
-                        } else {
-                          column(
-                            width = 10,
-                            align = "left",
-                            p(
-                              HTML(
-                                paste(
-                                  tags$span(style='color: white; font-size: 15px;', "Type at least two assemblies to display a distance matrix.")
-                                )
-                              )
-                            ),
-                            br(),
-                            br()
-                          )
-                        }
-                      }
-                    })
-                    
-                  }
-                })
-                
-                
-                # Render delete entry box UI
-                output$delete_box <- renderUI({
-                  box(
-                    solidHeader = TRUE,
-                    status = "primary",
-                    width = "100%",
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "center",
-                        h3(p("Delete Entries"), style = "color:white")
-                      )
-                    ),
-                    hr(),
-                    fluidRow(
-                      column(
-                        width = 2,
-                        offset = 1,
-                        align = "right",
-                        br(),
-                        h5("Index", style = "color:white; margin-bottom: 0px;")
-                      ),
-                      column(
-                        width = 6,
-                        align = "center",
-                        uiOutput("delete_select")
-                      ),
-                      column(
-                        width = 2,
-                        align = "center",
-                        br(),
-                        uiOutput("del_bttn")
-                      )
-                    ),
-                    br()
-                  )
-                })
-                
-                # Render loci comparison box UI
-                output$compare_allele_box <- renderUI({
-                  box(
-                    solidHeader = TRUE,
-                    status = "primary",
-                    width = "100%",
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "center",
-                        h3(p("Compare Loci"), style = "color:white")
-                      )
-                    ),
-                    hr(),
-                    column(
-                      width = 12,
-                      align = "center",
-                      br(),
-                      uiOutput("compare_select"),
-                      br(),
-                      column(2),
-                      column(
-                        width = 10,
-                        align = "left",
-                        uiOutput("compare_difference_box")
-                      )
-                    ),
-                    br()
-                  )
-                })
-                
-                # Render entry table download box UI
-                output$download_entries <- renderUI({
-                  fluidRow(
-                    column(
-                      width = 12,
-                      box(
-                        solidHeader = TRUE,
-                        status = "primary",
-                        width = "100%",
-                        fluidRow(
-                          column(
-                            width = 12,
-                            align = "center",
-                            h3(p("Download Table"), style = "color:white")
-                          )
-                        ),
-                        hr(),
-                        fluidRow(
-                          column(2),
-                          column(
-                            width = 10,
-                            align = "left",
-                            br(),
-                            div(
-                              class = "mat-switch-db",
-                              materialSwitch(
-                                "download_table_include",
-                                h5(p("Only Included Entries"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            ),
-                            div(
-                              class = "mat-switch-db",
-                              materialSwitch(
-                                "download_table_loci",
-                                h5(p("Include Displayed Loci"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            ),
-                            br(),
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 12,
-                            align = "center",
-                            downloadBttn(
-                              "download_entry_table",
-                              style = "simple",
-                              label = "",
-                              size = "sm",
-                              icon = icon("download"),
-                              color = "primary"
-                            )
-                          )
-                        ),
-                        br()
-                      )
-                    ),
-                    column(
-                      width = 12,
-                      fluidRow(
-                        column(
-                          width = 2,
-                          div(
-                            class = "rectangle-blue" 
-                          ),
-                          div(
-                            class = "rectangle-orange" 
-                          ),
-                          div(
-                            class = "rectangle-red" 
-                          ),
-                          div(
-                            class = "rectangle-green" 
-                          )
-                        ),
-                        column(
-                          width = 10,
-                          align = "left",
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -12px", " = included for analyses")
-                              )
-                            )
-                          ),
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -13px", " =  duplicated name/ID")
-                              )
-                            )
-                          ),
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -14px", " =  ≥ 5% of loci missing")
-                              )
-                            )
-                          ),
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -15px", " =  locus contains multiple variants")
-                              )
-                            )
-                          ),
-                        )
-                      )
-                    )
-                  )
-                })
-                
-                # Render entry deletion select input
-                output$delete_select <- renderUI({
-                  pickerInput("select_delete",
-                              label = "",
-                              choices = DB$data[, "Index"],
-                              options = list(
-                                `live-search` = TRUE,
-                                `actions-box` = TRUE,
-                                size = 10,
-                                style = "background-color: white; border-radius: 5px;"
-                              ),
-                              multiple = TRUE)
-                })
-                
-                # Render delete entry button
-                output$del_bttn <- renderUI({
-                  actionBttn(
-                    "del_button",
-                    label = "",
-                    color = "danger",
-                    size = "sm",
-                    style = "material-circle",
-                    icon = icon("xmark")
-                  )
-                })
-                
-                #### Missing Values UI ----
-                
-                # Missing values calculations and table 
-                observe({
-                  
-                  if (!is.null(DB$allelic_profile)) {
-                    NA_table <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) != 0]
-                    
-                    NA_table <- NA_table[rowSums(is.na(NA_table)) != 0,]
-                    
-                    NA_table[is.na(NA_table)] <- "NA"
-                    
-                    NA_table <- NA_table %>% 
-                      cbind("Assembly Name" = DB$meta[rownames(NA_table),]$`Assembly Name`) %>%
-                      cbind("Errors" = DB$meta[rownames(NA_table),]$Errors) %>%
-                      relocate("Assembly Name", "Errors")
-                    
-                    DB$na_table <- NA_table
-                    
-                    if(!is.null(input$miss_val_height)) {
-                      if(nrow(DB$na_table) < 31) {
-                        output$table_missing_values <- renderRHandsontable({
-                          rhandsontable(
-                            DB$na_table,
-                            readOnly = TRUE,
-                            rowHeaders = NULL,
-                            contextMenu = FALSE,
-                            highlightCol = TRUE, 
-                            highlightRow = TRUE,
-                            error_highlight = err_thresh_na() - 1
-                          ) %>%
-                            hot_cols(fixedColumnsLeft = 1) %>%
-                            hot_rows(fixedRowsTop = 0) %>%
-                            hot_col(1:ncol(DB$na_table), valign = "htMiddle", halign = "htLeft") %>%
-                            hot_col(2, renderer = "
-                            function (instance, td, row, col, prop, value, cellProperties) {
-                              Handsontable.renderers.TextRenderer.apply(this, arguments);
-                              if (instance.params) {
-                                hrows = instance.params.error_highlight
-                                hrows = hrows instanceof Array ? hrows : [hrows]
-                                if (hrows.includes(row)) { 
-                                  td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
-                                }
-                              }
-                            }") %>%
-                            hot_col(3:ncol(DB$na_table), renderer = htmlwidgets::JS(
-                              "function(instance, td, row, col, prop, value, cellProperties) {
-                                if (value.length > 8) {
-                                  value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                                }
-                                td.innerHTML = value;
-                                td.style.textAlign = 'center';
-                                return td;
-                               }"
-                            ))
-                        })
-                      } else {
-                        output$table_missing_values <- renderRHandsontable({
-                          rhandsontable(
-                            DB$na_table,
-                            readOnly = TRUE,
-                            rowHeaders = NULL,
-                            height = miss.val.height(),
-                            contextMenu = FALSE,
-                            highlightCol = TRUE, 
-                            highlightRow = TRUE,
-                            error_highlight = err_thresh() - 1
-                          ) %>%
-                            hot_cols(fixedColumnsLeft = 1) %>%
-                            hot_rows(fixedRowsTop = 0) %>%
-                            hot_col(1:ncol(DB$na_table), valign = "htMiddle", halign = "htLeft") %>%
-                            hot_col(2, renderer = "
-                            function (instance, td, row, col, prop, value, cellProperties) {
-                              Handsontable.renderers.TextRenderer.apply(this, arguments);
-                              if (instance.params) {
-                                hrows = instance.params.error_highlight
-                                hrows = hrows instanceof Array ? hrows : [hrows]
-                                if (hrows.includes(row)) { 
-                                  td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
-                                }
-                              }
-                            }") %>%
-                            hot_col(3:ncol(DB$na_table), renderer = htmlwidgets::JS(
-                              "function(instance, td, row, col, prop, value, cellProperties) {
-                                if (value.length > 8) {
-                                  value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                                }
-                                td.innerHTML = value;
-                                td.style.textAlign = 'center';
-                                return td;
-                               }"
-                            ))
-                        })
-                      }
-                    }
-                  }
-                  
-                })
-                
-                # Render missing value informatiojn box UI
-                output$missing_values <- renderUI({
-                  div(
-                    class = "miss_val_box",
-                    box(
-                      solidHeader = TRUE,
-                      status = "primary",
-                      width = "100%",
-                      fluidRow(
-                        div(
-                          class = "white",
-                          column(
-                            width = 12,
-                            align = "left",
-                            br(), 
-                            HTML(
-                              paste0("There are ", 
-                                     strong(as.character(sum(is.na(DB$data)))), 
-                                     " unsuccessful allele allocations (NA). ",
-                                     strong(sum(sapply(DB$allelic_profile, anyNA))),
-                                     " out of ",
-                                     strong(ncol(DB$allelic_profile)),
-                                     " total loci in this scheme contain NA's (",
-                                     strong(round((sum(sapply(DB$allelic_profile, anyNA)) / ncol(DB$allelic_profile) * 100), 1)),
-                                     " %). ",
-                                     "Decide how these missing values should be treated:")
-                              
-                            ),
-                            br()
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(1),
-                        column(
-                          width = 11,
-                          align = "left",
-                          br(),
-                          prettyRadioButtons(
-                            "na_handling",
-                            "",
-                            choiceNames = c("Ignore missing values for pairwise comparison",
-                                            "Omit loci with missing values for all assemblies",
-                                            "Treat missing values as allele variant"),
-                            choiceValues = c("ignore_na", "omit", "category"),
-                            shape = "curve",
-                            selected = c("ignore_na")
-                          ),
-                          br()
-                        )
-                      )
-                    )
-                  )
-                })  
-                
-              } else { 
-                #if no typed assemblies present
-                
-                # null underlying database
-                
-                DB$data <- NULL
-                DB$meta <- NULL
-                DB$meta_gs <- NULL
-                DB$meta_true <- NULL
-                DB$allelic_profile <- NULL
-                DB$allelic_profile_trunc <- NULL
-                DB$allelic_profile_true <- NULL
-                
-                # Render menu without missing values tab
-                output$menu <- renderMenu(
-                  sidebarMenu(
-                    menuItem(
-                      text = "Database Browser",
-                      tabName = "database",
-                      icon = icon("hard-drive"),
-                      startExpanded = TRUE,
-                      selected = TRUE,
-                      menuSubItem(
-                        text = "Browse Entries",
-                        tabName = "db_browse_entries"
-                      ),
-                      menuSubItem(
-                        text = "Scheme Info",
-                        tabName = "db_schemeinfo"
-                      ),
-                      menuSubItem(
-                        text = "Loci Info",
-                        tabName = "db_loci_info"
-                      ),
-                      menuSubItem(
-                        text = "Distance Matrix",
-                        tabName = "db_distmatrix"
-                      )
-                    ),
-                    menuItem(
-                      text = "Manage Schemes",
-                      tabName = "init",
-                      icon = icon("layer-group")
-                    ),
-                    menuItem(
-                      text = "Allelic Typing",
-                      tabName = "typing",
-                      icon = icon("gears")
-                    ),
-                    menuItem(
-                      text = "Resistance Profile",
-                      tabName = "gene_screening",
-                      icon = icon("dna"),
-                      startExpanded = TRUE,
-                      menuSubItem(
-                        text = "Browse Entries",
-                        tabName = "gs_profile"
-                      ),
-                      menuSubItem(
-                        text = "Screening",
-                        tabName = "gs_screening"
-                      )
-                    ),
-                    menuItem(
-                      text = "Visualization",
-                      tabName = "visualization",
-                      icon = icon("circle-nodes")
-                    ),
-                    menuItem(
-                      text = "Utilities",
-                      tabName = "utilities",
-                      icon = icon("screwdriver-wrench")
-                    )
-                  )
-                )
-                
-                observe({
-                  if(is.null(DB$data)) {
-                    if(check_new_entry()) {
-                      output$db_no_entries <- renderUI(
-                        column(
-                          width = 12,
-                          fluidRow(
-                            column(1),
-                            column(
-                              width = 3,
-                              align = "left",
-                              HTML(
-                                paste(
-                                  tags$span(style='color: white; font-size: 15px; position: absolute; bottom: -30px; right: -5px', 'New entries - reload database')
-                                )
-                              )
-                            ),
-                            column(
-                              width = 4,
-                              actionButton(
-                                "load",
-                                "",
-                                icon = icon("rotate"),
-                                class = "pulsating-button"
-                              )
-                            )
-                          )
-                        )
-                      )
-                    } else {
-                      output$db_no_entries <- renderUI(
-                        column(
-                          width = 12,
-                          fluidRow(
-                            column(1),
-                            column(
-                              width = 11,
-                              align = "left",
-                              HTML(
-                                paste(
-                                  "<span style='color: white;'>",
-                                  "No Entries for this scheme available.\n",
-                                  "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
-                                  sep = '<br/>'
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    }
-                  }
-                })
-                
-                output$distancematrix_no_entries <- renderUI(
-                  fluidRow(
-                    column(1),
-                    column(
-                      width = 11,
-                      align = "left",
-                      HTML(paste(
-                        "<span style='color: white;'>",
-                        "No Entries for this scheme available.",
-                        "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
-                        sep = '<br/>'
-                      ))
-                    )
-                  )
-                )
-                
-                output$db_entries <- NULL
-                output$edit_index <- NULL
-                output$edit_scheme_d <- NULL
-                output$edit_entries <- NULL
-                output$compare_select <- NULL
-                output$delete_select <- NULL
-                output$del_bttn <- NULL
-                output$compare_allele_box <- NULL
-                output$download_entries <- NULL
-                output$missing_values <- NULL
-                output$delete_box <- NULL
-                output$entry_table_controls <- NULL
-                output$multi_stop <- NULL
-                output$metadata_multi_box <- NULL
-                output$start_multi_typing_ui <- NULL
-                output$pending_typing <- NULL
-                output$multi_typing_results <- NULL
-                output$single_typing_progress <- NULL
-                output$metadata_single_box <- NULL
-                output$start_typing_ui <- NULL
-                
-                output$initiate_typing_ui <- renderUI({
-                  column(
-                    width = 4,
-                    align = "center",
-                    br(),
-                    br(),
-                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-                    br(),
-                    br(),
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "center",
-                        shinyFilesButton(
-                          "genome_file",
-                          "Browse" ,
-                          icon = icon("file"),
-                          title = "Select the assembly in .fasta/.fna/.fa format:",
-                          multiple = FALSE,
-                          buttonType = "default",
-                          class = NULL,
-                          root = path_home()
-                        ),
-                        br(),
-                        br(),
-                        uiOutput("genome_path"),
-                        br()
-                      )
-                    )
-                  )
-                })
-                
-                output$initiate_typing_ui <- renderUI({
-                  column(
-                    width = 4,
-                    align = "center",
-                    br(),
-                    br(),
-                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-                    br(),
-                    br(),
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "center",
-                        shinyFilesButton(
-                          "genome_file",
-                          "Browse" ,
-                          icon = icon("file"),
-                          title = "Select the assembly in .fasta/.fna/.fa format:",
-                          multiple = FALSE,
-                          buttonType = "default",
-                          class = NULL,
-                          root = path_home()
-                        ),
-                        br(),
-                        br(),
-                        uiOutput("genome_path"),
-                        br()
-                      )
-                    )
-                  )
-                })
-                
-                output$initiate_multi_typing_ui <- renderUI({
-                  column(
-                    width = 4,
-                    align = "center",
-                    br(),
-                    br(),
-                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-                    br(), br(),
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "center",
-                        shinyDirButton(
-                          "genome_file_multi",
-                          "Browse",
-                          icon = icon("folder-open"),
-                          title = "Select the folder containing the genome assemblies (FASTA)",
-                          buttonType = "default",
-                          root = path_home()
-                        ),
-                        br(),
-                        br(),
-                        uiOutput("multi_select_info"),
-                        br()
-                      )
-                    ),
-                    uiOutput("multi_select_tab_ctrls"),
-                    br(),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "left",
-                        rHandsontableOutput("multi_select_table")
-                      )
-                    )
-                  )
-                })
-              }
-            }
-          }
-        }
-      } else {
-        
-        log_print("Invalid scheme folder")
-        show_toast(
-          title = "Invalid scheme folder",
-          type = "warning",
-          position = "bottom-end",
-          timer = 4000
-        )
-      }
-    }
-    
-  })
-  
-  # _______________________ ####
-  
-  ## Database ----
-  
-  ### Conditional UI Elements rendering ----
-  
-  # Contro custom variables table
-  output$cust_var_select <- renderUI({
-    if(nrow(DB$cust_var) > 5) {
-      selectInput(
-        "cust_var_select",
-        "",
-        choices = 1:ceiling(nrow(DB$cust_var) / 5 )
-      )
-    }
-  })
-  
-  output$cust_var_info <- renderUI({
-    if((!is.null(DB$cust_var)) & (!is.null(input$cust_var_select))) {
-      if(nrow(DB$cust_var) > 5) {
-        low <- -4
-        high <- 0
-        for (i in 1:input$cust_var_select) {
-          low <- low + 5
-          if((nrow(DB$cust_var) %% 5) != 0) {
-            if(i == ceiling(nrow(DB$cust_var) / 5 )) {
-              high <- high + nrow(DB$cust_var) %% 5
-            } else {
-              high <- high + 5
-            }
-          } else {
-            high <- high + 5
-          }
-        }
-        h5(paste0("Showing ", low, " to ", high," of ", nrow(DB$cust_var), " variables"), style = "color: white; font-size: 10px;")
-      }
-    }
-  })
-  
-  # Message on Database tabs if no scheme available yet
-  observe({
-    if(!is.null(DB$exist)) {
-      if(DB$exist){
-        
-        # Message for tab Browse Entries
-        output$no_scheme_entries <- renderUI({
-          fluidRow(
-            column(1),
-            column(
-              width = 4,
-              align = "left",
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'No scheme available.')
-                  )
-                )
-              ),
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'Download a scheme first and type assemblies in the section Allelic Typing.')
-                  )
-                )
-              )
-            )
-          )
-        })
-        
-        # Message for Tab Scheme Info
-        output$no_scheme_info <- renderUI({
-          fluidRow(
-            column(1),
-            column(
-              width = 10,
-              align = "left",
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'No scheme available.')
-                  )
-                )
-              ),
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'Download a scheme first and type assemblies in the section Allelic Typing.')
-                  )
-                )
-              )
-            )
-          )
-        })
-        
-        # Message for Tab Distance Matrix
-        output$no_scheme_distancematrix <- renderUI({
-          fluidRow(
-            column(1),
-            column(
-              width = 10,
-              align = "left",
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'No scheme available.')
-                  )
-                )
-              ),
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'Download a scheme first and type assemblies in the section Allelic Typing.')
-                  )
-                )
-              )
-            )
-          )
-        })
-        
-      } else {
-        output$no_scheme_entries <- NULL
-        output$no_scheme_info <- NULL
-        output$no_scheme_distancematrix <- NULL
-      }
-    }
-    
-  })
-  
-  observe({
-    # Conditional Missing Values Tab
-    if(!is.null(DB$allelic_profile)) {
-      if(anyNA(DB$allelic_profile)) {
-        if(DB$no_na_switch == FALSE) {
-          output$menu <- renderMenu(
-            sidebarMenu(
-              menuItem(
-                text = "Database Browser",
-                tabName = "database",
-                icon = icon("hard-drive"),
-                startExpanded = TRUE,
-                menuSubItem(
-                  text = "Browse Entries",
-                  tabName = "db_browse_entries"
-                ),
-                menuSubItem(
-                  text = "Scheme Info",
-                  tabName = "db_schemeinfo"
-                ),
-                menuSubItem(
-                  text = "Loci Info",
-                  tabName = "db_loci_info"
-                ),
-                menuSubItem(
-                  text = "Distance Matrix",
-                  tabName = "db_distmatrix"
-                ),
-                menuSubItem(
-                  text = "Missing Values",
-                  tabName = "db_missing_values",
-                  selected = TRUE,
-                  icon = icon("triangle-exclamation")
-                )
-              ),
-              menuItem(
-                text = "Manage Schemes",
-                tabName = "init",
-                icon = icon("layer-group")
-              ),
-              menuItem(
-                text = "Allelic Typing",
-                tabName = "typing",
-                icon = icon("gears")
-              ),
-              menuItem(
-                text = "Resistance Profile",
-                tabName = "gene_screening",
-                icon = icon("dna"),
-                startExpanded = TRUE,
-                menuSubItem(
-                  text = "Browse Entries",
-                  tabName = "gs_profile"
-                ),
-                menuSubItem(
-                  text = "Screening",
-                  tabName = "gs_screening"
-                )
-              ),
-              menuItem(
-                text = "Visualization",
-                tabName = "visualization",
-                icon = icon("circle-nodes")
-              ),
-              menuItem(
-                text = "Utilities",
-                tabName = "utilities",
-                icon = icon("screwdriver-wrench")
-              )
-            )
-          )
-        }
-        
-      } else {
-        output$menu <- renderMenu(
-          sidebarMenu(
-            menuItem(
-              text = "Database Browser",
-              tabName = "database",
-              icon = icon("hard-drive"),
-              startExpanded = TRUE,
-              menuSubItem(
-                text = "Browse Entries",
-                tabName = "db_browse_entries"
-              ),
-              menuSubItem(
-                text = "Scheme Info",
-                tabName = "db_schemeinfo"
-              ),
-              menuSubItem(
-                text = "Loci Info",
-                tabName = "db_loci_info"
-              ),
-              menuSubItem(
-                text = "Distance Matrix",
-                tabName = "db_distmatrix"
-              )
-            ),
-            menuItem(
-              text = "Manage Schemes",
-              tabName = "init",
-              icon = icon("layer-group")
-            ),
-            menuItem(
-              text = "Allelic Typing",
-              tabName = "typing",
-              icon = icon("gears")
-            ),
-            menuItem(
-              text = "Resistance Profile",
-              tabName = "gene_screening",
-              icon = icon("dna"),
-              startExpanded = TRUE,
-              menuSubItem(
-                text = "Browse Entries",
-                tabName = "gs_profile"
-              ),
-              menuSubItem(
-                text = "Screening",
-                tabName = "gs_screening"
-              )
-            ),
-            menuItem(
-              text = "Visualization",
-              tabName = "visualization",
-              icon = icon("circle-nodes")
-            ),
-            menuItem(
-              text = "Utilities",
-              tabName = "utilities",
-              icon = icon("screwdriver-wrench")
-            )
-          )
-        )
-      }
-    }
-    
-  })
-  
-  observe({
-    
-    if (!is.null(DB$available)) {
-      output$scheme_db <- renderUI({
-        if (length(DB$available) > 5) {
-          selectInput(
-            "scheme_db",
-            label = "",
-            choices = if(!is.null(Typing$last_scheme)) {
-              Typing$last_scheme
-            } else {DB$available},
-            selected = if(!is.null(Typing$last_scheme)) {
-              Typing$last_scheme
-            } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}
-          )
-        } else {
-          prettyRadioButtons(
-            "scheme_db",
-            label = "",
-            choices = if(!is.null(Typing$last_scheme)) {
-              Typing$last_scheme
-            } else {DB$available},
-            selected = if(!is.null(Typing$last_scheme)) {
-              Typing$last_scheme
-            } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}
-          )
-        }
-      })
-      
-      if (!is.null(DB$schemeinfo)) {
-        
-        output$scheme_info <- renderTable({
-          DB$schemeinfo
-        })
-        
-        output$scheme_header <- renderUI(h3(p("cgMLST Scheme"), style = "color:white"))
-        
-      } else {
-        
-        output$scheme_info <- NULL
-        output$scheme_header <- NULL
-        
-      }
-      
-      if (!is.null(DB$loci_info)) {
-        loci_info <- DB$loci_info
-        names(loci_info)[6] <- "Allele Count"
-        
-        output$db_loci <- renderDataTable(
-          loci_info,
-          selection = "single",
-          options = list(pageLength = 10,
-                         columnDefs = list(list(searchable = TRUE,
-                                                targets = "_all")),
-                         initComplete = DT::JS(
-                           "function(settings, json) {",
-                           "$('th:first-child').css({'border-top-left-radius': '5px'});",
-                           "$('th:last-child').css({'border-top-right-radius': '5px'});",
-                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                           "}"
-                         ),
-                         drawCallback = DT::JS(
-                           "function(settings) {",
-                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                           "}"
-                         ))
-        )
-        
-        output$loci_header <- renderUI(h3(p("Loci"), style = "color:white"))
-        
-      } else {
-        output$db_loci <- NULL
-        output$loci_header <- NULL
-      }
-    } 
-  })
-  
-  # If only one entry available disable varying loci checkbox
-  
-  output$compare_difference_box <- renderUI({
-    if(!is.null(DB$data)) {
-      if(nrow(DB$data) > 1) {
-        div(
-          class = "mat-switch-db",
-          materialSwitch(
-            "compare_difference",
-            h5(p("Only Varying Loci"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-            value = FALSE,
-            right = TRUE
-          )
-        )
-      }
-    }
-  })
-  
-  ### Database Events ----
-  
-  # Invalid entries table input
-  observe({
-    req(DB$data, input$db_entries)
-    if (isTRUE(input$invalid_date)) {
-      show_toast(
-        title = "Invalid date",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-      DB$inhibit_change <- TRUE
-    } else if (isTRUE(input$empty_name)) {
-      show_toast(
-        title = "Empty name",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-      DB$inhibit_change <- TRUE
-    } else if (isTRUE(input$empty_id)) {
-      show_toast(
-        title = "Empty ID",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-      DB$inhibit_change <- TRUE
-    } else {
-      DB$inhibit_change <- FALSE
-    }
-  })
-  
-  # Change scheme
-  observeEvent(input$reload_db, {
-    log_print("Input reload_db")
-    
-    if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
-      show_toast(
-        title = "Pending Multi Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
-      show_toast(
-        title = "Pending Single Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if(Screening$status == "started") {
-      show_toast(
-        title = "Pending Screening",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      showModal(
-        modalDialog(
-          selectInput(
-            "scheme_db",
-            label = "",
-            choices = DB$available,
-            selected = DB$scheme),
-          title = "Select a local database to load.",
-          easyClose = TRUE,
-          footer = tagList(
-            modalButton("Cancel"),
-            actionButton("load", "Load", class = "btn btn-default")
-          )
-        )
-      )
-    }
-  })
-  
-  # Create new database
-  observe({
-    shinyDirChoose(input,
-                   "create_new_db",
-                   roots = c(Home = path_home(), Root = "/"),
-                   defaultRoot = "Home",
-                   session = session)
-    
-    if(!is.null(input$create_new_db)) {
-      DB$new_database <- as.character(
-        parseDirPath(
-          roots = c(Home = path_home(), Root = "/"),
-          input$create_new_db
-        )
-      )
-    }
-  })
-  
-  # Undo db changes
-  observeEvent(input$undo_changes, {
-    log_print("Input undo_changes")
-    
-    DB$inhibit_change <- FALSE
-    
-    Data <- readRDS(paste0(
-      DB$database, "/",
-      gsub(" ", "_", DB$scheme),
-      "/Typing.rds"
-    ))
-    
-    DB$data <- Data[["Typing"]]
-    
-    if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-      cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-      DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
-    } else {
-      DB$cust_var <- data.frame()
-    }
-    
-    DB$change <- FALSE
-    DB$count <- 0
-    DB$no_na_switch <- TRUE
-    DB$meta_gs <- select(DB$data, c(1, 3:13))
-    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
-    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-    DB$deleted_entries <- character(0)
-    
-    observe({
-      if (!is.null(DB$data)) {
-        if (nrow(DB$data) == 1) {
-          if(!is.null(DB$data) & !is.null(DB$cust_var)) {
-            output$db_entries <- renderRHandsontable({
-              rhandsontable(
-                select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                error_highlight = err_thresh() - 1,                              
-                rowHeaders = NULL,
-                contextMenu = FALSE,
-                highlightCol = TRUE, 
-                highlightRow = TRUE
-              ) %>%
-                hot_col(1, 
-                        valign = "htMiddle",
-                        halign = "htCenter") %>%
-                hot_col(3, readOnly = TRUE) %>%
-                hot_col(c(1, 5, 10, 11, 12, 13),
-                        readOnly = TRUE) %>%
-                hot_col(3:(13 + nrow(DB$cust_var)), 
-                        valign = "htMiddle",
-                        halign = "htLeft") %>%
-                hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                hot_col(8, type = "dropdown", source = country_names) %>%
-                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                        validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                hot_cols(fixedColumnsLeft = 1) %>%
-                hot_col(2, type = "checkbox", width = "auto",
-                        valign = "htTop",
-                        halign = "htCenter") %>%
-                hot_rows(fixedRowsTop = 0) %>%
-                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-            })
-          }
-        } else if (between(nrow(DB$data), 1, 40)) {
-          if (length(input$compare_select) > 0) {
-            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
-              output$db_entries <- renderRHandsontable({
-                
-                entry_data <- DB$data %>%
-                  select(1:(13 + nrow(DB$cust_var))) %>%
-                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
-                
-                rhandsontable(
-                  entry_data,
-                  col_highlight = diff_allele() - 1,
-                  dup_names_high = duplicated_names() - 1,
-                  dup_ids_high = duplicated_ids() - 1,
-                  row_highlight = true_rows() - 1,
-                  error_highlight = err_thresh() - 1,
-                  rowHeaders = NULL,
-                  highlightCol = TRUE, 
-                  highlightRow = TRUE,
-                  contextMenu = FALSE
-                )  %>%
-                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
-                          valign = "htMiddle",
-                          halign = "htCenter",
-                          readOnly = TRUE) %>%
-                  hot_col(1, 
-                          valign = "htMiddle",
-                          halign = "htCenter") %>%
-                  hot_col(3, readOnly = TRUE) %>%
-                  hot_col(c(1, 5, 10, 11, 12, 13),
-                          readOnly = TRUE) %>%
-                  hot_col(3:(13 + nrow(DB$cust_var)), 
-                          valign = "htMiddle",
-                          halign = "htLeft") %>%
-                  hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(8, type = "dropdown", source = country_names) %>%
-                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                          validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                  hot_col(2, type = "checkbox", width = "auto",
-                          valign = "htTop",
-                          halign = "htCenter",
-                          strict = TRUE,
-                          allowInvalid = FALSE,
-                          copyable = TRUE) %>%
-                  hot_cols(fixedColumnsLeft = 1) %>%
-                  hot_rows(fixedRowsTop = 0) %>%
-                  hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-  
-                       }
-              }") %>%
-                  hot_col(diff_allele(),
-                          renderer = "
-                  function(instance, td, row, col, prop, value, cellProperties) {
-                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
-  
-                    if (instance.params) {
-                          hcols = instance.params.col_highlight;
-                          hcols = hcols instanceof Array ? hcols : [hcols];
-                        }
-  
-                    if (instance.params && hcols.includes(col)) {
-                      td.style.background = 'rgb(116, 188, 139)';
-                    }
-                }"
-                  ) %>%
-                  hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-              })
-            }
-          } else {
-            if(!is.null(DB$data) & !is.null(DB$cust_var)) {
-              output$db_entries <- renderRHandsontable({
-                rhandsontable(
-                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                  rowHeaders = NULL,
-                  row_highlight = true_rows() - 1,
-                  dup_names_high = duplicated_names()- 1,
-                  dup_ids_high = duplicated_ids() - 1,
-                  error_highlight = err_thresh() - 1,
-                  contextMenu = FALSE,
-                  highlightCol = TRUE, 
-                  highlightRow = TRUE
-                ) %>%
-                  hot_cols(fixedColumnsLeft = 1) %>%
-                  hot_col(1, 
-                          valign = "htMiddle",
-                          halign = "htCenter") %>%
-                  hot_col(3, readOnly = TRUE) %>%
-                  hot_col(c(1, 5, 10, 11, 12, 13),
-                          readOnly = TRUE) %>%
-                  hot_col(3:(13 + nrow(DB$cust_var)), 
-                          valign = "htMiddle",
-                          halign = "htLeft") %>%
-                  hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(8, type = "dropdown", source = country_names) %>%
-                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                          validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                  hot_col(2, type = "checkbox", width = "auto",
-                          valign = "htTop",
-                          halign = "htCenter") %>%
-                  hot_rows(fixedRowsTop = 0) %>%
-                  hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-  
-                       }
-              }") %>%
-                  hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-              })    
-            }
-          }
-        } else {
-          if (length(input$compare_select) > 0) {
-            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
-              output$db_entries <- renderRHandsontable({
-                
-                entry_data <- DB$data %>%
-                  select(1:(13 + nrow(DB$cust_var))) %>%
-                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
-                
-                rhandsontable(
-                  entry_data,
-                  col_highlight = diff_allele() - 1,
-                  rowHeaders = NULL,
-                  height = table_height(),
-                  row_highlight = true_rows() - 1,
-                  dup_names_high = duplicated_names() - 1,
-                  dup_ids_high = duplicated_ids() - 1,
-                  error_highlight = err_thresh() - 1,
-                  contextMenu = FALSE,
-                  highlightCol = TRUE, 
-                  highlightRow = TRUE
-                ) %>%
-                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
-                          readOnly = TRUE, 
-                          valign = "htMiddle",
-                          halign = "htCenter") %>%
-                  hot_col(3:(13 + nrow(DB$cust_var)), 
-                          valign = "htMiddle",
-                          halign = "htLeft") %>%
-                  hot_col(3, readOnly = TRUE) %>%
-                  hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(c(1, 5, 10, 11, 12, 13),
-                          readOnly = TRUE) %>%
-                  hot_col(8, type = "dropdown", source = country_names) %>%
-                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                          validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                  hot_col(1, 
-                          valign = "htMiddle",
-                          halign = "htCenter") %>%
-                  hot_col(2, type = "checkbox", width = "auto",
-                          valign = "htTop",
-                          halign = "htCenter",
-                          allowInvalid = FALSE,
-                          copyable = TRUE) %>%
-                  hot_cols(fixedColumnsLeft = 1) %>%
-                  hot_rows(fixedRowsTop = 0) %>%
-                  hot_col(1, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.row_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                                                             }
-                                                           }
-                                                       }") %>%
-                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") %>%
-                  hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(diff_allele(),
-                          renderer = "
-                  function(instance, td, row, col, prop, value, cellProperties) {
-                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
-  
-                    if (instance.params) {
-                          hcols = instance.params.col_highlight;
-                          hcols = hcols instanceof Array ? hcols : [hcols];
-                        }
-  
-                    if (instance.params && hcols.includes(col)) {
-                      td.style.background = 'rgb(116, 188, 139)';
-                    }
-                }") 
-              })    
-            }
-          } else {
-            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
-              output$db_entries <- renderRHandsontable({
-                rhandsontable(
-                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                  rowHeaders = NULL,
-                  height = table_height(),
-                  dup_names_high = duplicated_names() - 1,
-                  dup_ids_high = duplicated_ids() - 1,
-                  row_highlight = true_rows() - 1,
-                  error_highlight = err_thresh() - 1,
-                  contextMenu = FALSE,
-                  highlightCol = TRUE, 
-                  highlightRow = TRUE
-                ) %>%
-                  hot_cols(fixedColumnsLeft = 1) %>%
-                  hot_col(1, 
-                          valign = "htMiddle",
-                          halign = "htCenter") %>%
-                  hot_col(c(1, 5, 10, 11, 12, 13),
-                          readOnly = TRUE) %>%
-                  hot_col(3, readOnly = TRUE) %>%
-                  hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(8, type = "dropdown", source = country_names) %>%
-                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                          validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                  hot_col(3:(13 + nrow(DB$cust_var)), 
-                          valign = "htMiddle",
-                          halign = "htLeft") %>%
-                  hot_rows(fixedRowsTop = 0) %>%
-                  hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(2, type = "checkbox", width = "auto",
-                          valign = "htTop", halign = "htCenter") %>%
-                  hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-              })
-            }
-          }
-        }
-      }
-    })
-  })
-  
-  observe({
-    if(!is.null(DB$data)){
-      if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-        cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-        DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
-        
-      } else {
-        DB$cust_var <- data.frame()
-      }
-    }
-  })
-  
-  DB$count <- 0
-  
-  observeEvent(input$add_new_variable, {
-    log_print("Input add_new_variable")
-    
-    if(nchar(input$new_var_name) > 12) {
-      log_print("Add variable; max. 10 character")
-      show_toast(
-        title = "Max. 10 characters",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      if (input$new_var_name == "") {
-        log_print("Add variable; min. 1 character")
-        show_toast(
-          title = "Min. 1 character",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-      } else {
-        if(trimws(input$new_var_name) %in% names(DB$meta)) {
-          log_print("Add variable; name already existing")
-          show_toast(
-            title = "Variable name already existing",
-            type = "warning",
-            position = "bottom-end",
-            timer = 6000
-          )
-        } else {
-          showModal(
-            modalDialog(
-              selectInput(
-                "new_var_type",
-                label = "",
-                choices = c("Categorical (character)",
-                            "Continous (numeric)")),
-              title = paste0("Select Data Type"),
-              easyClose = TRUE,
-              footer = tagList(
-                modalButton("Cancel"),
-                actionButton("conf_new_var", "Confirm", class = "btn btn-default")
-              )
-            )
-          )
-        }
-      }
-    }
-  })
-  
-  observeEvent(input$conf_new_var, {
-    log_print("Input conf_new_var")
-    
-    # User feedback variables
-    removeModal()
-    DB$count <- DB$count + 1
-    DB$change <- TRUE
-    
-    # Format variable name
-    name <- trimws(input$new_var_name)
-    
-    if(input$new_var_type == "Categorical (character)") {
-      DB$data <- DB$data %>%
-        mutate("{name}" := character(nrow(DB$data)), .after = 13)
-      
-      DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "categ"))
-    } else {
-      DB$data <- DB$data %>%
-        mutate("{name}" := numeric(nrow(DB$data)), .after = 13)
-      
-      DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "cont"))
-    }
-    
-    DB$meta_gs <- select(DB$data, c(1, 3:13))
-    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-    
-    log_print(paste0("New custom variable added: ", input$new_var_name))
-    
-    show_toast(
-      title = paste0("Variable ", trimws(input$new_var_name), " added"),
-      type = "success",
-      position = "bottom-end",
-      timer = 6000
-    )
-    
-  })
-  
-  observeEvent(input$delete_new_variable, {
-    log_print("Input delete_new_variable")
-    
-    if (input$del_which_var == "") {
-      log_print("Delete custom variables; no custom variable")
-      show_toast(
-        title = "No custom variables",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      showModal(
-        modalDialog(
-          paste0(
-            "Confirmation will lead to irreversible deletion of the custom ",
-            input$del_which_var,
-            " variable. Continue?"
-          ),
-          title = "Delete custom variables",
-          fade = TRUE,
-          easyClose = TRUE,
-          footer = tagList(
-            modalButton("Cancel"),
-            actionButton("conf_var_del", "Delete", class = "btn btn-danger")
-          )
-        )
-      )
-    }
-  })
-  
-  observeEvent(input$conf_var_del, {
-    log_print("Input conf_var_del")
-    
-    DB$change <- TRUE
-    
-    removeModal()
-    
-    if(DB$count >= 1) {
-      DB$count <- DB$count - 1
-    } 
-    
-    show_toast(
-      title = paste0("Variable ", input$del_which_var, " removed"),
-      type = "warning",
-      position = "bottom-end",
-      timer = 6000
-    )
-    
-    log_print(paste0("Variable ", input$del_which_var, " removed"))
-    
-    DB$cust_var <- DB$cust_var[-which(DB$cust_var$Variable == input$del_which_var),]
-    DB$data <- select(DB$data, -(input$del_which_var))
-    DB$meta_gs <- select(DB$data, c(1, 3:13))
-    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
-    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-  })
-  
-  # Select all button
-  
-  observeEvent(input$sel_all_entries, {
-    log_print("Input sel_all_entries")
-    
-    DB$data$Include <- TRUE
-  })
-  
-  observeEvent(input$desel_all_entries, {
-    log_print("Input desel_all_entries")
-    
-    DB$data$Include <- FALSE
-  })
-  
-  # Switch to entry table
-  
-  observeEvent(input$change_entries, {
-    log_print("Input change_entries")
-    
-    removeModal()
-    updateTabItems(session, "tabs", selected = "db_browse_entries")
-  })
-  
-  #### Save Missing Value as CSV ----
-  
-  output$download_na_matrix <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save missing values table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")))
-      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")
-    },
-    content = function(file) {
-      download_matrix <- hot_to_r(input$table_missing_values)
-      write.csv(download_matrix, file, sep = ",", row.names=FALSE, quote=FALSE) 
-    }
-  )
-  
-  #### Save scheme info table as CSV ----
-  
-  output$download_schemeinfo <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save scheme info table ", paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")))
-      
-      paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")
-    },
-    content = function(file) {
-      pub_index <- which(DB$schemeinfo[,1] == "Publications")
-      write.table(
-        DB$schemeinfo[1:(pub_index-1),],
-        file, 
-        sep = ";",
-        row.names = FALSE, 
-        quote = FALSE
-      ) 
-    }
-  )
-  
-  #### Save Loci info table as CSV ----
-  
-  output$download_loci_info <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save loci info table ", paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")))
-      
-      paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")
-    },
-    content = function(file) {
-      write.table(
-        DB$loci_info,
-        file, 
-        sep = ";",
-        row.names = FALSE, 
-        quote = FALSE
-      ) 
-    }
-  )
-  
-  #### Save entry table as CSV ----
-  
-  output$download_entry_table <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save entry table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")))
-      
-      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")
-    },
-    content = function(file) {
-      download_matrix <- hot_to_r(input$db_entries)
-      
-      if (input$download_table_include == TRUE) {
-        download_matrix <- download_matrix[which(download_matrix$Include == TRUE),]
-      }
-      
-      if (input$download_table_loci == FALSE) {
-        download_matrix <- select(download_matrix, 1:(13 + nrow(DB$cust_var)))
-      } 
-      
-      write.csv(download_matrix, file, row.names=FALSE, quote=FALSE) 
-    }
-  )
-  
-  # Save Edits Button
-  
-  observeEvent(input$edit_button, {
-    if(nrow(hot_to_r(input$db_entries)) > nrow(DB$data)) {
-      show_toast(
-        title = "Invalid rows entered. Saving not possible.",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      if(!isTRUE(DB$inhibit_change)) {
-        log_print("Input edit_button")
-        
-        showModal(
-          modalDialog(
-            if(length(DB$deleted_entries > 0)) {
-              paste0(
-                "Overwriting previous metadata of local ",
-                DB$scheme,
-                " database. Deleted entries will be irreversibly removed. Continue?"
-              )
-            } else {
-              paste0(
-                "Overwriting previous metadata of local ",
-                DB$scheme,
-                " database. Continue?"
-              )
-            },
-            title = "Save Database",
-            fade = TRUE,
-            easyClose = TRUE,
-            footer = tagList(
-              modalButton("Cancel"),
-              actionButton("conf_db_save", "Save", class = "btn btn-default")
-            )
-          )
-        )
-      } else {
-        log_print("Input edit_button, invalid values.")
-        show_toast(
-          title = "Invalid values entered. Saving not possible.",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-      }
-    }
-  })
-  
-  observeEvent(input$Cancel, {
-    log_print("Input Cancel")
-    removeModal()
-  })
-  
-  observeEvent(input$conf_db_save, {
-    log_print("Input conf_db_save")
-    
-    # Remove isolate assembly file if present
-    if(!is.null(DB$remove_iso)) {
-      if(length(DB$remove_iso) > 0) {
-        lapply(DB$remove_iso, unlink, recursive = TRUE, force = FALSE, expand = TRUE)
-      }
-    }
-    DB$remove_iso <- NULL
-    
-    Data <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
-    
-    if ((ncol(Data[["Typing"]]) - 13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-      cust_vars_pre <- select(Data[["Typing"]], 
-                              14:(ncol(Data[["Typing"]]) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-      cust_vars_pre <- names(cust_vars_pre)
-    } else {
-      cust_vars_pre <- character()
-    }
-    
-    Data[["Typing"]] <- select(Data[["Typing"]], -(1:(13 + length(cust_vars_pre))))
-    
-    meta_hot <- hot_to_r(input$db_entries)
-    
-    if(length(DB$deleted_entries > 0)) {
-      
-      meta_hot <- mutate(meta_hot, Index = as.character(1:nrow(DB$data)))
-      
-      Data[["Typing"]] <- mutate(Data[["Typing"]][-as.numeric(DB$deleted_entries),  ], 
-                                 meta_hot, .before = 1)
-      rownames(Data[["Typing"]]) <- Data[["Typing"]]$Index
-    } else {
-      Data[["Typing"]] <- mutate(Data[["Typing"]], meta_hot, .before = 1)
-    }
-    
-    # Ensure correct logical data type
-    Data[["Typing"]][["Include"]] <- as.logical(Data[["Typing"]][["Include"]])
-    saveRDS(Data, file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
-    
-    # Load database from files  
-    Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
-    
-    DB$data <- Database[["Typing"]]
-    
-    if(!is.null(DB$data)){
-      if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-        cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-        DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
-      } else {
-        DB$cust_var <- data.frame()
-      }
-    }
-    
-    DB$change <- FALSE
-    DB$count <- 0
-    DB$no_na_switch <- TRUE
-    DB$meta_gs <- select(DB$data, c(1, 3:13))
-    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
-    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-    DB$deleted_entries <- character(0)
-    
-    removeModal()
-    
-    show_toast(
-      title = "Database successfully saved",
-      type = "success",
-      position = "bottom-end",
-      timer = 4000
-    )
-  })
-  
-  observeEvent(input$del_button, {
-    log_print("Input del_button")
-    
-    if (length(input$select_delete) < 1) {
-      log_print("Delete entries; no entry selected")
-      show_toast(
-        title = "No entry selected",
-        type = "warning",
-        position = "bottom-end",
-        timer = 4000
-      )
-    } else if((readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") |
-              (tail(readLogFile(), 1) != "0")) {
-      log_print("Delete entries; pending typing")
-      
-      show_toast(
-        title = "Pending Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 4000
-      )
-    } else {
-      if( (length(input$select_delete) - nrow(DB$data) ) == 0) {
-        showModal(
-          modalDialog(
-            paste0("Deleting will lead to removal of all entries and assemblies from local ", DB$scheme, " database. The data can not be recovered afterwards. Continue?"),
-            easyClose = TRUE,
-            title = "Deleting Entries",
-            footer = tagList(
-              modalButton("Cancel"),
-              actionButton("conf_delete_all", "Delete", class = "btn btn-danger")
-            )
-          )
-        )
-      } else {
-        showModal(
-          modalDialog(
-            paste0(
-              "Confirmation will lead to irreversible removal of selected entries and the respectively saved assembly. Continue?"
-            ),
-            title = "Deleting Entries",
-            fade = TRUE,
-            easyClose = TRUE,
-            footer = tagList(
-              modalButton("Cancel"),
-              actionButton(
-                "conf_delete", 
-                "Delete", 
-                class = "btn btn-danger")
-            )
-          )
-        )
-      }
-    }
-  })
-  
-  observeEvent(input$conf_delete_all, {
-    log_print("Input conf_delete_all")
-    
-    # remove file with typing data
-    file.remove(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
-    unlink(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates"), recursive = TRUE, force = FALSE, expand =TRUE)
-    
-    showModal(
-      modalDialog(
-        selectInput(
-          "scheme_db",
-          label = "",
-          choices = if(!is.null(Typing$last_scheme)) {
-            Typing$last_scheme
-          } else {DB$available},
-          selected = if(!is.null(Typing$last_scheme)) {
-            Typing$last_scheme
-          } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}),
-        title = "All entries have been removed. Select a local database to load.",
-        footer = tagList(
-          actionButton("load", "Load", class = "btn btn-default")
-        )
-      )
-    )
-    
-  })
-  
-  DB$deleted_entries <- character(0)
-  
-  observeEvent(input$conf_delete, {
-    
-    log_print("Input conf_delete")
-    
-    # Get isolates selected for deletion
-    DB$deleted_entries <- append(DB$deleted_entries, DB$data$Index[as.numeric(input$select_delete)])
-    
-    # Set reactive status variables
-    DB$no_na_switch <- TRUE
-    DB$change <- TRUE
-    DB$check_new_entries <- FALSE
-    
-    # Set isolate directory deletion variables
-    isopath <- dir_ls(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates"))
-    DB$remove_iso <- isopath[which(basename(isopath) == DB$data$`Assembly ID`[as.numeric(input$select_delete)])]
-    
-    # Reload updated database reactive variables
-    DB$data <- DB$data[!(DB$data$Index %in% as.numeric(input$select_delete)),]
-    DB$meta_gs <- select(DB$data, c(1, 3:13))
-    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
-    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-    
-    # User feedback
-    removeModal()
-    
-    if(length(input$select_delete) > 1) {
-      show_toast(
-        title = "Entries deleted",
-        type = "success",
-        position = "bottom-end",
-        timer = 4000
-      )
-    } else {
-      show_toast(
-        title = "Entry deleted",
-        type = "success",
-        position = "bottom-end",
-        timer = 4000
-      )
-    }
-  })
-  
-  
-  ### Distance Matrix ---- 
-  
-  hamming_df <- reactive({
-    if(input$distmatrix_true == TRUE) {
-      if(anyNA(DB$allelic_profile)) {
-        if(input$na_handling == "omit") {
-          allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
-          
-          allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
-          
-          hamming_mat <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
-          
-        } else if(input$na_handling == "ignore_na"){
-          hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
-          
-        } else {
-          hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
-          
-        } 
-      } else {
-        hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
-      }
-    } else {
-      if(anyNA(DB$allelic_profile)) {
-        if(input$na_handling == "omit") {
-          allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
-          hamming_mat <- compute.distMatrix(allelic_profile_noNA, hamming.dist)
-        } else if(input$na_handling == "ignore_na"){
-          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distIgnore)
-        } else {
-          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distCategory)
-        }  
-      } else {
-        hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.dist)
-      }
-    }
-    
-    # Extreme values for distance matrix heatmap display
-    DB$matrix_min <- min(hamming_mat, na.rm = TRUE)
-    DB$matrix_max <- max(hamming_mat, na.rm = TRUE)
-    
-    if(input$distmatrix_triangle == FALSE) {
-      hamming_mat[upper.tri(hamming_mat, diag = !input$distmatrix_diag)] <- NA
-    } 
-    
-    # Row- and colnames change
-    if(input$distmatrix_true == TRUE) {
-      rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label][which(DB$data$Include == TRUE),])
-    } else {
-      rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label])
-    }
-    colnames(hamming_mat) <- rownames(hamming_mat)
-    
-    mode(hamming_mat) <- "integer"
-    
-    DB$ham_matrix <- hamming_mat %>%
-      as.data.frame() %>%
-      mutate(Index = colnames(hamming_mat)) %>%
-      relocate(Index)
-    DB$distancematrix_nrow <- nrow(DB$ham_matrix)
-    
-    DB$ham_matrix
-  })
-  
-  output$download_distmatrix <- downloadHandler(
-    filename = function() {
-      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Distance_Matrix.csv")
-    },
-    content = function(file) {
-      download_matrix <- hot_to_r(input$db_distancematrix)
-      download_matrix[is.na(download_matrix)] <- ""
-      write.csv(download_matrix, file, row.names=FALSE, quote=FALSE) 
-    }
-  )
-  
-  # _______________________ ####
-  
-  ## Locus sequences ----
-  
-  observe({
-    if(!is.null(DB$database) & !is.null(DB$scheme)) {
-      DB$loci <- list.files(
-        path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
-        pattern = "\\.(fasta|fa|fna)$",
-        full.names = TRUE
-      )
-    }
-  })
-  
-  output$loci_sequences <- renderUI({
-    req(input$db_loci_rows_selected, DB$database, DB$scheme, input$seq_sel)
-    
-    DB$loci <- list.files(
-      path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
-      pattern = "\\.(fasta|fa|fna)$",
-      full.names = TRUE
-    )
-    
-    fasta <- format_fasta(DB$loci[input$db_loci_rows_selected])
-    
-    seq <- fasta[[which(fasta == paste0(">", gsub("Allele ", "", sub(" -.*", "", input$seq_sel)))) + 1]]
-    
-    DB$seq <- seq
-    
-    column(
-      width = 12,
-      HTML(
-        paste(
-          tags$span(style='color: white; font-size: 15px; position: relative; top: -15px; left: -50px', 
-                    sub(" -.*", "", input$seq_sel))
-        )
-      ),
-      tags$pre(HTML(color_sequence(seq)), class = "sequence")
-    )
-  })
-  
-  output$sequence_selector <- renderUI({
-    if(!is.null(input$db_loci_rows_selected)) {
-      
-      req(input$db_loci_rows_selected, DB$database, DB$scheme)
-      
-      DB$loci <- list.files(
-        path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
-        pattern = "\\.(fasta|fa|fna)$",
-        full.names = TRUE
-      )
-      
-      fasta <- format_fasta(DB$loci[input$db_loci_rows_selected])
-      
-      seq_names <- c()
-      for (i in seq_along(fasta)) {
-        if (startsWith(fasta[[i]], ">")) {
-          name <- sub(">", "", fasta[[i]])
-          seq_names <- c(seq_names, name)
-        }
-      }
-      
-      var_count <- table(DB$allelic_profile[gsub(".fasta", "", (basename(DB$loci[input$db_loci_rows_selected])))])
-      
-      vec <- prop.table(var_count)
-      
-      perc <- sapply(unname(vec), scales::percent, accuracy = 0.1)
-      
-      names(perc) <- names(vec)
-      
-      choices <- seq_names
-      
-      present <- which(choices %in% names(vec))
-      absent <- which(!(choices %in% names(vec)))
-      
-      choices[present] <- paste0("Allele ", choices[present], " - ", unname(var_count), " times in DB (", unname(perc), ")")
-      
-      choices[absent] <- paste0("Allele ", choices[absent], " - not present")
-      
-      choices <- c(choices[present], choices[absent])
-      
-      names(choices) <- sapply(choices, function(x) {
-        x <- strsplit(x, " ")[[1]]
-        x[2] <- paste0(substr(x[2], 1, 4), "...", substr(x[2], nchar(x[2])-3, nchar(x[2])))
-        paste(x, collapse = " ")
-      })
-      
-      column(
-        width = 3,
-        selectInput(
-          "seq_sel",
-          h5("Select Variant", style = "color:white;"),
-          choices = choices,
-          width = "80%"
-        ),
-        br(),
-        fluidRow(
-          column(
-            width = 8,
-            align = "left",
-            actionButton("copy_seq", "Copy Sequence",
-                         icon = icon("copy")),
-            bsTooltip("copy_seq", "Copy the variant sequence <br> to clipboard", placement = "top", trigger = "hover")
-          )
-        ),
-        br(),
-        fluidRow(
-          column(
-            width = 8,
-            align = "left",
-            downloadBttn(
-              "get_locus",
-              style = "simple",
-              label = "Save .fasta",
-              size = "sm",
-              icon = icon("download")
-            ),
-            bsTooltip("get_locus_bttn", "Save locus file with all variants", placement = "top", trigger = "hover")
-          )
-        ),
-        br(), br(), br(), br(), br(), br(), br()
-      )
-    }
-  })
-  
-  observeEvent(input$copy_seq, {
-    if(!is.null(DB$seq)) {
-      session$sendCustomMessage("txt", DB$seq)
-    }
-    show_toast(
-      title = "Copied sequence",
-      type = "success",
-      position = "bottom-end",
-      timer = 3000
-    )
-  })
-  
-  output$get_locus <- downloadHandler(
-    filename = function() {
-      fname <- basename(DB$loci[input$db_loci_rows_selected])
-      log_print(paste0("Get locus fasta ", fname))
-      fname
-    },
-    content = function(file) {
-      cont <- readLines(DB$loci[input$db_loci_rows_selected])
-      writeLines(cont, file)
-    }
-  )
-  
-  # _______________________ ####
-  
-  ## Download cgMLST ----
-  
-  observe({
-    if (input$select_cgmlst == "Acinetobacter baumanii") {
-      species <- "Abaumannii1907"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- Scheme$folder_name <- "Acinetobacter_baumanii"
-    } else if (input$select_cgmlst == "Bacillus anthracis") {
-      species <- "Banthracis1917"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Bacillus_anthracis"
-    } else if (input$select_cgmlst == "Bordetella pertussis") {
-      species <- "Bpertussis1917"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Bordetella_pertussis"
-    } else if (input$select_cgmlst == "Brucella melitensis") {
-      species <- "Bmelitensis1912"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Brucella_melitensis"
-    } else if (input$select_cgmlst == "Brucella spp.") {
-      species <- "Brucella1914"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Brucella_spp"
-    } else if (input$select_cgmlst == "Burkholderia mallei (FLI)") {
-      species <- "Bmallei_fli1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Burkholderia_mallei_FLI"
-    } else if (input$select_cgmlst == "Burkholderia mallei (RKI)") {
-      species <- "Bmallei_rki1909"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Burkholderia_mallei_RKI"
-    } else if (input$select_cgmlst == "Burkholderia pseudomallei") {
-      species <- "Bpseudomallei1906"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Burkholderia_pseudomallei"
-    } else if (input$select_cgmlst == "Campylobacter jejuni/coli") {
-      species <- "Cjejuni1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Campylobacter_jejuni_coli"
-    } else if (input$select_cgmlst == "Clostridioides difficile") {
-      species <- "Cdifficile1905"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Clostridioides_difficile"
-    } else if (input$select_cgmlst == "Clostridium perfringens") {
-      species <- "Cperfringens1907"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Clostridium_perfringens"
-    } else if (input$select_cgmlst == "Corynebacterium diphtheriae") {
-      species <- "Cdiphtheriae1907"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Corynebacterium_diphtheriae"
-    } else if (input$select_cgmlst == "Cronobacter sakazakii/malonaticus") {
-      species <- "Csakazakii1910"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Cronobacter_sakazakii_malonaticus"
-    } else if (input$select_cgmlst == "Enterococcus faecalis") {
-      species <- "Efaecalis1912"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Enterococcus_faecalis"
-    } else if (input$select_cgmlst == "Enterococcus faecium") {
-      species <- "Efaecium1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Enterococcus_faecium"
-    } else if (input$select_cgmlst == "Escherichia coli") {
-      species <- "Ecoli1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Escherichia_coli"
-    } else if (input$select_cgmlst == "Francisella tularensis") {
-      species <- "Ftularensis1913"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Francisella_tularensis"
-    } else if (input$select_cgmlst == "Klebsiella oxytoca sensu lato") {
-      species <- "Koxytoca717"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Klebsiella_oxytoca_sensu_lato"
-    } else if (input$select_cgmlst == "Klebsiella pneumoniae sensu lato") {
-      species <- "Kpneumoniae1909"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Klebsiella_pneumoniae_sensu_lato"
-    } else if (input$select_cgmlst == "Legionella pneumophila") {
-      species <- "Lpneumophila1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Legionella_pneumophila"
-    } else if (input$select_cgmlst == "Listeria monocytogenes") {
-      species <- "Lmonocytogenes1910"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Listeria_monocytogenes"
-    } else if (input$select_cgmlst == "Mycobacterium tuberculosis complex") {
-      species <- "Mtuberculosis1909"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Mycobacterium_tuberculosis_complex"
-    } else if (input$select_cgmlst == "Mycobacteroides abscessus") {
-      species <- "Mabscessus1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Mycobacteroides_abscessus"
-    } else if (input$select_cgmlst == "Mycoplasma gallisepticum") {
-      species <- "Mgallisepticum1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Mycoplasma_gallisepticum"
-    } else if (input$select_cgmlst == "Paenibacillus larvae") {
-      species <- "Plarvae1902"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Paenibacillus_larvae"
-    } else if (input$select_cgmlst == "Pseudomonas aeruginosa") {
-      species <- "Paeruginosa1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Pseudomonas_aeruginosa"
-    } else if (input$select_cgmlst == "Salmonella enterica") {
-      species <- "Senterica1913"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Salmonella_enterica"
-    } else if (input$select_cgmlst == "Serratia marcescens") {
-      species <- "Smarcescens1912"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Serratia_marcescens"
-    } else if (input$select_cgmlst == "Staphylococcus aureus") {
-      species <- "Saureus1908"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Staphylococcus_aureus"
-    } else if (input$select_cgmlst == "Staphylococcus capitis") {
-      species <- "Scapitis1905"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Staphylococcus_capitis"
-    } else if (input$select_cgmlst == "Streptococcus pyogenes") {
-      species <- "Spyogenes1904"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Streptococcus_pyogenes"
-    }
-  })
-  
-  observeEvent(input$download_cgMLST, {
-    log_print(paste0("Started download of scheme for ", Scheme$folder_name))
-    
-    shinyjs::hide("download_cgMLST")
-    shinyjs::show("loading")
-    
-    output$statustext <- renderUI(
-      fluidRow(
-        tags$li(
-          class = "dropdown", 
-          tags$span(HTML(
-            paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                  "Status:&nbsp;&nbsp;&nbsp; <i>Downloading scheme...</i>")),
-            style = "color:white;")
-        )
-      )
-    )
-    
-    show_toast(
-      title = "Download started",
-      type = "success",
-      position = "bottom-end",
-      timer = 5000
-    )
-    
-    if(length(DB$available) == 0) {
-      saveRDS(DB$new_database, paste0(getwd(), "/execute/new_db.rds"))
-      dir.create(file.path(readRDS(paste0(getwd(), "/execute/new_db.rds")), "Database"), recursive = TRUE)
-    }
-    
-    DB$load_selected <- TRUE
-    
-    # Check if .downloaded_schemes folder exists and if not create it
-    if (!dir.exists(file.path(DB$database, ".downloaded_schemes"))) {
-      dir.create(file.path(DB$database, ".downloaded_schemes"), recursive = TRUE)
-    }
-    
-    # Check if remains of old temporary folder exists and remove them
-    if (dir.exists(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")))) {
-      unlink(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")), recursive = TRUE)
-    }
-    
-    # Download Loci Fasta Files
-    options(timeout = 600)
-    
-    tryCatch({
-      download.file(Scheme$link_cgmlst, 
-                    file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")))
-      "Download successful!"
-    }, error = function(e) {
-      paste("Error: ", e$message)
-    })
-    
-    # Unzip the scheme in temporary folder
-    unzip(
-      zipfile = file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")),
-      exdir = file.path(DB$database, 
-                        Scheme$folder_name, 
-                        paste0(Scheme$folder_name, ".tmp")
-      )
-    )
-    
-    log_print("Hashing downloaded database")
-    # Hash temporary folder
-    hash_database(file.path(DB$database, 
-                            Scheme$folder_name, 
-                            paste0(Scheme$folder_name, ".tmp")))
-    
-    # Get list from local database
-    local_db_filelist <- list.files(file.path(DB$database, 
-                                              Scheme$folder_name, 
-                                              paste0(Scheme$folder_name, "_alleles")))
-    if (!is_empty(local_db_filelist)) {
-      # Get list from temporary database
-      tmp_db_filelist <- list.files(file.path(DB$database,
-                                              Scheme$folder_name,
-                                              paste0(Scheme$folder_name, ".tmp")))
-      
-      # Find the difference (extra files in local database)
-      local_db_extra <- setdiff(local_db_filelist, tmp_db_filelist)
-      
-      # Copy extra files to temporary folder
-      file.copy(file.path(DB$database,
-                          Scheme$folder_name, 
-                          paste0(Scheme$folder_name, "_alleles"), local_db_extra),
-                file.path(DB$database,
-                          Scheme$folder_name,
-                          paste0(Scheme$folder_name, ".tmp")))
-      
-      # Check differences in file pairs
-      local_db_hashes <- tools::md5sum(file.path(DB$database,
-                                                 Scheme$folder_name,
-                                                 paste0(Scheme$folder_name, "_alleles"),
-                                                 local_db_filelist))
-      tmp_db_hashes <- tools::md5sum(file.path(DB$database,
-                                               Scheme$folder_name,
-                                               paste0(Scheme$folder_name, ".tmp"),
-                                               local_db_filelist))
-      
-      diff_files <- local_db_hashes %in% tmp_db_hashes
-      diff_loci <- names(local_db_hashes)[diff_files == FALSE]
-      diff_loci <- sapply(strsplit(diff_loci, "/"), function(x) x[length(x)])
-      
-      # Check locus hashes
-      for (locus in diff_loci) {
-        local_db_hashes <- get_locus_hashes(file.path(DB$database,
-                                                      Scheme$folder_name,
-                                                      paste0(Scheme$folder_name, "_alleles"),
-                                                      locus))
-        tmp_db_hashes <- get_locus_hashes(file.path(DB$database,
-                                                    Scheme$folder_name,
-                                                    paste0(Scheme$folder_name, ".tmp"),
-                                                    locus))
-        diff_hashes <- setdiff(local_db_hashes, tmp_db_hashes)
-        
-        sequences <- extract_seq(file.path(DB$database,
-                                           Scheme$folder_name,
-                                           paste0(Scheme$folder_name, "_alleles"),
-                                           locus), diff_hashes)
-        if (!is_empty(sequences$idx) && !is_empty(sequences$seq) &&
-            length(sequences$idx) == length(sequences$seq)) {
-          add_new_sequences(file.path(DB$database,
-                                      Scheme$folder_name,
-                                      paste0(Scheme$folder_name, ".tmp"),
-                                      locus), sequences)
-        }
-      }
-    }
-    
-    unlink(file.path(DB$database, Scheme$folder_name, 
-                     paste0(Scheme$folder_name, "_alleles")), recursive = TRUE)
-    
-    file.rename(file.path(DB$database, Scheme$folder_name,
-                          paste0(Scheme$folder_name, ".tmp")),
-                file.path(DB$database, Scheme$folder_name,
-                          paste0(Scheme$folder_name, "_alleles")))
-    
-    # Download Scheme Info
-    download(
-      Scheme$link_scheme,
-      dest = file.path(DB$database, Scheme$folder_name, "scheme_info.html"),
-      mode = "wb"
-    )
-    
-    # Download Loci Info	
-    download(	
-      Scheme$link_targets,	
-      dest = file.path(DB$database, Scheme$folder_name, "targets.csv"),
-      mode = "wb"
-    )
-    
-    # Send downloaded scheme to database browser overview
-    DB$available <- gsub("_", " ", basename(dir_ls(DB$database)))
-    
-    Scheme$target_table <- read.csv(
-      file.path(DB$database, Scheme$folder_name, "targets.csv"),
-      header = TRUE,	
-      sep = "\t",	
-      row.names = NULL,	
-      colClasses = c(	
-        "NULL",	
-        "character",	
-        "character",	
-        "integer",	
-        "integer",	
-        "character",	
-        "integer",	
-        "NULL"	
-      )	
-    )
-    
-    DB$exist <- length(dir_ls(DB$database)) == 0
-    
-    shinyjs::show("download_cgMLST")
-    shinyjs::hide("loading")
-    
-    output$statustext <- renderUI(
-      fluidRow(
-        tags$li(
-          class = "dropdown", 
-          tags$span(HTML(
-            paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
-                  "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
-            style = "color:white;")
-        )
-      )
-    )
-    
-    show_toast(
-      title = "Download successful",
-      type = "success",
-      position = "bottom-end",
-      timer = 5000
-    )
-    
-    log_print("Download successful")
-    
-    showModal(
-      modalDialog(
-        selectInput(
-          "scheme_db",
-          label = "",
-          choices = if(!is.null(Typing$last_scheme)) {
-            Typing$last_scheme
-          } else {DB$available},
-          selected = if(!is.null(Typing$last_scheme)) {
-            Typing$last_scheme
-          } else {if(!is.null(DB$scheme)) {input$select_cgmlst} else {DB$available[1]}}),
-        title = "Select a local database to load.",
-        footer = tagList(
-          actionButton("load", "Load", class = "btn btn-default")
-        )
-      )
-    )
-  })
-  
-  # Download Target Info (CSV Table)
-  observe({
-    input$download_cgMLST
-    
-    scheme_overview <- read_html(Scheme$link_scheme) %>%
-      html_table(header = FALSE) %>%
-      as.data.frame(stringsAsFactors = FALSE)
-    
-    last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"],
-                                   format = "%B %d, %Y, %H:%M %p")
-    names(scheme_overview) <- NULL
-    
-    last_file_change <- format(
-      file.info(file.path(DB$database,
-                          ".downloaded_schemes",
-                          paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
-    
-    output$cgmlst_scheme <- renderTable({scheme_overview})
-    output$scheme_update_info <- renderText({
-      req(last_file_change)
-      if (last_file_change < last_scheme_change) {
-        "(Newer scheme available \u274c)"
-      } else {
-        "(Scheme is up-to-date \u2705)"
-      }
-    })
-  })
-  
-  # _______________________ ####
-  
-  ## Visualization ----
-  
-  # Render placeholder image
-  
-  output$placeholder <- renderImage({
-    # Path to your PNG image with a transparent background
-    image_path <- paste0(getwd(), "/www/PhyloTrace.png")
-    
-    # Use HTML to display the image with the <img> tag
-    list(src = image_path,
-         height = 180)
-  }, deleteFile = FALSE)
-  
-  # Render tree plot fields
-  
-  output$nj_field <- renderUI(
-    fluidRow(
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
-    )
-  )
-  
-  output$mst_field <- renderUI(
-    fluidRow(
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
-    )
-  )
-  
-  output$upgma_field <- renderUI(
-    fluidRow(
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
-    )
-  )
-  
-  ### Render Visualization Controls ----
-  
-  #### NJ and UPGMA controls ----
-  
-  # Control enable/disable of variable mapping inputs
-  observe({
-    shinyjs::toggleState(id = "nj_color_mapping", condition = isTRUE(input$nj_mapping_show))
-    shinyjs::toggleState(id = "nj_tiplab_scale", condition = isTRUE(input$nj_mapping_show))
-    shinyjs::toggleState(id = "upgma_color_mapping", condition = isTRUE(input$upgma_mapping_show))
-    shinyjs::toggleState(id = "upgma_tiplab_scale", condition = isTRUE(input$upgma_mapping_show))
-    
-    shinyjs::toggleState(id = "nj_tipcolor_mapping", condition = isTRUE(input$nj_tipcolor_mapping_show))
-    shinyjs::toggleState(id = "nj_tippoint_scale", condition = isTRUE(input$nj_tipcolor_mapping_show))
-    shinyjs::toggleState(id = "upgma_tipcolor_mapping", condition = isTRUE(input$upgma_tipcolor_mapping_show))
-    shinyjs::toggleState(id = "upgma_tippoint_scale", condition = isTRUE(input$upgma_tipcolor_mapping_show))
-    
-    shinyjs::toggleState(id = "nj_tipshape_mapping", condition = isTRUE(input$nj_tipshape_mapping_show))
-    shinyjs::toggleState(id = "upgma_tipshape_mapping", condition = isTRUE(input$upgma_tipshape_mapping_show))
-    
-    shinyjs::toggleState(id = "nj_fruit_variable", condition = isTRUE(input$nj_tiles_show_1))
-    shinyjs::toggleState(id = "upgma_fruit_variable", condition = isTRUE(input$upgma_tiles_show_1))
-    shinyjs::toggleState(id = "nj_fruit_variable_2", condition = isTRUE(input$nj_tiles_show_2))
-    shinyjs::toggleState(id = "upgma_fruit_variable_2", condition = isTRUE(input$upgma_tiles_show_2))
-    shinyjs::toggleState(id = "nj_fruit_variable_3", condition = isTRUE(input$nj_tiles_show_3))
-    shinyjs::toggleState(id = "upgma_fruit_variable_3", condition = isTRUE(input$upgma_tiles_show_3))
-    shinyjs::toggleState(id = "nj_fruit_variable_4", condition = isTRUE(input$nj_tiles_show_4))
-    shinyjs::toggleState(id = "upgma_fruit_variable_4", condition = isTRUE(input$upgma_tiles_show_4))
-    shinyjs::toggleState(id = "nj_fruit_variable_5", condition = isTRUE(input$nj_tiles_show_5))
-    shinyjs::toggleState(id = "upgma_fruit_variable_5", condition = isTRUE(input$upgma_tiles_show_5))
-    shinyjs::toggleState(id = "nj_tiles_scale_1", condition = isTRUE(input$nj_tiles_show_1))
-    shinyjs::toggleState(id = "upgma_tiles_scale_1", condition = isTRUE(input$upgma_tiles_show_1))
-    shinyjs::toggleState(id = "nj_tiles_scale_2", condition = isTRUE(input$nj_tiles_show_2))
-    shinyjs::toggleState(id = "upgma_tiles_scale_2", condition = isTRUE(input$upgma_tiles_show_2))
-    shinyjs::toggleState(id = "nj_tiles_scale_3", condition = isTRUE(input$nj_tiles_show_3))
-    shinyjs::toggleState(id = "upgma_tiles_scale_3", condition = isTRUE(input$upgma_tiles_show_3))
-    shinyjs::toggleState(id = "nj_tiles_scale_4", condition = isTRUE(input$nj_tiles_show_4))
-    shinyjs::toggleState(id = "upgma_tiles_scale_4", condition = isTRUE(input$upgma_tiles_show_4))
-    shinyjs::toggleState(id = "nj_tiles_scale_5", condition = isTRUE(input$nj_tiles_show_5))
-    shinyjs::toggleState(id = "upgma_tiles_scale_5", condition = isTRUE(input$upgma_tiles_show_5))
-    
-    shinyjs::toggleState(id = "nj_heatmap_sel", condition = isTRUE(input$nj_heatmap_show))
-    shinyjs::toggleState(id = "nj_heatmap_scale", condition = isTRUE(input$nj_heatmap_show))
-    shinyjs::toggleState(id = "upgma_heatmap_sel", condition = isTRUE(input$upgma_heatmap_show))
-    shinyjs::toggleState(id = "upgma_heatmap_scale", condition = isTRUE(input$upgma_heatmap_show))
-  })
-  
-  # Size scaling NJ
-  observe({
-    req(input$nj_ratio)
-    if(input$nj_ratio == "1.6") {
-      updateSliderInput(session, "nj_scale",
-                        step = 5, value = 800, min = 500, max = 1200)
-    } else if(input$nj_ratio == "1.77777777777778") {
-      updateSliderInput(session, "nj_scale",
-                        step = 9, value = 801, min = 504, max = 1197)
-    } else if(input$nj_ratio == "1.33333333333333"){
-      updateSliderInput(session, "nj_scale",
-                        step = 3, value = 801, min = 501, max = 1200)
-    }
-  })
-  
-  # Size scaling UPGMA
-  observe({
-    req(input$upgma_ratio)
-    if(input$upgma_ratio == "1.6") {
-      updateSliderInput(session, "upgma_scale",
-                        step = 5, value = 800, min = 500, max = 1200)
-    } else if(input$upgma_ratio == "1.77777777777778") {
-      updateSliderInput(session, "upgma_scale",
-                        step = 9, value = 801, min = 504, max = 1197)
-    } else if(input$upgma_ratio == "1.33333333333333"){
-      updateSliderInput(session, "upgma_scale",
-                        step = 3, value = 801, min = 501, max = 1200)
-    }
-  })
-  
-  # Size scaling MST
-  observe({
-    req(input$mst_ratio)
-    if(input$mst_ratio == "1.6") {
-      updateSliderInput(session, "mst_scale",
-                        step = 5, value = 800, min = 500, max = 1200)
-    } else if(input$mst_ratio == "1.77777777777778") {
-      updateSliderInput(session, "mst_scale",
-                        step = 9, value = 801, min = 504, max = 1197)
-    } else if(input$mst_ratio == "1.33333333333333"){
-      updateSliderInput(session, "mst_scale",
-                        step = 3, value = 801, min = 501, max = 1200)
-    }
-  })
-  
-  # Custom Labels
-  
-  # Add custom label
-  observeEvent(input$nj_add_new_label, {
-    
-    if(nchar(input$nj_new_label_name) > 0) {
-      if(!(input$nj_new_label_name %in% Vis$custom_label_nj)) {
-        Vis$custom_label_nj <- rbind(Vis$custom_label_nj, input$nj_new_label_name) 
-        if(!(nrow(Vis$custom_label_nj) == 1)) {
-          updateSelectInput(session, "nj_custom_label_sel", selected = input$nj_new_label_name)
-        }
-      } else {
-        show_toast(
-          title = "Label already exists",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-      }
-    } else {
-      show_toast(
-        title = "Min. 1 character",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    }
-  })
-  
-  observeEvent(input$upgma_add_new_label, {
-    
-    if(nchar(input$upgma_new_label_name) > 0) {
-      if(!(input$upgma_new_label_name %in% Vis$custom_label_upgma)) {
-        Vis$custom_label_upgma <- rbind(Vis$custom_label_upgma, input$upgma_new_label_name) 
-        if(!(nrow(Vis$custom_label_upgma) == 1)) {
-          updateSelectInput(session, "upgma_custom_label_sel", selected = input$upgma_new_label_name)
-        }
-      } else {
-        show_toast(
-          title = "Label already exists",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-      }
-    } else {
-      show_toast(
-        title = "Min. 1 character",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    }
-  })
-  
-  # Delete custom label
-  observeEvent(input$nj_del_label, {
-    
-    if(nrow(Vis$custom_label_nj) > 1) {
-      Vis$custom_label_nj <- Vis$custom_label_nj[-which(Vis$custom_label_nj[,1] == input$nj_custom_label_sel), , drop = FALSE]
-    } else if (nrow(Vis$custom_label_nj) == 1) {
-      Vis$nj_label_pos_x <- list()
-      Vis$nj_label_pos_y <- list()
-      Vis$nj_label_size <- list()
-      Vis$custom_label_nj <- data.frame()
-    }
-  })
-  
-  observeEvent(input$upgma_del_label, {
-    
-    if(nrow(Vis$custom_label_upgma) > 1) {
-      Vis$custom_label_upgma <- Vis$custom_label_upgma[-which(Vis$custom_label_upgma[,1] == input$upgma_custom_label_sel), , drop = FALSE]
-    } else if (nrow(Vis$custom_label_upgma) == 1) {
-      Vis$upgma_label_pos_x <- list()
-      Vis$upgma_label_pos_y <- list()
-      Vis$upgma_label_size <- list()
-      Vis$custom_label_upgma <- data.frame()
-    }
-  })
-  
-  # Select custom labels
-  output$nj_custom_label_select <- renderUI({
-    if(nrow(Vis$custom_label_nj) > 0) {
-      selectInput(
-        "nj_custom_label_sel",
-        "",
-        choices = Vis$custom_label_nj[,1]
-      )
-    }
-  })
-  
-  output$upgma_custom_label_select <- renderUI({
-    if(nrow(Vis$custom_label_upgma) > 0) {
-      selectInput(
-        "upgma_custom_label_sel",
-        "",
-        choices = Vis$custom_label_upgma[,1]
-      )
-    }
-  })
-  
-  # Select custom labels
-  output$nj_cust_label_save <- renderUI({
-    if(nrow(Vis$custom_label_nj) > 0) {
-      actionButton(
-        "nj_cust_label_save",
-        "Apply"
-      )
-    } else {
-      column(
-        width = 12,
-        br(), br(), br(), br(), br(), br(),
-        h5("test", style = "color: transparent; margin-bottom: 3px")
-      )
-    }
-  })
-  
-  output$upgma_cust_label_save <- renderUI({
-    if(nrow(Vis$custom_label_upgma) > 0) {
-      actionButton(
-        "upgma_cust_label_save",
-        "Apply"
-      )
-    } else {
-      column(
-        width = 12,
-        br(), br(), br(), br(), br(), br(),
-        h5("test", style = "color: transparent; margin-bottom: 3px")
-      )
-    }
-  })
-  
-  # Custom Label Size
-  output$nj_custom_labelsize <- renderUI({
-    if(length(Vis$custom_label_nj) > 0) {
-      if(!is.null(Vis$nj_label_size[[input$nj_custom_label_sel]])) {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_size"),
-                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
-                    min = 0, max = 10, step = 0.5, ticks = F,
-                    value = Vis$nj_label_size[[input$nj_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_size"),
-                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
-                    min = 0, max = 10, step = 0.5, ticks = F, value = 5,
-                    width = "150px")
-      }
-    } 
-  })
-  
-  output$upgma_custom_labelsize <- renderUI({
-    if(length(Vis$custom_label_upgma) > 0) {
-      if(!is.null(Vis$upgma_label_size[[input$upgma_custom_label_sel]])) {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_size"),
-                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
-                    min = 0, max = 10, step = 0.5, ticks = F,
-                    value = Vis$upgma_label_size[[input$upgma_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_size"),
-                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
-                    min = 0, max = 10, step = 0.5, ticks = F, value = 5,
-                    width = "150px")
-      }
-    } 
-  })
-  
-  # Render slider input based on selected label
-  output$nj_sliderInput_y <- renderUI({
-    if(length(Vis$custom_label_nj) > 0) {
-      if(!is.null(Vis$nj_label_pos_y[[input$nj_custom_label_sel]])) {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_y"),
-                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = 50, step = 1, ticks = F,
-                    value = Vis$nj_label_pos_y[[input$nj_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_y"),
-                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = sum(DB$data$Include), step = 1, ticks = F, 
-                    value = sum(DB$data$Include) / 2,
-                    width = "150px")
-      }
-    } 
-  })
-  
-  output$upgma_sliderInput_y <- renderUI({
-    if(length(Vis$custom_label_upgma) > 0) {
-      if(!is.null(Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]])) {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_y"),
-                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = 50, step = 1, ticks = F,
-                    value = Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_y"),
-                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = sum(DB$data$Include), step = 1, ticks = F, 
-                    value = sum(DB$data$Include) / 2,
-                    width = "150px")
-      }
-    } 
-  })
-  
-  output$nj_sliderInput_x <- renderUI({
-    if(length(Vis$custom_label_nj) > 0) {
-      if(!is.null(Vis$nj_label_pos_x[[input$nj_custom_label_sel]])) {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_x"),
-                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = 50, step = 1, ticks = F,
-                    value = Vis$nj_label_pos_x[[input$nj_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_x"),
-                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = round(Vis$nj_max_x, 0), step = 1, ticks = F, 
-                    value = round(Vis$nj_max_x / 2, 0),
-                    width = "150px")
-      }
-    }
-  })
-  
-  output$upgma_sliderInput_x <- renderUI({
-    if(length(Vis$custom_label_upgma) > 0) {
-      if(!is.null(Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]])) {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_x"),
-                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = 50, step = 1, ticks = F,
-                    value = Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_x"),
-                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = round(Vis$upgma_max_x, 0), step = 1, ticks = F, 
-                    value = round(Vis$upgma_max_x / 2, 0),
-                    width = "150px")
-      }
-    }
-  })
-  
-  # Apply custom label changes
-  observeEvent(input$nj_cust_label_save, {
-    
-    if(!is.null(Vis$nj_label_pos_y) &
-       !is.null(Vis$nj_label_pos_x) &
-       !is.null(Vis$nj_label_size) &
-       !is.null(input$nj_custom_label_sel)) {
-      Vis$nj_label_pos_y[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_y")]]
-      Vis$nj_label_pos_x[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_x")]]
-      Vis$nj_label_size[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_size")]]
-    }
-  })
-  
-  observeEvent(input$upgma_cust_label_save, {
-    
-    if(!is.null(Vis$upgma_label_pos_y) &
-       !is.null(Vis$upgma_label_pos_x) &
-       !is.null(Vis$upgma_label_size) &
-       !is.null(input$upgma_custom_label_sel)) {
-      Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_y")]]
-      Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_x")]]
-      Vis$upgma_label_size[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_size")]]
-    }
-  })
-  
-  # Show delete custom label button if custam label added
-  output$nj_del_label <- renderUI({
-    if(nrow(Vis$custom_label_nj) > 0) {
-      actionButton(
-        "nj_del_label",
-        "",
-        icon = icon("minus")
-      )
-    } else {NULL}
-  })
-  
-  output$upgma_del_label <- renderUI({
-    if(nrow(Vis$custom_label_upgma) > 0) {
-      actionButton(
-        "upgma_del_label",
-        "",
-        icon = icon("minus")
-      )
-    } else {NULL}
-  })
-  
-  # Mapping value number information
-  output$nj_tiplab_mapping_info <- renderUI({
-    if(!is.null(input$nj_color_mapping) & (!is.null(Vis$meta_nj))) {
-      if(is.numeric(unlist(Vis$meta_nj[input$nj_color_mapping]))) {
-        if(input$nj_tiplab_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-          column(
-            width = 3,
-            fluidRow(
-              column(
-                width = 4,
-                h5("Midpoint", style = "color: white; margin-top: 22px;")
-              ),
-              column(
-                width = 8,
-                div(
-                  class = "divmid-sel1",
-                  selectInput(
-                    "nj_color_mapping_div_mid",
-                    label = "",
-                    choices = c("Zero", "Mean", "Median"),
-                    selected = "Mean"
-                  )
-                )
-              )
-            )
-          )
-        } else {
-          column(
-            width = 3,
-            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
-          ) 
-        }
-      } else {
-        if(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))) > 7) {
-          column(
-            width = 3,
-            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$upgma_tiplab_mapping_info <- renderUI({
-    if(!is.null(input$upgma_color_mapping) & (!is.null(Vis$meta_upgma))) {
-      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) {
-        if(input$upgma_tiplab_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-          column(
-            width = 3,
-            fluidRow(
-              column(
-                width = 4,
-                h5("Midpoint", style = "color: white; margin-top: 22px;")
-              ),
-              column(
-                width = 8,
-                div(
-                  class = "divmid-sel1",
-                  selectInput(
-                    "upgma_color_mapping_div_mid",
-                    label = "",
-                    choices = c("Zero", "Mean", "Median"),
-                    selected = "Mean"
-                  )
-                )
-              )
-            )
-          )
-        } else {
-          column(
-            width = 3,
-            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
-          ) 
-        }
-      } else {
-        if(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) > 7) {
-          column(
-            width = 3,
-            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$nj_tipcolor_mapping_info <- renderUI({
-    if(!is.null(input$nj_tipcolor_mapping) & (!is.null(Vis$meta_nj))) {
-      if(is.numeric(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) {
-        if(input$nj_tippoint_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-          column(
-            width = 3,
-            fluidRow(
-              column(
-                width = 4,
-                h5("Midpoint", style = "color: white; margin-top: 22px;")
-              ),
-              column(
-                width = 8,
-                div(
-                  class = "divmid-sel1",
-                  selectInput(
-                    "nj_tipcolor_mapping_div_mid",
-                    label = "",
-                    choices = c("Zero", "Mean", "Median"),
-                    selected = "Mean"
-                  )
-                )
-              )
-            )
-          )
-        } else {
-          column(
-            width = 3,
-            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-          ) 
-        }
-      } else {
-        if(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) > 7) {
-          column(
-            width = 3,
-            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$upgma_tipcolor_mapping_info <- renderUI({
-    if(!is.null(input$upgma_tipcolor_mapping) & (!is.null(Vis$meta_upgma))) {
-      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) {
-        if(input$upgma_tippoint_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-          column(
-            width = 3,
-            fluidRow(
-              column(
-                width = 4,
-                h5("Midpoint", style = "color: white; margin-top: 22px;")
-              ),
-              column(
-                width = 8,
-                div(
-                  class = "divmid-sel1",
-                  selectInput(
-                    "upgma_tipcolor_mapping_div_mid",
-                    label = "",
-                    choices = c("Zero", "Mean", "Median"),
-                    selected = "Mean"
-                  )
-                )
-              )
-            )
-          )
-        } else {
-          column(
-            width = 3,
-            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-          ) 
-        }
-      } else {
-        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) > 7) {
-          column(
-            width = 3,
-            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$nj_tipshape_mapping_info <- renderUI({
-    if(!is.null(input$nj_tipshape_mapping) & (!is.null(Vis$meta_nj))) {
-      if(is.numeric(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))) {
-        column(
-          width = 3,
-          h5("Mapping continous variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
-        )
-      } else {
-        if(length(unique(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))) > 6) {
-          column(
-            width = 3,
-            h5("Mapping > 6 variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )    
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$upgma_tipshape_mapping_info <- renderUI({
-    if(!is.null(input$upgma_tipshape_mapping) & (!is.null(Vis$meta_upgma))) {
-      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))) {
-        column(
-          width = 3,
-          h5("Mapping continous variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
-        )
-      } else {
-        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))) > 6) {
-          column(
-            width = 3,
-            h5("Mapping > 6 variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )    
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$nj_fruit_mapping_info <- renderUI({
-    if(input$nj_tile_num == 1) {
-      if(!is.null(input$nj_fruit_variable) & (!is.null(Vis$meta_nj))) {
-        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable]))) {
-          if(input$nj_tiles_scale_1 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_tiles_mapping_div_mid_1",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$nj_tile_num == 2) {
-      if(!is.null(input$nj_fruit_variable_2) & (!is.null(Vis$meta_nj))) {
-        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) {
-          if(input$nj_tiles_scale_2 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_tiles_mapping_div_mid_2",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$nj_tile_num == 3) {
-      if(!is.null(input$nj_fruit_variable_3) & (!is.null(Vis$meta_nj))) {
-        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) {
-          if(input$nj_tiles_scale_3 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_tiles_mapping_div_mid_3",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$nj_tile_num == 4) {
-      if(!is.null(input$nj_fruit_variable_4) & (!is.null(Vis$meta_nj))) {
-        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) {
-          if(input$nj_tiles_scale_4 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_tiles_mapping_div_mid_4",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$nj_tile_num == 5) {
-      if(!is.null(input$nj_fruit_variable_5) & (!is.null(Vis$meta_nj))) {
-        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) {
-          if(input$nj_tiles_scale_5 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_tiles_mapping_div_mid_5",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  output$upgma_fruit_mapping_info <- renderUI({
-    if(input$upgma_tile_num == 1) {
-      if(!is.null(input$upgma_fruit_variable) & (!is.null(Vis$meta_upgma))) {
-        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) {
-          if(input$upgma_tiles_scale_1 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_tiles_mapping_div_mid_1",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$upgma_tile_num == 2) {
-      if(!is.null(input$upgma_fruit_variable_2) & (!is.null(Vis$meta_upgma))) {
-        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) {
-          if(input$upgma_tiles_scale_2 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_tiles_mapping_div_mid_2",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$upgma_tile_num == 3) {
-      if(!is.null(input$upgma_fruit_variable_3) & (!is.null(Vis$meta_upgma))) {
-        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) {
-          if(input$upgma_tiles_scale_3 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_tiles_mapping_div_mid_3",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$upgma_tile_num == 4) {
-      if(!is.null(input$upgma_fruit_variable_4) & (!is.null(Vis$meta_upgma))) {
-        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) {
-          if(input$upgma_tiles_scale_4 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_tiles_mapping_div_mid_4",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$upgma_tile_num == 5) {
-      if(!is.null(input$upgma_fruit_variable_5) & (!is.null(Vis$meta_upgma))) {
-        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) {
-          if(input$upgma_tiles_scale_5 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_tiles_mapping_div_mid_5",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  output$nj_heatmap_mapping_info <- renderUI({
-    if(!is.null(input$nj_heatmap_select) & (!is.null(Vis$meta_nj))) {
-      if (any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)) & 
-          any(!sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric))) {
-        column(
-          width = 3,
-          h5("Heatmap with categorical and continous values not possible", 
-             style = "color: #E18B00; font-size: 12px; font-style: italic; margin-top: 15px;  margin-left: 40px")
-        ) 
-      } else {
-        if(any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric))) {
-          if(input$nj_heatmap_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_heatmap_div_mid",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_heatmap_select]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Categorical values", style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$upgma_heatmap_mapping_info <- renderUI({
-    if(!is.null(input$upgma_heatmap_select) & (!is.null(Vis$meta_upgma))) {
-      if (any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)) & 
-          any(!sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric))) {
-        column(
-          width = 3,
-          h5("Heatmap with categorical and continous values not possible", 
-             style = "color: #E18B00; font-size: 12px; font-style: italic; margin-top: 15px;  margin-left: 40px")
-        ) 
-      } else {
-        if(any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric))) {
-          if(input$upgma_heatmap_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_heatmap_div_mid",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_heatmap_select]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Categorical values", style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      }
-    } else {NULL}
-  })
-  
-  # Tiles offset
-  output$nj_fruit_offset_circ <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "nj_fruit_offset_circ",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_fruit_offset_circ",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_fruit_offset_circ <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        offset <- 0.15
-        step <- 0.1
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.05
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "upgma_fruit_offset_circ",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_fruit_offset_circ",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.05,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$nj_fruit_offset_circ_2 <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "nj_fruit_offset_circ_2",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_fruit_offset_circ_2",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_fruit_offset_circ_2 <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "upgma_fruit_offset_circ_2",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_fruit_offset_circ_2",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$nj_fruit_offset_circ_3 <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "nj_fruit_offset_circ_3",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_fruit_offset_circ_3",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_fruit_offset_circ_3 <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "upgma_fruit_offset_circ_3",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_fruit_offset_circ_3",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$nj_fruit_offset_circ_4 <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "nj_fruit_offset_circ_4",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_fruit_offset_circ_4",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_fruit_offset_circ_4 <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "upgma_fruit_offset_circ_4",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_fruit_offset_circ_4",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$nj_fruit_offset_circ_5 <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "nj_fruit_offset_circ_5",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_fruit_offset_circ_5",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_fruit_offset_circ_5 <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "upgma_fruit_offset_circ_5",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_fruit_offset_circ_5",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  # For Layout change update tiles offset position
-  observeEvent(input$nj_layout, {
-    
-    if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-      offset <- 0.05
-      step <- 0.01
-      min <- -0.2
-      max <- 0.2
-    } else {
-      offset <- 0.15
-      step <- 0.03
-      min <- -0.6
-      max <- 0.6
-    }
-    
-    updateSliderInput(session, "nj_fruit_offset_circ", min = min, step = step, max = max)
-    updateSliderInput(session, "nj_fruit_offset_circ_2", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "nj_fruit_offset_circ_3", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "nj_fruit_offset_circ_4", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "nj_fruit_offset_circ_5", min = min, step = step, max = max, value = offset) 
-  })
-  
-  observeEvent(input$upgma_layout, {
-    
-    if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-      offset <- 0.05
-      step <- 0.01
-      min <- -0.2
-      max <- 0.2
-    } else {
-      offset <- 0.15
-      step <- 0.03
-      min <- -0.6
-      max <- 0.6
-    }
-    
-    updateSliderInput(session, "upgma_fruit_offset_circ", min = min, step = step, max = max)
-    updateSliderInput(session, "upgma_fruit_offset_circ_2", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "upgma_fruit_offset_circ_3", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "upgma_fruit_offset_circ_4", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "upgma_fruit_offset_circ_5", min = min, step = step, max = max, value = offset) 
-  })
-  
-  # Heatmap width
-  output$nj_heatmap_width <- renderUI({
-    if(!is.null(input$nj_heatmap_select)) {
-      length_input <- length(input$nj_heatmap_select)
-      if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
-        if(length_input < 3) {
-          width <- 0.1
-        } else {
-          if (length_input >= 3 && length_input <= 50) {
-            width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-          } else {
-            width <- 1.5
-          }   
-        }
-      } else {
-        if(length_input < 3) {
-          width <- 0.3
-        } else if (length_input >= 3 && length_input <= 27) {
-          width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 3
-        }
-      }
-      
-      sliderInput(
-        "nj_heatmap_width",
-        label = "",
-        min = 0.05,
-        max = 1.5,
-        value = width,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_heatmap_width",
-        label = "",
-        min = 0.05,
-        max = 1.5,
-        value = 0.1,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_heatmap_width <- renderUI({
-    if(!is.null(input$upgma_heatmap_select)) {
-      length_input <- length(input$upgma_heatmap_select)
-      if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
-        if(length_input < 3) {
-          width <- 0.1
-        } else {
-          if (length_input >= 3 && length_input <= 50) {
-            width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-          } else {
-            width <- 1.5
-          }   
-        }
-      } else {
-        if(length_input < 3) {
-          width <- 0.3
-        } else if (length_input >= 3 && length_input <= 27) {
-          width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 3
-        }
-      }
-      
-      sliderInput(
-        "upgma_heatmap_width",
-        label = "",
-        min = 0.05,
-        max = 1.5,
-        value = width,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_heatmap_width",
-        label = "",
-        min = 0.05,
-        max = 1.5,
-        value = 0.1,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  # Update value if new variables added
-  observeEvent(input$nj_heatmap_select, {
-    
-    length_input <- length(input$nj_heatmap_select)
-    if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
-      if(length_input < 3) {
-        width <- 0.1
-      } else {
-        if (length_input >= 3 && length_input <= 50) {
-          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 1.5
-        }   
-      }
-    } else {
-      if(length_input < 3) {
-        width <- 0.3
-      } else if (length_input >= 3 && length_input <= 27) {
-        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-      } else {
-        width <- 3
-      }
-    }
-    updateSliderInput(session, "nj_heatmap_width", value = width)
-  })
-  
-  observeEvent(input$upgma_heatmap_select, {
-    
-    length_input <- length(input$upgma_heatmap_select)
-    if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
-      if(length_input < 3) {
-        width <- 0.1
-      } else {
-        if (length_input >= 3 && length_input <= 50) {
-          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 1.5
-        }   
-      }
-    } else {
-      if(length_input < 3) {
-        width <- 0.3
-      } else if (length_input >= 3 && length_input <= 27) {
-        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-      } else {
-        width <- 3
-      }
-    }
-    updateSliderInput(session, "upgma_heatmap_width", value = width)
-  })
-  
-  # Update value if layout changed
-  observeEvent(input$nj_layout, {
-    length_input <- length(input$nj_heatmap_select)
-    if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
-      if(length_input < 3) {
-        width <- 0.1
-      } else {
-        if (length_input >= 3 && length_input <= 50) {
-          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 1.5
-        }   
-      }
-    } else {
-      if(length_input < 3) {
-        width <- 0.3
-      } else if (length_input >= 3 && length_input <= 27) {
-        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-      } else {
-        width <- 3
-      }
-    }
-    updateSliderInput(session, "nj_heatmap_width", value = width)
-  })
-  
-  observeEvent(input$upgma_layout, {
-    length_input <- length(input$upgma_heatmap_select)
-    if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
-      if(length_input < 3) {
-        width <- 0.1
-      } else {
-        if (length_input >= 3 && length_input <= 50) {
-          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 1.5
-        }   
-      }
-    } else {
-      if(length_input < 3) {
-        width <- 0.3
-      } else if (length_input >= 3 && length_input <= 27) {
-        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-      } else {
-        width <- 3
-      }
-    }
-    updateSliderInput(session, "upgma_heatmap_width", value = width)
-  })
-  
-  # Heatmap column titles position
-  observeEvent(input$nj_layout, {
-    if(!(input$nj_layout == "inward" | input$nj_layout == "circular")) {
-      updateSliderInput(session, "nj_colnames_y", value = -1)
-    } else {
-      updateSliderInput(session, "nj_colnames_y", value = 0)
-    }
-  })
-  
-  observeEvent(input$upgma_layout, {
-    if(!(input$upgma_layout == "inward" | input$upgma_layout == "circular")) {
-      updateSliderInput(session, "upgma_colnames_y", value = -1)
-    } else {
-      updateSliderInput(session, "upgma_colnames_y", value = 0)
-    }
-  })
-  
-  output$nj_colnames_y <- renderUI({
-    if(!is.null(sum(DB$data$Include))) {
-      if(input$nj_layout == "inward" | input$nj_layout == "circular") {
-        min <- 0
-        val <- 0
-      } else {
-        val <- -1
-        if((sum(DB$data$Include) * -0.1) > -2) {
-          min <- -2
-        } else {
-          min <- round(sum(DB$data$Include) * -0.1, 0)
-        }
-      }
-      sliderInput(
-        "nj_colnames_y",
-        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
-        min = min,
-        max = sum(DB$data$Include),
-        value = val,
-        step = 1,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_colnames_y",
-        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
-        min = -10,
-        max = 10,
-        value = 0,
-        step = 1,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_colnames_y <- renderUI({
-    if(!is.null(sum(DB$data$Include))) {
-      if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
-        min <- 0
-        val <- 0
-      } else {
-        val <- -1
-        if((sum(DB$data$Include) * -0.1) > -2) {
-          min <- -2
-        } else {
-          min <- round(sum(DB$data$Include) * -0.1, 0)
-        }
-      }
-      sliderInput(
-        "upgma_colnames_y",
-        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
-        min = min,
-        max = sum(DB$data$Include),
-        value = val,
-        step = 1,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_colnames_y",
-        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
-        min = -10,
-        max = 10,
-        value = 0,
-        step = 1,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  # Heatmap column titles angle
-  output$nj_colnames_angle <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        angle <- 90
-      } else {angle <- -90}
-      sliderInput(
-        "nj_colnames_angle",
-        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
-        min = -90,
-        max = 90,
-        value = angle,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_colnames_angle",
-        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
-        min = -90,
-        max = 90,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_colnames_angle <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        angle <- 90
-      } else {angle <- -90}
-      sliderInput(
-        "upgma_colnames_angle",
-        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
-        min = -90,
-        max = 90,
-        value = angle,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_colnames_angle",
-        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
-        min = -90,
-        max = 90,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  # Change heatmap column titles angle and label align when switching layout
-  observeEvent(input$nj_layout, {
-    if(input$nj_layout == "circular" | input$nj_layout == "inward"){
-      angle <- 90
-      val <- TRUE
-    } else {
-      angle <- -90
-      val <- FALSE
-    }
-    updateSwitchInput(session, "nj_align", value = val)
-    updateSliderInput(session, "nj_colnames_angle", value = angle)
-  })
-  
-  observeEvent(input$upgma_layout, {
-    if(input$upgma_layout == "circular" | input$upgma_layout == "inward"){
-      angle <- 90
-      val <- TRUE
-    } else {
-      angle <- -90
-      val <- FALSE
-    }
-    updateSwitchInput(session, "upgma_align", value = val)
-    updateSliderInput(session, "upgma_colnames_angle", value = angle)
-  })
-  
-  # Tile number selector update each other
-  observeEvent(input$nj_tile_num, {
-    updateSelectInput(session, "nj_tile_number", selected = input$nj_tile_num)
-  })
-  
-  observeEvent(input$nj_tile_number, {
-    updateSelectInput(session, "nj_tile_num", selected = input$nj_tile_number)
-  })
-  
-  observeEvent(input$upgma_tile_num, {
-    updateSelectInput(session, "upgma_tile_number", selected = input$upgma_tile_num)
-  })
-  
-  observeEvent(input$upgma_tile_number, {
-    updateSelectInput(session, "upgma_tile_num", selected = input$upgma_tile_number)
-  })
-  
-  # Clade coloring
-  output$nj_clade_scale <- renderUI({
-    if(length(input$nj_parentnode) <= 1) {
-      fluidRow(
-        column(
-          width = 5,
-          h5("Color", style = "color:white; position: relative; right: -15px; margin-top: 30px")
-        ),
-        column(
-          width = 7,
-          align = "center",
-          colorPickr(
-            inputId = "nj_clade_scale",
-            selected = "#D0F221",
-            label = "",
-            update = "changestop",
-            interaction = list(clear = FALSE,
-                               save = FALSE),
-            position = "right-start",
-            width = "100%"
-          )
-        )
-      )
-    } else {
-      fluidRow(
-        column(
-          width = 5,
-          h5("Scale", style = "color:white; position: relative; right: -15px; margin-top: 30px")
-        ),
-        column(
-          width = 7,
-          align = "center",
-          div(
-            class = "sel-clade-scale",
-            selectInput(
-              "nj_clade_scale",
-              "",
-              choices = list(
-                Qualitative = list(
-                  "Set1",
-                  "Set2",
-                  "Set3",
-                  "Pastel1",
-                  "Pastel2",
-                  "Paired",
-                  "Dark2",
-                  "Accent"
-                ),
-                Sequential = list(
-                  "YlOrRd",
-                  "YlOrBr",
-                  "YlGnBu",
-                  "YlGn",
-                  "Reds",
-                  "RdPu",
-                  "Purples",
-                  "PuRd",
-                  "PuBuGn",
-                  "PuBu",
-                  "OrRd",
-                  "Oranges",
-                  "Greys",
-                  "Greens",
-                  "GnBu",
-                  "BuPu",
-                  "BuGn",
-                  "Blues"
-                )
-              )
-            )
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_clade_scale <- renderUI({
-    if(length(input$upgma_parentnode) <= 1) {
-      fluidRow(
-        column(
-          width = 5,
-          h5("Color", style = "color:white; position: relative; right: -15px; margin-top: 30px")
-        ),
-        column(
-          width = 7,
-          align = "center",
-          colorPickr(
-            inputId = "upgma_clade_scale",
-            selected = "#D0F221",
-            label = "",
-            update = "changestop",
-            interaction = list(clear = FALSE,
-                               save = FALSE),
-            position = "right-start",
-            width = "100%"
-          )
-        )
-      )
-    } else {
-      fluidRow(
-        column(
-          width = 5,
-          h5("Scale", style = "color:white; position: relative; right: -15px; margin-top: 30px")
-        ),
-        column(
-          width = 7,
-          align = "center",
-          div(
-            class = "sel-clade-scale",
-            selectInput(
-              "upgma_clade_scale",
-              "",
-              choices = list(
-                Qualitative = list(
-                  "Set1",
-                  "Set2",
-                  "Set3",
-                  "Pastel1",
-                  "Pastel2",
-                  "Paired",
-                  "Dark2",
-                  "Accent"
-                ),
-                Sequential = list(
-                  "YlOrRd",
-                  "YlOrBr",
-                  "YlGnBu",
-                  "YlGn",
-                  "Reds",
-                  "RdPu",
-                  "Purples",
-                  "PuRd",
-                  "PuBuGn",
-                  "PuBu",
-                  "OrRd",
-                  "Oranges",
-                  "Greys",
-                  "Greens",
-                  "GnBu",
-                  "BuPu",
-                  "BuGn",
-                  "Blues"
-                )
-              )
-            )
-          )
-        )
-      )
-    }
-  })
-  
-  # Heatmap variable color scale
-  output$nj_heatmap_scale <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_heatmap_select])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_heatmap_scale",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_heatmap_select]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_heatmap_scale",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_heatmap_scale",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Paired"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_heatmap_scale <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_heatmap_select])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_heatmap_scale",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_heatmap_select]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_heatmap_scale",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_heatmap_scale",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Paired"
-          )
-        )
-      }
-    }
-  })
-  
-  # Tiles variable color scale
-  output$nj_tiles_scale_1 <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiles_scale_1",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_1",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_1",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiles_scale_1 <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiles_scale_1",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_1",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_1",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$nj_tiles_scale_2 <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_2])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiles_scale_2",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_2",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_2",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiles_scale_2 <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiles_scale_2",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_2",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_2",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$nj_tiles_scale_3 <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_3])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiles_scale_3",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_3",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_3",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiles_scale_3 <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiles_scale_3",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_3",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_3",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$nj_tiles_scale_4 <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_4])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiles_scale_4",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) > 7) {
-        shinyjs::disabled(selectInput(
-          "nj_tiles_scale_4",
-          "",
-          choices = list(
-            Gradient = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            )
-          ),
-          selected = "turbo"
-        ))
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_4",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiles_scale_4 <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiles_scale_4",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_4",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_4",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$nj_tiles_scale_5 <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_5])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiles_scale_5",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_5",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_5",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiles_scale_5 <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiles_scale_5",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_5",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_5",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  # Tip Labels Variable Color Scale
-  output$nj_tiplab_scale <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_color_mapping])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiplab_scale",
-          "",
-          selectize = FALSE,
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiplab_scale",
-            "",
-            selectize = FALSE,
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiplab_scale",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            )
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiplab_scale <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_color_mapping])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiplab_scale",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiplab_scale",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiplab_scale",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            )
-          )
-        )
-      }
-    }
-  })
-  
-  # Tippoint Scale
-  output$nj_tippoint_scale <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      if(class(unlist(Vis$meta_nj[input$nj_tipcolor_mapping])) == "numeric") {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tippoint_scale",
-            "",
-            choices = list(
-              Continous = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              ),
-              Diverging = list(
-                "Spectral",
-                "RdYlGn",
-                "RdYlBu",
-                "RdGy",
-                "RdBu",
-                "PuOr",
-                "PRGn",
-                "PiYG",
-                "BrBG"
-              )
-            )
-          )
-        )
-      } else {
-        if(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) > 7) {
-          shinyjs::disabled(
-            selectInput(
-              "nj_tippoint_scale",
-              "",
-              choices = list(
-                Gradient = list(
-                  "Magma" = "magma",
-                  "Inferno" = "inferno",
-                  "Plasma" = "plasma",
-                  "Viridis" = "viridis",
-                  "Cividis" = "cividis",
-                  "Rocket" = "rocket",
-                  "Mako" = "mako",
-                  "Turbo" = "turbo"
-                )
-              ),
-              selected = "turbo"
-            )
-          )
-        } else {
-          shinyjs::disabled(
-            selectInput(
-              "nj_tippoint_scale",
-              "",
-              choices = list(
-                Qualitative = list(
-                  "Set1",
-                  "Set2",
-                  "Set3",
-                  "Pastel1",
-                  "Pastel2",
-                  "Paired",
-                  "Dark2",
-                  "Accent"
-                ),
-                Sequential = list(
-                  "YlOrRd",
-                  "YlOrBr",
-                  "YlGnBu",
-                  "YlGn",
-                  "Reds",
-                  "RdPu",
-                  "Purples",
-                  "PuRd",
-                  "PuBuGn",
-                  "PuBu",
-                  "OrRd",
-                  "Oranges",
-                  "Greys",
-                  "Greens",
-                  "GnBu",
-                  "BuPu",
-                  "BuGn",
-                  "Blues"
-                )
-              ),
-              selected = "Set2"
-            )
-          )
-        }
-      }
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tippoint_scale",
-          "",
-          choices = list(
-            Qualitative = list(
-              "Set1",
-              "Set2",
-              "Set3",
-              "Pastel1",
-              "Pastel2",
-              "Paired",
-              "Dark2",
-              "Accent"
-            ),
-            Sequential = list(
-              "YlOrRd",
-              "YlOrBr",
-              "YlGnBu",
-              "YlGn",
-              "Reds",
-              "RdPu",
-              "Purples",
-              "PuRd",
-              "PuBuGn",
-              "PuBu",
-              "OrRd",
-              "Oranges",
-              "Greys",
-              "Greens",
-              "GnBu",
-              "BuPu",
-              "BuGn",
-              "Blues"
-            )
-          ),
-          selected = "Set2"
-        )
-      )
-    }
-  })
-  
-  output$upgma_tippoint_scale <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      if(class(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping])) == "numeric") {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tippoint_scale",
-            "",
-            choices = list(
-              Continous = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              ),
-              Diverging = list(
-                "Spectral",
-                "RdYlGn",
-                "RdYlBu",
-                "RdGy",
-                "RdBu",
-                "PuOr",
-                "PRGn",
-                "PiYG",
-                "BrBG"
-              )
-            ),
-            selected = c("Viridis" = "viridis")
-          )
-        )
-      } else {
-        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) > 7) {
-          shinyjs::disabled(
-            selectInput(
-              "upgma_tippoint_scale",
-              "",
-              choices = list(
-                Gradient = list(
-                  "Magma" = "magma",
-                  "Inferno" = "inferno",
-                  "Plasma" = "plasma",
-                  "Viridis" = "viridis",
-                  "Cividis" = "cividis",
-                  "Rocket" = "rocket",
-                  "Mako" = "mako",
-                  "Turbo" = "turbo"
-                )
-              ),
-              selected = "turbo"
-            )
-          )
-        } else {
-          shinyjs::disabled(
-            selectInput(
-              "upgma_tippoint_scale",
-              "",
-              choices = list(
-                Qualitative = list(
-                  "Set1",
-                  "Set2",
-                  "Set3",
-                  "Pastel1",
-                  "Pastel2",
-                  "Paired",
-                  "Dark2",
-                  "Accent"
-                ),
-                Sequential = list(
-                  "YlOrRd",
-                  "YlOrBr",
-                  "YlGnBu",
-                  "YlGn",
-                  "Reds",
-                  "RdPu",
-                  "Purples",
-                  "PuRd",
-                  "PuBuGn",
-                  "PuBu",
-                  "OrRd",
-                  "Oranges",
-                  "Greys",
-                  "Greens",
-                  "GnBu",
-                  "BuPu",
-                  "BuGn",
-                  "Blues"
-                )
-              ),
-              selected = "Set2"
-            )
-          )
-        }
-      }
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tippoint_scale",
-          "",
-          choices = list(
-            Qualitative = list(
-              "Set1",
-              "Set2",
-              "Set3",
-              "Pastel1",
-              "Pastel2",
-              "Paired",
-              "Dark2",
-              "Accent"
-            ),
-            Sequential = list(
-              "YlOrRd",
-              "YlOrBr",
-              "YlGnBu",
-              "YlGn",
-              "Reds",
-              "RdPu",
-              "Purples",
-              "PuRd",
-              "PuBuGn",
-              "PuBu",
-              "OrRd",
-              "Oranges",
-              "Greys",
-              "Greens",
-              "GnBu",
-              "BuPu",
-              "BuGn",
-              "Blues"
-            )
-          ),
-          selected = "Set2"
-        )
-      )
-    }
-  })
-  
-  # Clade Highlights
-  output$nj_parentnode <- renderUI({
-    if(!is.null(Vis$nj_parentnodes)) {
-      pickerInput(
-        "nj_parentnode",
-        label = "",
-        choices = sort(unique(as.numeric(Vis$nj_parentnodes))),
-        multiple = TRUE,
-        options = list(
-          `live-search` = TRUE,
-          size = 10,
-          style = "background-color: white; border-radius: 5px;"
-        ),
-        width = "99%"
-      )
-    } else {
-      pickerInput(
-        "nj_parentnode",
-        label = "",
-        choices = c(),
-        multiple = TRUE,
-        options = list(
-          `live-search` = TRUE,
-          size = 10,
-          style = "background-color: white; border-radius: 5px;"
-        ),
-        width = "99%"
-      )
-    }
-  })
-  
-  output$upgma_parentnode <- renderUI({
-    if(!is.null(Vis$upgma_parentnodes)) {
-      pickerInput(
-        "upgma_parentnode",
-        label = "",
-        choices = sort(unique(as.numeric(Vis$upgma_parentnodes))),
-        multiple = TRUE,
-        options = list(
-          `live-search` = TRUE,
-          size = 10,
-          style = "background-color: white; border-radius: 5px;"
-        ),
-        width = "99%"
-      )
-    } else {
-      pickerInput(
-        "upgma_parentnode",
-        label = "",
-        choices = c(),
-        multiple = TRUE,
-        options = list(
-          `live-search` = TRUE,
-          size = 10,
-          style = "background-color: white; border-radius: 5px;"
-        ),
-        width = "99%"
-      )
-    }
-  })
-  
-  # Branch label size
-  output$nj_branch_size <- renderUI(
-    numericInput(
-      "nj_branch_size",
-      label = h5("Size", style = "color:white; margin-bottom: 0px"),
-      min = 2,
-      max = 10,
-      step = 0.5,
-      value = Vis$branch_size_nj,
-      width = "80px"
-    )
-  )
-  
-  output$upgma_branch_size <- renderUI(
-    numericInput(
-      "upgma_branch_size",
-      label = h5("Size", style = "color:white; margin-bottom: 0px"),
-      min = 2,
-      max = 10,
-      step = 0.5,
-      value = Vis$branch_size_upgma,
-      width = "80px"
-    )
-  )
-  
-  # Tippanel size
-  output$nj_tiplab_padding <- renderUI(
-    if(!is.null(Vis$tiplab_padding_nj)) {
-      sliderInput(
-        inputId = "nj_tiplab_padding",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 0.05,
-        max = 1,
-        value = Vis$tiplab_padding_nj,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "nj_tiplab_padding",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 0.05,
-        max = 1,
-        value = 0.2,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  output$upgma_tiplab_padding <- renderUI(
-    if(!is.null(Vis$tiplab_padding_upgma)) {
-      sliderInput(
-        inputId = "upgma_tiplab_padding",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 0.05,
-        max = 1,
-        value = Vis$tiplab_padding_upgma,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "upgma_tiplab_padding",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 0.05,
-        max = 1,
-        value = 0.2,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  # Nodepoint size
-  output$nj_nodepoint_size <- renderUI(
-    if(!is.null(Vis$nodepointsize_nj)) {
-      sliderInput(
-        inputId = "nj_nodepoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        value = Vis$nodepointsize_nj,
-        step = 0.5,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "nj_nodepoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        value = 2.5,
-        step = 0.5,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  output$upgma_nodepoint_size <- renderUI(
-    if(!is.null(Vis$nodepointsize_upgma)) {
-      sliderInput(
-        inputId = "upgma_nodepoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        value = Vis$nodepointsize_upgma,
-        step = 0.5,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "upgma_nodepoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        value = 2.5,
-        step = 0.5,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  # Tippoint size 
-  output$nj_tippoint_size <- renderUI(
-    if(!is.null(Vis$tippointsize_nj)) {
-      sliderInput(
-        inputId = "nj_tippoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        step = 0.5,
-        value = Vis$tippointsize_nj,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "nj_tippoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        step = 0.5,
-        value = 4,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  output$upgma_tippoint_size <- renderUI(
-    if(!is.null(Vis$tippointsize_upgma)) {
-      sliderInput(
-        inputId = "upgma_tippoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        step = 0.5,
-        value = Vis$tippointsize_upgma,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "upgma_tippoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        step = 0.5,
-        value = 4,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  # Tiplabel size
-  output$nj_tiplab_size <- renderUI(
-    if(!is.null(Vis$labelsize_nj)) {
-      numericInput(
-        "nj_tiplab_size",
-        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        step = 0.5,
-        value = Vis$labelsize_nj,
-        width = "80px"
-      )
-    } else {
-      numericInput(
-        "nj_tiplab_size",
-        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        step = 0.5,
-        value = 4,
-        width = "80px"
-      )
-    }
-  )
-  
-  output$upgma_tiplab_size <- renderUI(
-    if(!is.null(Vis$labelsize_upgma)) {
-      numericInput(
-        "upgma_tiplab_size",
-        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        step = 0.5,
-        value = Vis$labelsize_upgma,
-        width = "80px"
-      )
-    } else {
-      numericInput(
-        "upgma_tiplab_size",
-        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        step = 0.5,
-        value = 4,
-        width = "80px"
-      )
-    }
-  )
-  
-  # Rootedge length 
-  output$nj_rootedge_length <- renderUI({
-    if(!is.null(Vis$nj_max_x)) {
-      if(round(ceiling(Vis$nj_max_x) * 0.02, 0) < 1) {
-        min <- 1
-      } else {
-        min <- round(ceiling(Vis$nj_max_x) * 0.02, 0)  
-      }
-      max <- round(ceiling(Vis$nj_max_x) * 0.2, 0)
-      sliderInput(
-        "nj_rootedge_length",
-        label = h5("Rootedge Length", style = "color:white; margin-bottom: 0px"),
-        min = min,
-        max = max,
-        value = round(ceiling(Vis$nj_max_x) * 0.05, 0),
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_rootedge_length",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        value = 2,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_rootedge_length <- renderUI({
-    if(!is.null(Vis$upgma_max_x)) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.02, 0) < 1) {
-        min <- 1
-      } else {
-        min <- round(ceiling(Vis$upgma_max_x) * 0.02, 0)  
-      }
-      max <- round(ceiling(Vis$upgma_max_x) * 0.2, 0)
-      sliderInput(
-        "upgma_rootedge_length",
-        label = h5("Rootedge Length", style = "color:white; margin-bottom: 0px"),
-        min = min,
-        max = max,
-        value = round(ceiling(Vis$upgma_max_x) * 0.05, 0),
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_rootedge_length",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        value = 2,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  # Treescale 
-  output$nj_treescale_width <- renderUI({
-    if(!is.null(Vis$nj_max_x)) {
-      numericInput(
-        "nj_treescale_width",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        value = round(ceiling(Vis$nj_max_x) * 0.1, 0),
-        min = 1,
-        max = round(floor(Vis$nj_max_x) * 0.5, 0),
-        step = 1,
-        width = "80px"
-      )
-    } else {
-      numericInput(
-        "nj_treescale_width",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        value = 2,
-        min = 1,
-        max = 10,
-        step = 1,
-        width = "80px"
-      )
-    }
-  })
-  
-  output$upgma_treescale_width <- renderUI({
-    if(!is.null(Vis$upgma_max_x)) {
-      numericInput(
-        "upgma_treescale_width",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        value = round(ceiling(Vis$upgma_max_x) * 0.1, 0),
-        min = 1,
-        max = round(floor(Vis$upgma_max_x) * 0.5, 0),
-        step = 1,
-        width = "80px"
-      )
-    } else {
-      numericInput(
-        "upgma_treescale_width",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        value = 2,
-        min = 1,
-        max = 10,
-        step = 1,
-        width = "80px"
-      )
-    }
-  })
-  
-  output$nj_treescale_x <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(ceiling(Vis$nj_min_x) < 1) {
-        floor <- 1
-      } else {
-        floor <- ceiling(Vis$nj_min_x)
-      }
-      sliderInput(
-        "nj_treescale_x",
-        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-        min = floor,
-        max = round(floor(Vis$nj_max_x)),
-        value = round(ceiling(Vis$nj_max_x) * 0.2, 0),
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_treescale_x",
-        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        value = 2,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_treescale_x <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(ceiling(Vis$upgma_min_x) < 1) {
-        floor <- 1
-      } else {
-        floor <- ceiling(Vis$upgma_min_x)
-      }
-      sliderInput(
-        "upgma_treescale_x",
-        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-        min = floor,
-        max = round(floor(Vis$upgma_max_x)),
-        value = round(ceiling(Vis$upgma_max_x) * 0.2, 0),
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_treescale_x",
-        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        value = 2,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$nj_treescale_y <- renderUI({
-    if(!is.null(sum(DB$data$Include))) {
-      sliderInput(
-        "nj_treescale_y",
-        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-        min = 0,
-        max = sum(DB$data$Include),
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_treescale_y",
-        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-        min = 0,
-        max = 10,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_treescale_y <- renderUI({
-    if(!is.null(sum(DB$data$Include))) {
-      sliderInput(
-        "upgma_treescale_y",
-        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-        min = 0,
-        max = sum(DB$data$Include),
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_treescale_y",
-        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-        min = 0,
-        max = 10,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  ### Heatmap 
-  # Heatmap picker
-  output$nj_heatmap_sel <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      meta <- select(Vis$meta_nj, -c(taxa, Index, `Assembly ID`, `Assembly Name`,
-                                     Scheme, `Typing Date`, Successes, Errors))
-      
-      # Identify numeric columns
-      numeric_columns <- sapply(meta, is.numeric)
-      
-      numeric_column_names <- names(meta[numeric_columns])
-      
-      non_numeric_column_names <- names(meta)[!numeric_columns]
-      
-      choices <- list()
-      
-      # Add Continuous list only if there are numeric columns
-      if (length(numeric_column_names) > 0) {
-        choices$Continuous <- as.list(setNames(numeric_column_names, numeric_column_names))
-      }
-      
-      # Add Diverging list
-      choices$Categorical <- as.list(setNames(non_numeric_column_names, non_numeric_column_names))
-      
-      div(
-        class = "heatmap-picker",
-        shinyjs::disabled(
-          pickerInput(
-            inputId = "nj_heatmap_select",
-            label = "",
-            width = "100%",
-            choices = if(ncol(Vis$meta_nj) == 11) {
-              c(
-                `Isolation Date` = "Isolation Date",
-                Host = "Host",
-                Country = "Country",
-                City = "City"
-              )
-            } else {choices},
-            options = list(
-              `dropdown-align-center` = TRUE,
-              size = 10,
-              style = "background-color: white; border-radius: 5px;"
-            ),
-            multiple = TRUE
-          )
-        )
-      )
-    } else {
-      div(
-        class = "heatmap-picker",
-        shinyjs::disabled(
-          pickerInput(
-            inputId = "nj_heatmap_select",
-            label = "",
-            width = "100%",
-            choices = c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            ),
-            multiple = TRUE
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_heatmap_sel <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      meta <- select(Vis$meta_upgma, -c(taxa, Index, `Assembly ID`, `Assembly Name`,
-                                        Scheme, `Typing Date`, Successes, Errors))
-      
-      # Identify numeric columns
-      numeric_columns <- sapply(meta, is.numeric)
-      
-      numeric_column_names <- names(meta[numeric_columns])
-      
-      non_numeric_column_names <- names(meta)[!numeric_columns]
-      
-      choices <- list()
-      
-      # Add Continuous list only if there are numeric columns
-      if (length(numeric_column_names) > 0) {
-        choices$Continuous <- as.list(setNames(numeric_column_names, numeric_column_names))
-      }
-      
-      # Add Diverging list
-      choices$Categorical <- as.list(setNames(non_numeric_column_names, non_numeric_column_names))
-      
-      div(
-        class = "heatmap-picker",
-        shinyjs::disabled(
-          pickerInput(
-            inputId = "upgma_heatmap_select",
-            label = "",
-            width = "100%",
-            choices = if(ncol(Vis$meta_upgma) == 11) {
-              c(
-                `Isolation Date` = "Isolation Date",
-                Host = "Host",
-                Country = "Country",
-                City = "City"
-              )
-            } else {choices},
-            options = list(
-              `dropdown-align-center` = TRUE,
-              size = 10,
-              style = "background-color: white; border-radius: 5px;"
-            ),
-            multiple = TRUE
-          )
-        )
-      )
-    } else {
-      div(
-        class = "heatmap-picker",
-        shinyjs::disabled(
-          pickerInput(
-            inputId = "upgma_heatmap_select",
-            label = "",
-            width = "100%",
-            choices = c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            ),
-            multiple = TRUE
-          )
-        )
-      )
-    }
-  })
-  
-  # Heatmap offset
-  output$nj_heatmap_offset <- renderUI({
-    if(!is.null(Vis$nj_max_x)) {
-      sliderInput(
-        "nj_heatmap_offset",
-        label = "",
-        min = 0,
-        max = round(ceiling(Vis$nj_max_x)*1.5, 0),
-        step = 1,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_heatmap_offset",
-        label = "",
-        min = 0,
-        max = 10,
-        step = 1,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_heatmap_offset <- renderUI({
-    if(!is.null(Vis$upgma_max_x)) {
-      sliderInput(
-        "upgma_heatmap_offset",
-        label = "",
-        min = 0,
-        max = round(ceiling(Vis$upgma_max_x)*1.5, 0),
-        step = 1,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_heatmap_offset",
-        label = "",
-        min = 0,
-        max = 10,
-        step = 1,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  ### Tiling 
-  # Geom Fruit select Variable
-  output$nj_fruit_variable <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$nj_fruit_variable2 <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_2",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_2",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$nj_fruit_variable3 <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_3",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_3",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$nj_fruit_variable4 <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_4",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_4",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$nj_fruit_variable5 <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_5",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_5",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_fruit_variable <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_fruit_variable2 <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_2",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_2",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_fruit_variable3 <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(selectInput(
-        "upgma_fruit_variable_3",
-        "",
-        choices = if(ncol(Vis$meta_upgma) == 11) {
-          c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        } else {
-          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-        },
-        selected = c(`Isolation Date` = "Isolation Date"),
-        width = "100%"
-      ))
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_3",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_fruit_variable4 <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_4",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_4",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_fruit_variable5 <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_5",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_5",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  # Geom Fruit Width
-  output$nj_fruit_width <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "nj_fruit_width_circ",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        sliderInput(
-          "nj_fruit_width_circ",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "nj_fruit_width_circ",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$nj_fruit_width2 <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "nj_fruit_width_circ_2",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        sliderInput(
-          "nj_fruit_width_circ_2",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "nj_fruit_width_circ_2",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$nj_fruit_width3 <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "nj_fruit_width_circ_3",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        sliderInput(
-          "nj_fruit_width_circ_3",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "nj_fruit_width_circ_3",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$nj_fruit_width4 <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "nj_fruit_width_circ_4",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        sliderInput(
-          "nj_fruit_width_circ_4",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "nj_fruit_width_circ_4",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$nj_fruit_width5 <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "nj_fruit_width_circ_5",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        sliderInput(
-          "nj_fruit_width_circ_5",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "nj_fruit_width_circ_5",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$upgma_fruit_width <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "upgma_fruit_width_circ",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        sliderInput(
-          "upgma_fruit_width_circ",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "upgma_fruit_width_circ",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$upgma_fruit_width2 <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "upgma_fruit_width_circ_2",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        sliderInput(
-          "upgma_fruit_width_circ_2",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "upgma_fruit_width_circ_2",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$upgma_fruit_width3 <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "upgma_fruit_width_circ_3",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        sliderInput(
-          "upgma_fruit_width_circ_3",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "upgma_fruit_width_circ_3",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$upgma_fruit_width4 <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "upgma_fruit_width_circ_4",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        sliderInput(
-          "upgma_fruit_width_circ_4",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "upgma_fruit_width_circ_4",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$upgma_fruit_width5 <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "upgma_fruit_width_circ_5",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        sliderInput(
-          "upgma_fruit_width_circ_5",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "upgma_fruit_width_circ_5",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  # For Layout change update tiles 
-  observeEvent(input$nj_layout, {
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-        } else {
-          width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-        }
-      }
-      
-      updateSliderInput(session, "nj_fruit_width_circ", value = width)
-      updateSliderInput(session, "nj_fruit_width_circ_2", value = width)
-      updateSliderInput(session, "nj_fruit_width_circ_3", value = width)
-      updateSliderInput(session, "nj_fruit_width_circ_4", value = width)
-      updateSliderInput(session, "nj_fruit_width_circ_5", value = width) 
-    }
-  })
-  
-  observeEvent(input$upgma_layout, {
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-        } else {
-          width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-        }
-      }
-      
-      updateSliderInput(session, "upgma_fruit_width_circ", value = width)
-      updateSliderInput(session, "upgma_fruit_width_circ_2", value = width)
-      updateSliderInput(session, "upgma_fruit_width_circ_3", value = width)
-      updateSliderInput(session, "upgma_fruit_width_circ_4", value = width)
-      updateSliderInput(session, "upgma_fruit_width_circ_5", value = width) 
-    }
-  })
-  
-  # Tip color mapping 
-  output$nj_tipcolor_mapping <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tipcolor_mapping",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Assembly Name` = "Assembly Name",
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Assembly Name` = "Assembly Name", `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(City = "City"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tipcolor_mapping",
-          "",
-          choices = c(
-            `Assembly Name` = "Assembly Name",
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c(City = "City")
-        )
-      )
-    }
-  })
-  
-  output$upgma_tipcolor_mapping <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tipcolor_mapping",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Assembly Name` = "Assembly Name",
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Assembly Name` = "Assembly Name", `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(City = "City"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tipcolor_mapping",
-          "",
-          choices = c(
-            `Assembly Name` = "Assembly Name",
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c(City = "City")
-        )
-      )
-    }
-  })
-  
-  # Tip shape Mapping 
-  output$nj_tipshape_mapping <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tipshape_mapping",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c("Host" = "Host"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tipshape_mapping",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c("Host" = "Host"),
-          width = "100%"
-        )
-      )
-    }
-  })
-  
-  output$upgma_tipshape_mapping <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tipshape_mapping",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c("Host" = "Host"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tipshape_mapping",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c("Host" = "Host"),
-          width = "100%"
-        )
-      )
-    }
-  })
-  
-  # Branch label 
-  output$nj_branch_label <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      selectInput(
-        "nj_branch_label",
-        "",
-        choices = if(ncol(Vis$meta_nj) == 11) {
-          c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        } else {
-          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                 names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-        },
-        selected = c("Host" = "Host"),
-        width = "100%"
-      )
-    } else {
-      selectInput(
-        "nj_branch_label",
-        "",
-        choices = c(
-          `Isolation Date` = "Isolation Date",
-          Host = "Host",
-          Country = "Country",
-          City = "City"
-        ),
-        selected = c("Host" = "Host"),
-        width = "100%"
-      )
-    }
-  })
-  
-  output$upgma_branch_label <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      selectInput(
-        "upgma_branch_label",
-        "",
-        choices = if(ncol(Vis$meta_upgma) == 11) {
-          c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        } else {
-          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-        },
-        selected = c("Host" = "Host"),
-        width = "100%"
-      )
-    } else {
-      selectInput(
-        "upgma_branch_label",
-        "",
-        choices = c(
-          `Isolation Date` = "Isolation Date",
-          Host = "Host",
-          Country = "Country",
-          City = "City"
-        ),
-        selected = c("Host" = "Host"),
-        width = "100%"
-      )
-    }
-  })
-  
-  # Color mapping 
-  output$nj_color_mapping <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_color_mapping",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(Country = "Country"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_color_mapping",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c(Country = "Country"),
-          width = "100%"
-        )
-      )
-    }
-  })
-  
-  output$upgma_color_mapping <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_color_mapping",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(Country = "Country"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_color_mapping",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c(Country = "Country"),
-          width = "100%"
-        )
-      )
-    }
-  })
-  
-  # Tip labels 
-  output$nj_tiplab <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      selectInput(
-        "nj_tiplab",
-        label = "",
-        choices = if(ncol(Vis$meta_nj) == 11) {
-          c(
-            Index = "Index",
-            `Assembly ID` = "Assembly ID",
-            `Assembly Name` = "Assembly Name",
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        } else {
-          append(c(Index = "Index", `Assembly ID` = "Assembly ID", `Assembly Name` = "Assembly Name",
-                   `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                 names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-        },
-        selected = c(`Assembly Name` = "Assembly Name"),
-        width = "100%"
-      )
-    } else {
-      selectInput(
-        "nj_tiplab",
-        label = "",
-        choices = c(
-          Index = "Index",
-          `Assembly ID` = "Assembly ID",
-          `Assembly Name` = "Assembly Name",
-          `Isolation Date` = "Isolation Date",
-          Host = "Host",
-          Country = "Country",
-          City = "City"
-        ),
-        selected = c(`Assembly Name` = "Assembly Name"),
-        width = "100%"
-      )
-    }
-  })
-  
-  output$upgma_tiplab <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      selectInput(
-        "upgma_tiplab",
-        label = "",
-        choices = if(ncol(Vis$meta_upgma) == 11) {
-          c(
-            Index = "Index",
-            `Assembly ID` = "Assembly ID",
-            `Assembly Name` = "Assembly Name",
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        } else {
-          append(c(Index = "Index", `Assembly ID` = "Assembly ID", `Assembly Name` = "Assembly Name",
-                   `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-        },
-        selected = c(`Assembly Name` = "Assembly Name"),
-        width = "100%"
-      )
-    } else {
-      selectInput(
-        "upgma_tiplab",
-        label = "",
-        choices = c(
-          Index = "Index",
-          `Assembly ID` = "Assembly ID",
-          `Assembly Name` = "Assembly Name",
-          `Isolation Date` = "Isolation Date",
-          Host = "Host",
-          Country = "Country",
-          City = "City"
-        ),
-        selected = c(`Assembly Name` = "Assembly Name"),
-        width = "100%"
-      )
-    }
-  })
-  
-  #### MST controls ----
-  
-  # Clustering UI
-  output$mst_cluster <- renderUI({
-    req(DB$schemeinfo)
-    numericInput(
-      inputId = "mst_cluster_threshold",
-      label = NULL,
-      value = as.numeric(DB$schemeinfo[7, 2]),
-      min = 1,
-      max = 99
-    )
-  })
-  
-  # MST color mapping
-  output$mst_color_mapping <- renderUI({
-    if(input$mst_color_var == FALSE) {
-      fluidRow(
-        column(
-          width = 7,
-          div(
-            class = "node_color",
-            colorPickr(
-              inputId = "mst_color_node",
-              width = "100%",
-              selected = "#B2FACA",
-              label = "",
-              update = "changestop",
-              interaction = list(clear = FALSE,
-                                 save = FALSE),
-              position = "right-start"
-            )
-          )
-        ),
-        column(
-          width = 5,
-          dropMenu(
-            actionBttn(
-              "mst_node_menu",
-              label = "",
-              color = "default",
-              size = "sm",
-              style = "material-flat",
-              icon = icon("sliders")
-            ),
-            placement = "top-start",
-            theme = "translucent",
-            width = 5,
-            numericInput(
-              "node_opacity",
-              label = h5("Opacity", style = "color:white; margin-bottom: 0px;"),
-              value = 1,
-              step = 0.1,
-              min = 0,
-              max = 1,
-              width = "80px"
-            )
-          )
-        )
-      ) 
-    } else {
-      fluidRow(
-        column(
-          width = 9,
-          div(
-            class = "mst_col_sel",
-            selectInput(
-              "mst_col_var",
-              label = "",
-              choices = if(any(DB$cust_var[DB$cust_var$Variable[which(DB$cust_var$Variable %in% c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)]))],]$Type != "categ")) {
-                selection <- c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)])
-                cust_vars <- DB$cust_var$Variable[which(DB$cust_var$Variable %in% selection)]
-                selection[-which(selection == cust_vars[DB$cust_var[cust_vars,]$Type != "categ"])]
-              } else {c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)])},
-              width = "100%"
-            )
-          )
-        ),
-        column(
-          width = 3,
-          dropMenu(
-            actionBttn(
-              "mst_col_menu",
-              label = "",
-              color = "default",
-              size = "sm",
-              style = "material-flat",
-              icon = icon("sliders")
-            ),
-            placement = "top-start",
-            theme = "translucent",
-            width = 5,
-            selectInput(
-              "mst_col_scale",
-              label = h5("Color Scale", style = "color:white; margin-bottom: 0px;"),
-              choices = c("Viridis", "Rainbow"),
-              width = "150px"
-            ),
-            br(), br(), br(), br()
-          )
-        )
-      ) 
-    }
-  })
-  
-  observeEvent(input$mst_color_var, {
-    
-    if(input$mst_color_var == TRUE) {
-      updateSelectizeInput(session, inputId = "mst_node_shape", choices = c("Pie Nodes" = "custom"))
-      updateSelectizeInput(session, inputId = "mst_node_label", choices = c("Assembly Name"))
-    } else {
-      updateSelectizeInput(session, inputId = "mst_node_shape", 
-                           choices = list(`Label inside` = c("Circle" = "circle", "Box" = "box", "Text" = "text"),
-                                          `Label outside` = c("Diamond" = "diamond", "Hexagon" = "hexagon","Dot" = "dot", "Square" = "square")),
-                           selected = c("Dot" = "dot"))
-      updateSelectizeInput(session, inputId = "mst_node_label",
-                           choices = names(DB$meta)[c(1, 3, 4, 6, 7, 8, 9)],
-                           selected = "Assembly Name")
-    }
-  })
-  
-  # MST node labels 
-  output$mst_node_label <- renderUI({
-    selectInput(
-      "mst_node_label",
-      label = "",
-      choices = names(DB$meta)[c(1, 3, 4, 6, 7, 8, 9)],
-      selected = "Assembly Name",
-      width = "100%"
-    )
-  })
-  
-  ### Plot Reactives ----
-  
-  #### MST ----
-  
-  mst_tree <- reactive({
-    data <- toVisNetworkData(Vis$ggraph_1)
-    data$nodes <- mutate(data$nodes, 
-                                label = label_mst(),
-                                value = mst_node_scaling(),
-                                opacity = node_opacity())
-    
-    ctxRendererJS <- htmlwidgets::JS("({ctx, id, x, y, state: { selected, hover }, style, font, label, metadata}) => {
-                            var pieData = JSON.parse(metadata);
-                            var radius = style.size;
-                            var centerX = x;
-                            var centerY = y;
-                            var total = pieData.reduce((sum, slice) => sum + slice.value, 0)
-                            var startAngle = 0;
-
-                            const drawNode = () => {
-                                // Set shadow properties
-                                if (style.shadow) {
-                                  var shadowSize = style.shadowSize;
-                                  ctx.shadowColor = style.shadowColor;
-                                  ctx.shadowBlur = style.shadowSize;
-                                  ctx.shadowOffsetX = style.shadowX;
-                                  ctx.shadowOffsetY = style.shadowY;
-                                  
-                                  ctx.beginPath();
-                                  ctx.arc(centerX, centerY, radius, 0, 2 * Math.PI);
-                                  ctx.fill();
-                                  
-                                  ctx.shadowColor = 'transparent';
-                                  ctx.shadowBlur = 0;
-                                  ctx.shadowOffsetX = 0;
-                                  ctx.shadowOffsetY = 0;
-                                }
-
-                                pieData.forEach(slice => {
-                                    var sliceAngle = 2 * Math.PI * (slice.value / total);
-                                    ctx.beginPath();
-                                    ctx.moveTo(centerX, centerY);
-                                    ctx.arc(centerX, centerY, radius, startAngle, startAngle + sliceAngle);
-                                    ctx.closePath();
-                                    ctx.fillStyle = slice.color;
-                                    ctx.fill();
-                                     if (pieData.length > 1) {
-                ctx.strokeStyle = 'black';
-                ctx.lineWidth = 1;
-                ctx.stroke();
-            }
-                                    startAngle += sliceAngle;
-                                });
-                    
-                                // Draw a border
-                                ctx.beginPath();
-                                ctx.arc(centerX, centerY, radius, 0, 2 * Math.PI);
-                                ctx.strokeStyle = 'black';
-                                ctx.lineWidth = 1;
-                                ctx.stroke();
-                            };
-                            drawLabel = () => {
-                              //Draw the label
-                              var lines = label.split(`\n`);
-                              var lineHeight = font.size;
-                              ctx.font = `${font.size}px ${font.face}`;
-                              ctx.fillStyle = font.color;
-                              ctx.textAlign = 'center';
-                              ctx.textBaseline = 'middle';
-                              lines.forEach((line, index) => {
-                                ctx.fillText(line, centerX, 
-                                centerY + radius + (index + 1) * lineHeight);
-                              })
-                            }
-                            
-                            return {
-                                drawNode,
-                                drawExternalLabel: drawLabel,
-                                nodeDimensions: { width: 2 * radius, height: 2 * radius },
-                            };
-                        }")
-    
-    Vis$var_cols <- NULL
-    
-    # Generate pie charts as nodes
-    if(input$mst_color_var == TRUE & (!is.null(input$mst_col_var))) {
-      
-      group <- character(nrow(data$nodes))
-      for (i in 1:length(unique(Vis$meta_mst[[input$mst_col_var]]))) {
-        group[i] <- unique(Vis$meta_mst[[input$mst_col_var]])[i]
-      }
-      
-      data$nodes <- cbind(data$nodes, data.frame(metadata = character(nrow(data$nodes))))
-      
-      if(length(which(data$nodes$group == "")) != 0) {
-        data$nodes$group[which(data$nodes$group == "")] <- data$nodes$group[1]
-      }
-      
-      if(is.null(input$mst_col_scale)) {
-        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
-                                      color = viridis(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
-      } else if (input$mst_col_scale == "Rainbow") {
-        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
-                                      color = rainbow(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
-      } else if (input$mst_col_scale == "Viridis") {
-        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
-                                      color = viridis(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
-      }
-      
-      for(i in 1:nrow(data$nodes)) {
-        
-        iso_subset <- strsplit(data$nodes$label[i], split = "\n")[[1]]
-        variable <- Vis$meta_mst[[input$mst_col_var]]
-        values <- variable[which(Vis$meta_mst$`Assembly Name` %in% iso_subset)]
-        
-        for(j in 1:length(unique(values))) {
-          
-          share <- sum(unique(values)[j] == values) / length(values) * 100
-          color <- Vis$var_cols$color[Vis$var_cols$value == unique(values)[j]]
-          
-          if(j == 1) {
-            pie_vec <- paste0('{"value":', share,',"color":"', color,'"}')
-          } else {
-            pie_vec <- paste0(pie_vec, ',{"value":', share,',"color":"', color,'"}')
-          }
-        }
-        
-        data$nodes$metadata[i] <- paste0('[', pie_vec, ']')
-      }
-    }
-    
-    data$edges <- mutate(data$edges,
-                                length = if(input$mst_scale_edges == FALSE) {
-                                  input$mst_edge_length
-                                } else {
-                                  data$edges$weight * input$mst_edge_length_scale
-                                },
-                                label = as.character(data$edges$weight),
-                                opacity = input$mst_edge_opacity)
-    
-    if (input$mst_show_clusters) {
-      data$nodes$group <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
-    }
-    
-    visNetwork_graph <- visNetwork(data$nodes, data$edges,
-                                   main = mst_title(),
-                                   background = mst_background_color(),
-                                   submain = mst_subtitle()) %>%
-      visNodes(size = mst_node_size(),
-               shape = input$mst_node_shape,
-               shadow = input$mst_shadow,
-               color = mst_color_node(),
-               ctxRenderer = ctxRendererJS,
-               scaling = list(min = mst_node_size_min(),
-                              max = mst_node_size_max()),
-               font = list(color = node_font_color(),
-                           size = input$node_label_fontsize)) %>%
-      visEdges(color = mst_color_edge(),
-               font = list(color = mst_edge_font_color(),
-                           size = mst_edge_font_size(),
-                           strokeWidth = 4)) %>%
-      visOptions(collapse = TRUE) %>%
-      visInteraction(hover = TRUE) %>%
-      visLayout(randomSeed = 1) %>%
-      visLegend(useGroups = FALSE,
-                zoom = TRUE,
-                width = legend_width(),
-                position = input$mst_legend_ori,
-                ncol = legend_col(),
-                addNodes = mst_legend())
-    
-    if (input$mst_show_clusters) {
-      if (input$mst_cluster_col_scale == "Viridis") {
-        color_palette <- viridis(length(unique(data$nodes$group)))
-      } else {
-        color_palette <- rainbow(length(unique(data$nodes$group)))
-      }
-      
-      for (i in 1:length(unique(data$nodes$group))) {
-        visNetwork_graph <- visNetwork_graph %>% 
-          visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
-      }
-    }
-    visNetwork_graph
-  })
-  
-  # MST legend
-  legend_col <- reactive({
-    if(!is.null(Vis$var_cols)) {
-      if(nrow(Vis$var_cols) > 10) {
-        3
-      } else if(nrow(Vis$var_cols) > 5) {
-        2
-      } else {
-        1
-      }
-    } else {1}
-  })
-  
-  mst_legend <- reactive({
-    if(is.null(Vis$var_cols)) {
-      NULL
-    } else {
-      legend <- Vis$var_cols
-      names(legend)[1] <- "label"
-      mutate(legend, shape = "dot",
-             font.color = input$mst_legend_color,
-             size = input$mst_symbol_size,
-             font.size = input$mst_font_size)
-    }
-  })
-  
-  # Set MST legend width
-  legend_width <- reactive({
-    0.2
-  })
-  
-  # Set MST node shape
-  mst_node_shape <- reactive({
-    if(input$mst_node_shape == "Pie Nodes"){
-      "dot"
-    } else if(input$mst_node_shape %in% c("circle", "database", "box", "text")) {
-      shinyjs::disable('scale_nodes') 
-      updateCheckboxInput(session, "scale_nodes", value = FALSE)
-      shinyjs::disable('mst_node_size') 
-      shinyjs::disable('mst_node_scale')
-      input$mst_node_shape
-    } else {
-      shinyjs::enable('scale_nodes') 
-      shinyjs::enable('mst_node_size') 
-      shinyjs::enable('mst_node_scale')
-      input$mst_node_shape
-    }
-  })
-  
-  # Set MST label
-  label_mst <- reactive({
-    Vis$unique_meta[, colnames(Vis$unique_meta) %in% input$mst_node_label]
-  })
-  
-  # Set node color
-  mst_color_node <- reactive({
-    input$mst_color_node
-  })
-  
-  # Node Label Color
-  node_font_color <- reactive({
-    input$node_font_color
-  })
-  
-  
-  # Node Size Scaling
-  mst_node_scaling <- reactive({
-    if(input$scale_nodes == TRUE){
-      Vis$unique_meta$size
-    } else {NULL}
-  })
-  
-  # Node Size Min/May
-  mst_node_size_min <- reactive({
-    input$mst_node_scale[1]
-  })
-  
-  mst_node_size_max <- reactive({
-    input$mst_node_scale[2]
-  })
-  
-  # Node Size
-  mst_node_size <- reactive({
-    input$mst_node_size
-  })
-  
-  # Node Alpha/Opacity
-  node_opacity <- reactive({
-    input$node_opacity
-  })
-  
-  # Set Title
-  mst_title <- reactive({
-    if(!is.null(input$mst_title)) {
-      if(nchar(input$mst_title) < 1) {
-        list(text = "title",
-             style = paste0(
-               "font-family:Georgia, Times New Roman, Times, serif;",
-               "text-align:center;",
-               "font-size: ", as.character(input$mst_title_size), "px", 
-               "; color: ", as.character(mst_background_color()))
-        )
-      } else {
-        list(text = input$mst_title,
-             style = paste0(
-               "font-family:Georgia, Times New Roman, Times, serif;",
-               "text-align:center;",
-               "font-size: ", as.character(input$mst_title_size), "px", 
-               "; color: ", as.character(input$mst_title_color))
-        )
-      }
-    } else {
-      list(text = "title",
-           style = paste0(
-             "font-family:Georgia, Times New Roman, Times, serif;",
-             "text-align:center;",
-             "font-size: ", as.character(input$mst_title_size), "px", 
-             "; color: ", as.character(mst_background_color()))
-      )
-    }
-  })
-  
-  # Set Subtitle
-  mst_subtitle <- reactive({
-    list(text = input$mst_subtitle,
-         style = paste0(
-           "font-family:Georgia, Times New Roman, Times, serif;",
-           "text-align:center;",
-           "font-size: ", as.character(input$mst_subtitle_size), "px", 
-           "; color: ", as.character(input$mst_subtitle_color))
-    )
-  })
-  
-  # Background color
-  
-  mst_background_color <- reactive({
-    if(input$mst_background_transparent == TRUE) {
-      'rgba(0, 0, 0, 0)'
-    } else{
-      input$mst_background_color
-    }
-  })
-  
-  # Edge font color
-  mst_edge_font_color <- reactive({
-    input$mst_edge_font_color
-  })
-  
-  # Edge color
-  mst_color_edge <- reactive({
-    input$mst_color_edge
-  })
-  
-  # Edge font size
-  mst_edge_font_size <- reactive({
-    input$mst_edge_font_size
-  })
-  
-  #### NJ ----
-  
-  nj_tree <- reactive({
-    
-    # Convert negative edges 
-    Vis$nj[["edge.length"]] <- abs(Vis$nj[["edge.length"]])
-    
-    if(input$nj_nodelabel_show == TRUE) {
-      ggtree(Vis$nj, alpha = 0.2, layout = layout_nj()) + 
-        geom_nodelab(aes(label = node), color = "#29303A", size = nj_tiplab_size() + 1, hjust = 0.7) +
-        nj_limit() +
-        nj_inward() 
-    } else {
-      tree <- 
-        ggtree(Vis$nj, 
-               color = input$nj_color,
-               layout = layout_nj(),
-               ladderize = input$nj_ladder) %<+% Vis$meta_nj +
-        nj_clades() +
-        nj_tiplab() +
-        nj_tiplab_scale() + 
-        new_scale_color() +
-        nj_limit() +
-        nj_inward() +
-        nj_label_branch() +
-        nj_treescale() +
-        nj_nodepoint() +
-        nj_tippoint() +
-        nj_tippoint_scale() + 
-        new_scale_color() +
-        nj_clip_label() +
-        nj_rootedge() +
-        ggtitle(label = input$nj_title,
-                subtitle = input$nj_subtitle) +
-        theme_tree(bgcolor = input$nj_bg) +
-        theme(plot.title = element_text(colour = input$nj_title_color,
-                                        size = input$nj_title_size),
-              plot.subtitle = element_text(colour = input$nj_title_color,
-                                           size = input$nj_subtitle_size),
-              legend.background = element_rect(fill = input$nj_bg),
-              legend.direction = input$nj_legend_orientation,
-              legend.title = element_text(color = input$nj_color,
-                                          size = input$nj_legend_size*1.2),
-              legend.title.align = 0.5,
-              legend.position = nj_legend_pos(),
-              legend.text = element_text(color = input$nj_color, 
-                                         size = input$nj_legend_size),
-              legend.key = element_rect(fill = input$nj_bg),
-              legend.box.spacing = unit(1.5, "cm"),
-              legend.key.size = unit(0.05*input$nj_legend_size, 'cm'),
-              plot.background = element_rect(fill = input$nj_bg, color = input$nj_bg)) +
-        new_scale_fill() +
-        nj_fruit() +
-        nj_gradient() +
-        new_scale_fill() +
-        nj_fruit2() +
-        nj_gradient2() +
-        new_scale_fill() +
-        nj_fruit3() +
-        nj_gradient3() +
-        new_scale_fill() +
-        nj_fruit4() +
-        nj_gradient4() +
-        new_scale_fill() +
-        nj_fruit5() +
-        nj_gradient5() +
-        new_scale_fill() 
-      
-      # Add custom labels
-      if(length(Vis$custom_label_nj) > 0) {
-        
-        for(i in Vis$custom_label_nj[,1]) {
-          
-          if(!is.null(Vis$nj_label_pos_x[[i]])) {
-            x_pos <- Vis$nj_label_pos_x[[i]]
-          } else {
-            x_pos <- round(Vis$nj_max_x / 2, 0)
-          }
-          
-          if(!is.null(Vis$nj_label_pos_y[[i]])) {
-            y_pos <- Vis$nj_label_pos_y[[i]]
-          } else {
-            y_pos <- sum(DB$data$Include) / 2
-          }
-          
-          if(!is.null(Vis$nj_label_size[[i]])) {
-            size <- Vis$nj_label_size[[i]]
-          } else {
-            size <- 5
-          }
-          
-          tree <- tree + annotate("text",
-                                  x = x_pos,
-                                  y = y_pos, 
-                                  label = i,
-                                  size = size)
-        }
-      }
-      
-      # Add heatmap
-      if(input$nj_heatmap_show == TRUE & length(input$nj_heatmap_select) > 0) {
-        if (!(any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)) & 
-              any(!sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)))) {
-          tree <- gheatmap.mod(tree, 
-                               data = select(Vis$meta_nj, input$nj_heatmap_select),
-                               offset = nj_heatmap_offset(),
-                               width = nj_heatmap_width(),
-                               legend_title = input$nj_heatmap_title,
-                               colnames_angle = -nj_colnames_angle(),
-                               colnames_offset_y = nj_colnames_y(),
-                               colnames_color = input$nj_color) +
-            nj_heatmap_scale()
-        }
-      } 
-      
-      # Sizing control
-      Vis$nj_plot <- ggplotify::as.ggplot(tree, 
-                                          scale = input$nj_zoom,
-                                          hjust = input$nj_h,
-                                          vjust = input$nj_v)  
-      
-      Vis$nj_true <- TRUE
-      
-      # Correct background color if zoomed out
-      cowplot::ggdraw(Vis$nj_plot) + 
-        theme(plot.background = element_rect(fill = input$nj_bg, color = input$nj_bg))
-    }
-  })
-  
-  # Heatmap width
-  nj_heatmap_width <- reactive({
-    if(!is.null(input$nj_heatmap_width)) {
-      input$nj_heatmap_width
-    } else {
-      length_input <- length(input$nj_heatmap_select)
-      if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
-        if(length_input < 3) {
-          0.1
-        } else {
-          if (length_input >= 3 && length_input <= 50) {
-            min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-          } else {
-            1.5
-          }   
-        }
-      } else {
-        if(length_input < 3) {
-          0.3
-        } else if (length_input >= 3 && length_input <= 27) {
-          min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          3
-        }
-      }
-    }
-  })
-  
-  # Heatmap column titles position
-  nj_colnames_y <- reactive({
-    if(!is.null(input$nj_colnames_y)) {
-      input$nj_colnames_y
-    } else {
-      if(input$nj_layout == "inward" | input$nj_layout == "circular") {
-        0
-      } else {-1}
-    }
-  })
-  
-  # Heatmap column titles angle
-  nj_colnames_angle <- reactive({
-    if(!is.null(input$nj_colnames_angle)) {
-      input$nj_colnames_angle
-    } else {
-      if(!is.null(input$nj_layout)) {
-        if(input$nj_layout == "inward" | input$nj_layout == "circular") {
-          90
-        } else {-90}
-      } else {-90}
-    }
-  })
-  
-  # Heatmap scale
-  nj_heatmap_scale <- reactive({
-    if(!is.null(input$nj_heatmap_scale) & !is.null(input$nj_heatmap_div_mid)) {
-      if(input$nj_heatmap_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$nj_heatmap_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$nj_heatmap_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_heatmap_select]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_heatmap_select]), na.rm = TRUE)
-        }
-        scale_fill_gradient2(low = brewer.pal(3, input$nj_heatmap_scale)[1],
-                             mid = brewer.pal(3, input$nj_heatmap_scale)[2],
-                             high = brewer.pal(3, input$nj_heatmap_scale)[3],
-                             midpoint = midpoint,
-                             name = input$nj_heatmap_title)
-      } else {
-        if(input$nj_heatmap_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_nj[input$nj_heatmap_select])) == "numeric") {
-            if(input$nj_heatmap_scale == "magma") {
-              scale_fill_viridis(option = "A",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "inferno") {
-              scale_fill_viridis(option = "B",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "plasma") {
-              scale_fill_viridis(option = "C",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "viridis") {
-              scale_fill_viridis(option = "D",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "cividis") {
-              scale_fill_viridis(option = "E",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "rocket") {
-              scale_fill_viridis(option = "F",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "mako") {
-              scale_fill_viridis(option = "G",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "turbo") {
-              scale_fill_viridis(option = "H",
-                                 name = input$nj_heatmap_title)
-            } 
-          } else {
-            if(input$nj_heatmap_scale == "magma") {
-              scale_fill_viridis(discrete = TRUE, option = "A",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "inferno") {
-              scale_fill_viridis(discrete = TRUE, option = "B",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "plasma") {
-              scale_fill_viridis(discrete = TRUE, option = "C",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "viridis") {
-              scale_fill_viridis(discrete = TRUE, option = "D",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "cividis") {
-              scale_fill_viridis(discrete = TRUE, option = "E",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "rocket") {
-              scale_fill_viridis(discrete = TRUE, option = "F",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "mako") {
-              scale_fill_viridis(discrete = TRUE, option = "G",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "turbo") {
-              scale_fill_viridis(discrete = TRUE, option = "H",
-                                 name = input$nj_heatmap_title)
-            } 
-          }
-        } else {
-          scale_fill_brewer(palette = input$nj_heatmap_scale,
-                            name = input$nj_heatmap_title)
-        }
-      }
-    }
-  })
-  
-  # Tippoint Scale
-  nj_tippoint_scale <- reactive({
-    if(!is.null(input$nj_tippoint_scale) & !is.null(input$nj_tipcolor_mapping_div_mid)) {
-      if(input$nj_tippoint_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$nj_tipcolor_mapping_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$nj_tipcolor_mapping_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_tipcolor_mapping]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_tipcolor_mapping]), na.rm = TRUE)
-        }
-        scale_color_gradient2(low = brewer.pal(3, input$nj_tippoint_scale)[1],
-                              mid = brewer.pal(3, input$nj_tippoint_scale)[2],
-                              high = brewer.pal(3, input$nj_tippoint_scale)[3],
-                              midpoint = midpoint)
-      } else {
-        if(input$nj_tippoint_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_nj[input$nj_tipcolor_mapping])) == "numeric") {
-            if(input$nj_tippoint_scale == "magma") {
-              scale_color_viridis(option = "A")
-            } else if(input$nj_tippoint_scale == "inferno") {
-              scale_color_viridis(option = "B")
-            } else if(input$nj_tippoint_scale == "plasma") {
-              scale_color_viridis(option = "C")
-            } else if(input$nj_tippoint_scale == "viridis") {
-              scale_color_viridis(option = "D")
-            } else if(input$nj_tippoint_scale == "cividis") {
-              scale_color_viridis(option = "E")
-            } else if(input$nj_tippoint_scale == "rocket") {
-              scale_color_viridis(option = "F")
-            } else if(input$nj_tippoint_scale == "mako") {
-              scale_color_viridis(option = "G")
-            } else if(input$nj_tippoint_scale == "turbo") {
-              scale_color_viridis(option = "H")
-            } 
-          } else {
-            if(input$nj_tippoint_scale == "magma") {
-              scale_color_viridis(discrete = TRUE, option = "A")
-            } else if(input$nj_tippoint_scale == "inferno") {
-              scale_color_viridis(discrete = TRUE, option = "B")
-            } else if(input$nj_tippoint_scale == "plasma") {
-              scale_color_viridis(discrete = TRUE, option = "C")
-            } else if(input$nj_tippoint_scale == "viridis") {
-              scale_color_viridis(discrete = TRUE, option = "D")
-            } else if(input$nj_tippoint_scale == "cividis") {
-              scale_color_viridis(discrete = TRUE, option = "E")
-            } else if(input$nj_tippoint_scale == "rocket") {
-              scale_color_viridis(discrete = TRUE, option = "F")
-            } else if(input$nj_tippoint_scale == "mako") {
-              scale_color_viridis(discrete = TRUE, option = "G")
-            } else if(input$nj_tippoint_scale == "turbo") {
-              scale_color_viridis(discrete = TRUE, option = "H")
-            } 
-          }
-        } else {
-          scale_color_brewer(palette = input$nj_tippoint_scale)
-        }
-      }
-    }
-  })
-  
-  # Tiplab Scale
-  nj_tiplab_scale <- reactive({
-    if(!is.null(input$nj_tiplab_scale) & !is.null(input$nj_color_mapping_div_mid)) {
-      if(input$nj_tiplab_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$nj_color_mapping_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$nj_color_mapping_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_color_mapping]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_color_mapping]), na.rm = TRUE)
-        }
-        scale_color_gradient2(low = brewer.pal(3, input$nj_tiplab_scale)[1],
-                              mid = brewer.pal(3, input$nj_tiplab_scale)[2],
-                              high = brewer.pal(3, input$nj_tiplab_scale)[3],
-                              midpoint = midpoint)
-      } else {
-        if(input$nj_tiplab_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_nj[input$nj_color_mapping])) == "numeric") {
-            if(input$nj_tiplab_scale == "magma") {
-              scale_color_viridis(option = "A")
-            } else if(input$nj_tiplab_scale == "inferno") {
-              scale_color_viridis(option = "B")
-            } else if(input$nj_tiplab_scale == "plasma") {
-              scale_color_viridis(option = "C")
-            } else if(input$nj_tiplab_scale == "viridis") {
-              scale_color_viridis(option = "D")
-            } else if(input$nj_tiplab_scale == "cividis") {
-              scale_color_viridis(option = "E")
-            } else if(input$nj_tiplab_scale == "rocket") {
-              scale_color_viridis(option = "F")
-            } else if(input$nj_tiplab_scale == "mako") {
-              scale_color_viridis(option = "G")
-            } else if(input$nj_tiplab_scale == "turbo") {
-              scale_color_viridis(option = "H")
-            } 
-          } else {
-            if(input$nj_tiplab_scale == "magma") {
-              scale_color_viridis(discrete = TRUE, option = "A")
-            } else if(input$nj_tiplab_scale == "inferno") {
-              scale_color_viridis(discrete = TRUE, option = "B")
-            } else if(input$nj_tiplab_scale == "plasma") {
-              scale_color_viridis(discrete = TRUE, option = "C")
-            } else if(input$nj_tiplab_scale == "viridis") {
-              scale_color_viridis(discrete = TRUE, option = "D")
-            } else if(input$nj_tiplab_scale == "cividis") {
-              scale_color_viridis(discrete = TRUE, option = "E")
-            } else if(input$nj_tiplab_scale == "rocket") {
-              scale_color_viridis(discrete = TRUE, option = "F")
-            } else if(input$nj_tiplab_scale == "mako") {
-              scale_color_viridis(discrete = TRUE, option = "G")
-            } else if(input$nj_tiplab_scale == "turbo") {
-              scale_color_viridis(discrete = TRUE, option = "H")
-            } 
-          }
-        } else {
-          scale_color_brewer(palette = input$nj_tiplab_scale)
-        }
-      }
-    }
-  })
-  
-  # Clade Highlight
-  nj_clades <- reactive({
-    if(!is.null(input$nj_parentnode)) {
-      if(!length(input$nj_parentnode) == 0) {
-        if(length(input$nj_parentnode) == 1) {
-          fill <- input$nj_clade_scale
-        } else if (length(input$nj_parentnode) == 2) {
-          if(startsWith(input$nj_clade_scale, "#")) {
-            fill <- brewer.pal(3, "Set1")[1:2]
-          } else {
-            fill <- brewer.pal(3, input$nj_clade_scale)[1:2]
-          }
-        } else {
-          fill <- brewer.pal(length(input$nj_parentnode), input$nj_clade_scale)
-        }
-        geom_hilight(node = as.numeric(input$nj_parentnode),
-                     fill = fill,
-                     type = input$nj_clade_type,
-                     to.bottom = TRUE
-        )
-      } else {NULL}
-    }
-  })
-  
-  # Legend Position
-  nj_legend_pos <- reactive({
-    if(!is.null(input$nj_legend_x) & !is.null(input$nj_legend_y)) {
-      c(input$nj_legend_x, input$nj_legend_y)
-    } else {
-      c(0.1, 1)
-    }
-  })
-  
-  # Heatmap offset
-  nj_heatmap_offset <- reactive({
-    if(is.null(input$nj_heatmap_offset)) {
-      0
-    } else {input$nj_heatmap_offset}
-  })
-  
-  # Tiles fill color gradient
-  nj_gradient <- reactive({
-    if(!is.null(input$nj_tiles_show_1) & 
-       !is.null(input$nj_fruit_variable) & 
-       !is.null(input$nj_tiles_scale_1) & 
-       !is.null(input$nj_tiles_mapping_div_mid_1)) {
-      if(input$nj_tiles_show_1 == TRUE) {
-        if(input$nj_tiles_scale_1 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$nj_tiles_mapping_div_mid_1 == "Zero") {
-            midpoint <- 0
-          } else if(input$nj_tiles_mapping_div_mid_1 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable]), na.rm = TRUE)
-          }
-          scale_fill_gradient2(low = brewer.pal(3, input$nj_tiles_scale_1)[1],
-                               mid = brewer.pal(3, input$nj_tiles_scale_1)[2],
-                               high = brewer.pal(3, input$nj_tiles_scale_1)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$nj_tiles_scale_1 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
-              if(input$nj_tiles_scale_1 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$nj_tiles_scale_1 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$nj_tiles_scale_1 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$nj_tiles_scale_1 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$nj_tiles_scale_1 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$nj_tiles_scale_1 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$nj_tiles_scale_1 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$nj_tiles_scale_1 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$nj_tiles_scale_1 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$nj_tiles_scale_1 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$nj_tiles_scale_1 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$nj_tiles_scale_1 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$nj_tiles_scale_1 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$nj_tiles_scale_1 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$nj_tiles_scale_1 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$nj_tiles_scale_1 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$nj_tiles_scale_1)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_gradient2 <- reactive({
-    if(!is.null(input$nj_tiles_show_2) & 
-       !is.null(input$nj_fruit_variable_2) & 
-       !is.null(input$nj_tiles_scale_2) & 
-       !is.null(input$nj_tiles_mapping_div_mid_2)) {
-      if(input$nj_tiles_show_2 == TRUE) {
-        if(input$nj_tiles_scale_2 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$nj_tiles_mapping_div_mid_2 == "Zero") {
-            midpoint <- 0
-          } else if(input$nj_tiles_mapping_div_mid_2 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_2]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_2]), na.rm = TRUE)
-          }
-          scale_fill_gradient2(low = brewer.pal(3, input$nj_tiles_scale_2)[1],
-                               mid = brewer.pal(3, input$nj_tiles_scale_2)[2],
-                               high = brewer.pal(3, input$nj_tiles_scale_2)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$nj_tiles_scale_2 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_2])) == "numeric") {
-              if(input$nj_tiles_scale_2 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$nj_tiles_scale_2 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$nj_tiles_scale_2 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$nj_tiles_scale_2 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$nj_tiles_scale_2 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$nj_tiles_scale_2 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$nj_tiles_scale_2 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$nj_tiles_scale_2 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$nj_tiles_scale_2 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$nj_tiles_scale_2 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$nj_tiles_scale_2 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$nj_tiles_scale_2 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$nj_tiles_scale_2 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$nj_tiles_scale_2 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$nj_tiles_scale_2 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$nj_tiles_scale_2 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$nj_tiles_scale_2)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_gradient3 <- reactive({
-    if(!is.null(input$nj_tiles_show_3) & 
-       !is.null(input$nj_fruit_variable_3) & 
-       !is.null(input$nj_tiles_scale_3 & 
-                !is.null(input$nj_tiles_mapping_div_mid_3))) {
-      if(input$nj_tiles_show_3 == TRUE) {
-        if(input$nj_tiles_scale_3 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$nj_tiles_mapping_div_mid_3 == "Zero") {
-            midpoint <- 0
-          } else if(input$nj_tiles_mapping_div_mid_3 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_3]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_3]), na.rm = TRUE)
-          }
-          scale_fill_gradient3(low = brewer.pal(3, input$nj_tiles_scale_3)[1],
-                               mid = brewer.pal(3, input$nj_tiles_scale_3)[2],
-                               high = brewer.pal(3, input$nj_tiles_scale_3)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$nj_tiles_scale_3 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_3])) == "numeric") {
-              if(input$nj_tiles_scale_3 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$nj_tiles_scale_3 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$nj_tiles_scale_3 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$nj_tiles_scale_3 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$nj_tiles_scale_3 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$nj_tiles_scale_3 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$nj_tiles_scale_3 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$nj_tiles_scale_3 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$nj_tiles_scale_3 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$nj_tiles_scale_3 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$nj_tiles_scale_3 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$nj_tiles_scale_3 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$nj_tiles_scale_3 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$nj_tiles_scale_3 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$nj_tiles_scale_3 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$nj_tiles_scale_3 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$nj_tiles_scale_3)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_gradient4 <- reactive({
-    if(!is.null(input$nj_tiles_show_4) & 
-       !is.null(input$nj_fruit_variable_4) & 
-       !is.null(input$nj_tiles_scale_4) & 
-       !is.null(input$nj_tiles_mapping_div_mid_4)) {
-      if(input$nj_tiles_show_4 == TRUE) {
-        if(input$nj_tiles_scale_4 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$nj_tiles_mapping_div_mid_4 == "Zero") {
-            midpoint <- 0
-          } else if(input$nj_tiles_mapping_div_mid_4 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_4]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_4]), na.rm = TRUE)
-          }
-          scale_fill_gradient4(low = brewer.pal(3, input$nj_tiles_scale_4)[1],
-                               mid = brewer.pal(3, input$nj_tiles_scale_4)[2],
-                               high = brewer.pal(3, input$nj_tiles_scale_4)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$nj_tiles_scale_4 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
-              if(input$nj_tiles_scale_4 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$nj_tiles_scale_4 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$nj_tiles_scale_4 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$nj_tiles_scale_4 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$nj_tiles_scale_4 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$nj_tiles_scale_4 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$nj_tiles_scale_4 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$nj_tiles_scale_4 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$nj_tiles_scale_4 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$nj_tiles_scale_4 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$nj_tiles_scale_4 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$nj_tiles_scale_4 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$nj_tiles_scale_4 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$nj_tiles_scale_4 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$nj_tiles_scale_4 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$nj_tiles_scale_4 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$nj_tiles_scale_4)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_gradient5 <- reactive({
-    if(!is.null(input$nj_tiles_show_5) & 
-       !is.null(input$nj_fruit_variable_5) & 
-       !is.null(input$nj_tiles_scale_5) & 
-       !is.null(input$nj_tiles_mapping_div_mid_5)) {
-      if(input$nj_tiles_show_5 == TRUE) {
-        if(input$nj_tiles_scale_5 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$nj_tiles_mapping_div_mid_5 == "Zero") {
-            midpoint <- 0
-          } else if(input$nj_tiles_mapping_div_mid_5 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_5]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_5]), na.rm = TRUE)
-          }
-          scale_fill_gradient5(low = brewer.pal(3, input$nj_tiles_scale_5)[1],
-                               mid = brewer.pal(3, input$nj_tiles_scale_5)[2],
-                               high = brewer.pal(3, input$nj_tiles_scale_5)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$nj_tiles_scale_5 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_5])) == "numeric") {
-              if(input$nj_tiles_scale_5 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$nj_tiles_scale_5 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$nj_tiles_scale_5 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$nj_tiles_scale_5 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$nj_tiles_scale_5 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$nj_tiles_scale_5 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$nj_tiles_scale_5 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$nj_tiles_scale_5 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$nj_tiles_scale_5 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$nj_tiles_scale_5 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$nj_tiles_scale_5 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$nj_tiles_scale_5 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$nj_tiles_scale_5 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$nj_tiles_scale_5 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$nj_tiles_scale_5 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$nj_tiles_scale_5 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$nj_tiles_scale_5)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  # No label clip off for linear NJ tree
-  nj_clip_label <- reactive({
-    if(!(input$nj_layout == "circular" | input$nj_layout == "inward")) {
-      coord_cartesian(clip = "off")
-    } else {NULL}
-  })
-  
-  # Geom Fruit
-  nj_fruit <- reactive({
-    if((!is.null(input$nj_tiles_show_1)) & 
-       (!is.null(input$nj_fruit_variable)) & 
-       (!is.null(input$nj_layout)) & 
-       (!is.null(input$nj_fruit_offset_circ)) & 
-       (!is.null(input$nj_fruit_width_circ)) & 
-       (!is.null(input$nj_fruit_alpha))) {
-      if(input$nj_tiles_show_1 == TRUE) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
-            offset = input$nj_fruit_offset_circ,
-            width = input$nj_fruit_width_circ,
-            alpha = input$nj_fruit_alpha
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
-            offset = input$nj_fruit_offset_circ,
-            width = input$nj_fruit_width_circ,
-            alpha = input$nj_fruit_alpha
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$nj_tiles_show_1 == TRUE) {
-        if(!is.null(Vis$nj_max_x)) {
-          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
-            offset = 0,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
-            offset = 0,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  # Geom Fruit
-  nj_fruit2 <- reactive({
-    if((!is.null(input$nj_tiles_show_2)) & 
-       (!is.null(input$nj_fruit_variable_2)) & 
-       (!is.null(input$nj_layout)) & 
-       (!is.null(input$nj_fruit_offset_circ_2)) & 
-       (!is.null(input$nj_fruit_width_circ_2)) & 
-       (!is.null(input$nj_fruit_alpha_2))) {
-      if(input$nj_tiles_show_2 == TRUE) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_2)),
-            offset = input$nj_fruit_offset_circ_2,
-            width = input$nj_fruit_width_circ_2,
-            alpha = input$nj_fruit_alpha_2
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_2)),
-            offset = input$nj_fruit_offset_circ_2,
-            width = input$nj_fruit_width_circ_2,
-            alpha = input$nj_fruit_alpha_2
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$nj_tiles_show_2 == TRUE) {
-        if(!is.null(Vis$nj_max_x)) {
-          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_2)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_2)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_fruit3 <- reactive({
-    if((!is.null(input$nj_tiles_show_3)) & 
-       (!is.null(input$nj_fruit_variable_3)) & 
-       (!is.null(input$nj_layout)) & 
-       (!is.null(input$nj_fruit_offset_circ_3)) & 
-       (!is.null(input$nj_fruit_width_circ_3)) & 
-       (!is.null(input$nj_fruit_alpha_3))) {
-      if(input$nj_tiles_show_3 == TRUE) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_3)),
-            offset = input$nj_fruit_offset_circ_3,
-            width = input$nj_fruit_width_circ_3,
-            alpha = input$nj_fruit_alpha_3
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_3)),
-            offset = input$nj_fruit_offset_circ_3,
-            width = input$nj_fruit_width_circ_3,
-            alpha = input$nj_fruit_alpha_3
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$nj_tiles_show_3 == TRUE) {
-        if(!is.null(Vis$nj_max_x)) {
-          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_3)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_3)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_fruit4 <- reactive({
-    if((!is.null(input$nj_tiles_show_4)) & 
-       (!is.null(input$nj_fruit_variable_4)) & 
-       (!is.null(input$nj_layout)) & 
-       (!is.null(input$nj_fruit_offset_circ_4)) & 
-       (!is.null(input$nj_fruit_width_circ_4)) & 
-       (!is.null(input$nj_fruit_alpha_4))) {
-      if(input$nj_tiles_show_4 == TRUE) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_4)),
-            offset = input$nj_fruit_offset_circ_4,
-            width = input$nj_fruit_width_circ_4,
-            alpha = input$nj_fruit_alpha_4
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_4)),
-            offset = input$nj_fruit_offset_circ_4,
-            width = input$nj_fruit_width_circ_4,
-            alpha = input$nj_fruit_alpha_4
-          )
-        }
-      } else {
-        if(input$nj_tiles_show_4 == TRUE) {
-          if(!is.null(Vis$nj_max_x)) {
-            if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-              width <- 1
-            } else {
-              width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-            }
-          } else {
-            width <- 2
-          }
-          if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-            geom_fruit(
-              geom = geom_tile,
-              mapping = aes(fill= !!sym(input$nj_fruit_variable_4)),
-              offset = 0.15,
-              width = width * 3,
-              alpha = 1
-            )
-          } else {
-            geom_fruit(
-              geom = geom_tile,
-              mapping = aes(fill= !!sym(input$nj_fruit_variable_4)),
-              offset = 0.05,
-              width = width,
-              alpha = 1
-            )
-          }
-        } else {NULL}
-      }
-    }
-  })
-  
-  nj_fruit5 <- reactive({
-    if((!is.null(input$nj_tiles_show_5)) & 
-       (!is.null(input$nj_fruit_variable_5)) & 
-       (!is.null(input$nj_layout)) & 
-       (!is.null(input$nj_fruit_offset_circ_5)) & 
-       (!is.null(input$nj_fruit_width_circ_5)) & 
-       (!is.null(input$nj_fruit_alpha_5))) {
-      if(input$nj_tiles_show_5 == TRUE) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_5)),
-            offset = input$nj_fruit_offset_circ_5,
-            width = input$nj_fruit_width_circ_5,
-            alpha = input$nj_fruit_alpha_5
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_5)),
-            offset = input$nj_fruit_offset_circ_5,
-            width = input$nj_fruit_width_circ_5,
-            alpha = input$nj_fruit_alpha_5
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$nj_tiles_show_5 == TRUE) {
-        if(!is.null(Vis$nj_max_x)) {
-          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_5)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_5)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  # Xlim
-  nj_limit <- reactive({
-    if(input$nj_layout == "circular") {
-      xlim(input$nj_xlim, NA)
-    } else {NULL}
-  })
-  
-  # Treescale
-  nj_treescale <- reactive({
-    if(!input$nj_layout == "circular") {
-      if(input$nj_treescale_show == TRUE) {
-        geom_treescale(x = nj_treescale_x(),
-                       y = nj_treescale_y(),
-                       width = nj_treescale_width(),
-                       color = input$nj_color,
-                       fontsize = 4)
-      } else {NULL}
-    } else {NULL}
-  }) 
-  
-  # Treescale Y Position
-  nj_treescale_y <- reactive({
-    if(is.null(input$nj_treescale_y)) {
-      0
-    } else {input$nj_treescale_y}
-  })
-  
-  # Treescale X Position
-  nj_treescale_x <- reactive({
-    if(is.null(input$nj_treescale_x)) {
-      round(ceiling(Vis$nj_max_x) * 0.2, 0)
-    } else {input$nj_treescale_x}
-  })
-  
-  # Treescale width
-  nj_treescale_width <- reactive({
-    if(!is.null(input$nj_treescale_width)) {
-      input$nj_treescale_width
-    } else {
-      round(ceiling(Vis$nj_max_x) * 0.1, 0)
-    }
-  })
-  
-  # Label branches
-  nj_label_branch <- reactive({
-    if(!input$nj_layout == "circular" | !input$nj_layout == "inward") {
-      if(input$nj_show_branch_label == TRUE) {
-        geom_label(
-          aes(
-            x=!!sym("branch"), 
-            label= !!sym(input$nj_branch_label)),
-          fill = input$nj_branch_label_color,
-          size = nj_branch_size(),
-          label.r = unit(input$nj_branch_labelradius, "lines"),
-          nudge_x = input$nj_branch_x,
-          nudge_y = input$nj_branch_y,
-          fontface = input$nj_branchlab_fontface,
-          alpha = input$nj_branchlab_alpha
-        )
-      } else {NULL}
-    } else {NULL}
-  })
-  
-  # Branch label size
-  nj_branch_size <- reactive({
-    if(!is.null(input$nj_branch_size)) {
-      input$nj_branch_size
-    } else {
-      Vis$branch_size_nj
-    }
-  })
-  
-  # Rootedge
-  nj_rootedge <- reactive({
-    if(input$nj_rootedge_show == TRUE) {
-      if(is.null(input$nj_rootedge_length)) {
-        geom_rootedge(rootedge = round(ceiling(Vis$nj_max_x) * 0.05, 0),
-                      linetype = input$nj_rootedge_line)
-      } else {
-        geom_rootedge(rootedge = input$nj_rootedge_length,
-                      linetype = input$nj_rootedge_line)
-      }
-    } else {NULL}
-  })
-  
-  # Tippoints
-  nj_tippoint <- reactive({
-    if(input$nj_tippoint_show == TRUE | input$nj_tipcolor_mapping_show == TRUE | input$nj_tipshape_mapping_show == TRUE) {
-      if(input$nj_tipcolor_mapping_show == TRUE & input$nj_tipshape_mapping_show == FALSE) {
-        geom_tippoint(
-          aes(color = !!sym(input$nj_tipcolor_mapping)),
-          alpha = input$nj_tippoint_alpha,
-          shape = input$nj_tippoint_shape,
-          size = nj_tippoint_size()
-        )
-      } else if (input$nj_tipcolor_mapping_show == FALSE & input$nj_tipshape_mapping_show == TRUE) {
-        geom_tippoint(
-          aes(shape = !!sym(input$nj_tipshape_mapping)),
-          alpha = input$nj_tippoint_alpha,
-          color = input$nj_tippoint_color,
-          size = nj_tippoint_size()
-        )
-      } else if (input$nj_tipcolor_mapping_show == TRUE & input$nj_tipshape_mapping_show == TRUE) {
-        geom_tippoint(
-          aes(shape = !!sym(input$nj_tipshape_mapping),
-              color = !!sym(input$nj_tipcolor_mapping)),
-          alpha = input$nj_tippoint_alpha,
-          size = nj_tippoint_size()
-        )
-      } else {
-        geom_tippoint(
-          alpha = input$nj_tippoint_alpha,
-          colour = input$nj_tippoint_color,
-          fill = input$nj_tippoint_color,
-          shape = input$nj_tippoint_shape,
-          size = nj_tippoint_size()
-        )
-      } 
-    } else {NULL}
-  })
-  
-  # Nodepoints
-  nj_nodepoint <- reactive({
-    if(input$nj_nodepoint_show == TRUE) {
-      geom_nodepoint(
-        alpha = input$nj_nodepoint_alpha,
-        color = input$nj_nodepoint_color,
-        shape = input$nj_nodepoint_shape,
-        size = nj_nodepoint_size()
-      )
-    } else {NULL}
-  })
-  
-  # Nodepoint size
-  nj_nodepoint_size <- reactive({
-    if(!is.null(input$nj_nodepoint_size)) {
-      input$nj_nodepoint_size
-    } else {
-      Vis$nodepointsize_nj
-    }
-  })
-  
-  # NJ circular or not
-  nj_tiplab <- reactive({
-    if(input$nj_tiplab_show == TRUE) {
-      if(input$nj_layout == "circular") {
-        if(input$nj_mapping_show == TRUE) {
-          geom_tiplab(
-            nj_mapping_tiplab(), 
-            geom = "text",
-            size = nj_tiplab_size(),
-            alpha = input$nj_tiplab_alpha,
-            fontface = input$nj_tiplab_fontface,
-            align = as.logical(input$nj_align),
-            hjust = as.numeric(input$nj_tiplab_position),
-            check.overlap = input$nj_tiplab_overlap
-          )
-        } else {
-          geom_tiplab(
-            nj_mapping_tiplab(),
-            color = input$nj_tiplab_color,
-            geom = "text",
-            size = nj_tiplab_size(),
-            alpha = input$nj_tiplab_alpha,
-            fontface = input$nj_tiplab_fontface,
-            align = as.logical(input$nj_align),
-            hjust = as.numeric(input$nj_tiplab_position),
-            check.overlap = input$nj_tiplab_overlap
-          )
-        }
-      } else if (input$nj_layout == "inward") {
-        if(input$nj_mapping_show == TRUE) {
-          geom_tiplab(
-            nj_mapping_tiplab(), 
-            geom = "text",
-            size = nj_tiplab_size(),
-            alpha = input$nj_tiplab_alpha,
-            fontface = input$nj_tiplab_fontface,
-            align = as.logical(input$nj_align),
-            hjust = as.numeric(input$nj_tiplab_position_inw),
-            check.overlap = input$nj_tiplab_overlap
-          )
-        } else {
-          geom_tiplab(
-            nj_mapping_tiplab(),
-            color = input$nj_tiplab_color,
-            geom = "text",
-            size = nj_tiplab_size(),
-            alpha = input$nj_tiplab_alpha,
-            fontface = input$nj_tiplab_fontface,
-            align = as.logical(input$nj_align),
-            hjust = as.numeric(input$nj_tiplab_position_inw),
-            check.overlap = input$nj_tiplab_overlap
-          )
-        }
-      } else {
-        if(input$nj_mapping_show == TRUE) {
-          if(input$nj_geom == TRUE) {
-            geom_tiplab(
-              nj_mapping_tiplab(), 
-              geom = nj_geom(),
-              angle = input$nj_tiplab_angle,
-              size = nj_tiplab_size(),
-              alpha = input$nj_tiplab_alpha,
-              fontface = input$nj_tiplab_fontface,
-              align = as.logical(input$nj_align),
-              nudge_x = input$nj_tiplab_nudge_x,
-              check.overlap = input$nj_tiplab_overlap,
-              label.padding = unit(nj_tiplab_padding(), "lines"),
-              label.r = unit(input$nj_tiplab_labelradius, "lines"), 
-              fill = input$nj_tiplab_fill
-            )
-          } else {
-            geom_tiplab(
-              nj_mapping_tiplab(), 
-              geom = nj_geom(),
-              angle = input$nj_tiplab_angle,
-              size = nj_tiplab_size(),
-              alpha = input$nj_tiplab_alpha,
-              fontface = input$nj_tiplab_fontface,
-              align = as.logical(input$nj_align),
-              nudge_x = input$nj_tiplab_nudge_x,
-              check.overlap = input$nj_tiplab_overlap
-            )
-          }
-        } else {
-          if(input$nj_geom == TRUE) {
-            geom_tiplab(
-              nj_mapping_tiplab(), 
-              geom = nj_geom(),
-              color = input$nj_tiplab_color,
-              angle = input$nj_tiplab_angle,
-              size = nj_tiplab_size(),
-              alpha = input$nj_tiplab_alpha,
-              fontface = input$nj_tiplab_fontface,
-              align = as.logical(input$nj_align),
-              nudge_x = input$nj_tiplab_nudge_x,
-              check.overlap = input$nj_tiplab_overlap,
-              label.padding = unit(nj_tiplab_padding(), "lines"),
-              label.r = unit(input$nj_tiplab_labelradius, "lines"), 
-              fill = input$nj_tiplab_fill
-            )
-          } else {
-            geom_tiplab(
-              nj_mapping_tiplab(), 
-              geom = nj_geom(),
-              color = input$nj_tiplab_color,
-              angle = input$nj_tiplab_angle,
-              size = nj_tiplab_size(),
-              alpha = input$nj_tiplab_alpha,
-              fontface = input$nj_tiplab_fontface,
-              align = as.logical(input$nj_align),
-              nudge_x = input$nj_tiplab_nudge_x,
-              check.overlap = input$nj_tiplab_overlap
-            )
-          }
-        }
-      }
-    } else {NULL}
-  })
-  
-  # Tip panel size
-  nj_tiplab_padding <- reactive({
-    if(!is.null(input$nj_tiplab_padding)) {
-      input$nj_tiplab_padding
-    } else {
-      Vis$tiplab_padding_nj
-    }
-  })
-  
-  # Tiplab size
-  nj_tiplab_size <- reactive({
-    if(!is.null(input$nj_tiplab_size)) {
-      input$nj_tiplab_size
-    } else {
-      Vis$labelsize_nj
-    }
-  })
-  
-  # Tippoint size
-  nj_tippoint_size <- reactive({
-    if(!is.null(input$nj_tippoint_size)) {
-      input$nj_tippoint_size
-    } else {
-      Vis$tippointsize_nj
-    }
-  })
-  
-  # Show Label Panels?
-  nj_geom <- reactive({
-    if(input$nj_geom == TRUE) {
-      "label"
-    } else {"text"}
-  })
-  
-  # NJ Tiplab color
-  nj_mapping_tiplab <- reactive({
-    if(input$nj_mapping_show == TRUE) {
-      if(!is.null(input$nj_tiplab)) {
-        aes(label = !!sym(input$nj_tiplab),
-            color = !!sym(input$nj_color_mapping))
-      } else {
-        aes(label = !!sym("Assembly Name"),
-            color = !!sym(input$nj_color_mapping))
-      }
-    } else {
-      if(!is.null(input$nj_tiplab)) {
-        aes(label = !!sym(input$nj_tiplab))
-      } else {
-        aes(label = !!sym("Assembly Name"))
-      }
-    }
-  })
-  
-  # NJ Tree Layout
-  layout_nj <- reactive({
-    if(input$nj_layout == "inward") {
-      "circular"
-    } else {input$nj_layout}
-  })
-  
-  # NJ inward circular
-  nj_inward <- reactive({
-    if (input$nj_layout == "inward") {
-      layout_inward_circular(xlim = input$nj_inward_xlim)
-    } else {
-      NULL
-    }
-  })
-  
-  #### UPGMA ----
-  
-  upgma_tree <- reactive({
-    if(input$upgma_nodelabel_show == TRUE) {
-      ggtree(Vis$upgma, alpha = 0.2, layout = layout_upgma()) + 
-        geom_nodelab(aes(label = node), color = "#29303A", size = upgma_tiplab_size() + 1, hjust = 0.7) +
-        upgma_limit() +
-        upgma_inward() 
-    } else {
-      tree <-
-        ggtree(Vis$upgma, 
-               color = input$upgma_color,
-               layout = layout_upgma(),
-               ladderize = input$upgma_ladder) %<+% Vis$meta_upgma +
-        upgma_tiplab() +
-        upgma_tiplab_scale() + 
-        new_scale_color() +
-        upgma_limit() +
-        upgma_inward() +
-        upgma_label_branch() +
-        upgma_treescale() +
-        upgma_nodepoint() +
-        upgma_tippoint() +
-        upgma_tippoint_scale() + 
-        new_scale_color() +
-        upgma_clip_label() +
-        upgma_rootedge() +
-        upgma_clades() +
-        ggtitle(label = input$upgma_title,
-                subtitle = input$upgma_subtitle) +
-        theme_tree(bgcolor = input$upgma_bg) +
-        theme(plot.title = element_text(colour = input$upgma_title_color,
-                                        size = input$upgma_title_size),
-              plot.subtitle = element_text(colour = input$upgma_title_color,
-                                           size = input$upgma_subtitle_size),
-              legend.background = element_rect(fill = input$upgma_bg),
-              legend.direction = input$upgma_legend_orientation,
-              legend.title = element_text(color = input$upgma_color,
-                                          size = input$upgma_legend_size*1.2),
-              legend.title.align = 0.5,
-              legend.position = upgma_legend_pos(),
-              legend.text = element_text(color = input$upgma_color, 
-                                         size = input$upgma_legend_size),
-              legend.key = element_rect(fill = input$upgma_bg),
-              legend.box.spacing = unit(1.5, "cm"),
-              legend.key.size = unit(0.05*input$upgma_legend_size, 'cm'),
-              plot.background = element_rect(fill = input$upgma_bg, color = input$upgma_bg)) +
-        new_scale_fill() +
-        upgma_fruit() +
-        upgma_gradient() +
-        new_scale_fill() +
-        upgma_fruit2() +
-        upgma_gradient2() +
-        new_scale_fill() +
-        upgma_fruit3() +
-        upgma_gradient3() +
-        new_scale_fill() +
-        upgma_fruit4() +
-        upgma_gradient4() +
-        new_scale_fill() +
-        upgma_fruit5() +
-        upgma_gradient5() +
-        new_scale_fill() 
-      
-      # Add custom labels
-      if(length(Vis$custom_label_upgma) > 0) {
-        
-        for(i in Vis$custom_label_upgma[,1]) {
-          
-          if(!is.null(Vis$upgma_label_pos_x[[i]])) {
-            x_pos <- Vis$upgma_label_pos_x[[i]]
-          } else {
-            x_pos <- round(Vis$upgma_max_x / 2, 0)
-          }
-          
-          if(!is.null(Vis$upgma_label_pos_y[[i]])) {
-            y_pos <- Vis$upgma_label_pos_y[[i]]
-          } else {
-            y_pos <- sum(DB$data$Include) / 2
-          }
-          
-          if(!is.null(Vis$upgma_label_size[[i]])) {
-            size <- Vis$upgma_label_size[[i]]
-          } else {
-            size <- 5
-          }
-          
-          tree <- tree + annotate("text",
-                                  x = x_pos,
-                                  y = y_pos, 
-                                  label = i,
-                                  size = size)
-        }
-      }
-      
-      # Add heatmap
-      if(input$upgma_heatmap_show == TRUE & length(input$upgma_heatmap_select) > 0) {
-        if (!(any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)) & 
-              any(!sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)))) {
-          tree <- gheatmap.mod(tree, 
-                               data = select(Vis$meta_upgma, input$upgma_heatmap_select),
-                               offset = upgma_heatmap_offset(),
-                               width = upgma_heatmap_width(),
-                               legend_title = input$upgma_heatmap_title,
-                               colnames_angle = -upgma_colnames_angle(),
-                               colnames_offset_y = upgma_colnames_y(),
-                               colnames_color = input$upgma_color) +
-            upgma_heatmap_scale()
-        }
-      } 
-      
-      # Sizing control
-      Vis$upgma_plot <- ggplotify::as.ggplot(tree, 
-                                             scale = input$upgma_zoom,
-                                             hjust = input$upgma_h,
-                                             vjust = input$upgma_v)  
-      
-      # Correct background color if zoomed out
-      cowplot::ggdraw(Vis$upgma_plot) + 
-        theme(plot.background = element_rect(fill = input$upgma_bg, color = input$upgma_bg))
-    }
-  })
-  
-  # Heatmap width
-  upgma_heatmap_width <- reactive({
-    if(!is.null(input$upgma_heatmap_width)) {
-      input$upgma_heatmap_width
-    } else {
-      length_input <- length(input$upgma_heatmap_select)
-      if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
-        if(length_input < 3) {
-          0.1
-        } else {
-          if (length_input >= 3 && length_input <= 50) {
-            min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-          } else {
-            1.5
-          }   
-        }
-      } else {
-        if(length_input < 3) {
-          0.3
-        } else if (length_input >= 3 && length_input <= 27) {
-          min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          3
-        }
-      }
-    }
-  })
-  
-  # Heatmap column titles position
-  upgma_colnames_y <- reactive({
-    if(!is.null(input$upgma_colnames_y)) {
-      input$upgma_colnames_y
-    } else {
-      if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
-        0
-      } else {-1}
-    }
-  })
-  
-  # Heatmap column titles angle
-  upgma_colnames_angle <- reactive({
-    if(!is.null(input$upgma_colnames_angle)) {
-      input$upgma_colnames_angle
-    } else {
-      if(!is.null(input$upgma_layout)) {
-        if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
-          90
-        } else {-90}
-      } else {-90}
-    }
-  })
-  
-  # Heatmap scale
-  upgma_heatmap_scale <- reactive({
-    if(!is.null(input$upgma_heatmap_scale) & !is.null(input$upgma_heatmap_div_mid)) {
-      if(input$upgma_heatmap_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$upgma_heatmap_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$upgma_heatmap_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_heatmap_select]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_heatmap_select]), na.rm = TRUE)
-        }
-        scale_fill_gradient2(low = brewer.pal(3, input$upgma_heatmap_scale)[1],
-                             mid = brewer.pal(3, input$upgma_heatmap_scale)[2],
-                             high = brewer.pal(3, input$upgma_heatmap_scale)[3],
-                             midpoint = midpoint,
-                             name = input$upgma_heatmap_title)
-      } else {
-        if(input$upgma_heatmap_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_upgma[input$upgma_heatmap_select])) == "numeric") {
-            if(input$upgma_heatmap_scale == "magma") {
-              scale_fill_viridis(option = "A",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "inferno") {
-              scale_fill_viridis(option = "B",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "plasma") {
-              scale_fill_viridis(option = "C",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "viridis") {
-              scale_fill_viridis(option = "D",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "cividis") {
-              scale_fill_viridis(option = "E",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "rocket") {
-              scale_fill_viridis(option = "F",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "mako") {
-              scale_fill_viridis(option = "G",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "turbo") {
-              scale_fill_viridis(option = "H",
-                                 name = input$upgma_heatmap_title)
-            } 
-          } else {
-            if(input$upgma_heatmap_scale == "magma") {
-              scale_fill_viridis(discrete = TRUE, option = "A",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "inferno") {
-              scale_fill_viridis(discrete = TRUE, option = "B",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "plasma") {
-              scale_fill_viridis(discrete = TRUE, option = "C",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "viridis") {
-              scale_fill_viridis(discrete = TRUE, option = "D",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "cividis") {
-              scale_fill_viridis(discrete = TRUE, option = "E",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "rocket") {
-              scale_fill_viridis(discrete = TRUE, option = "F",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "mako") {
-              scale_fill_viridis(discrete = TRUE, option = "G",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "turbo") {
-              scale_fill_viridis(discrete = TRUE, option = "H",
-                                 name = input$upgma_heatmap_title)
-            } 
-          }
-        } else {
-          scale_fill_brewer(palette = input$upgma_heatmap_scale,
-                            name = input$upgma_heatmap_title)
-        }
-      }
-    }
-  })
-  
-  # Tippoint Scale
-  upgma_tippoint_scale <- reactive({
-    if(!is.null(input$upgma_tippoint_scale) & !is.null(input$upgma_tipcolor_mapping_div_mid)) {
-      if(input$upgma_tippoint_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$upgma_tipcolor_mapping_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$upgma_tipcolor_mapping_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_tipcolor_mapping]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_tipcolor_mapping]), na.rm = TRUE)
-        }
-        scale_color_gradient2(low = brewer.pal(3, input$upgma_tippoint_scale)[1],
-                              mid = brewer.pal(3, input$upgma_tippoint_scale)[2],
-                              high = brewer.pal(3, input$upgma_tippoint_scale)[3],
-                              midpoint = midpoint)
-      } else {
-        if(input$upgma_tippoint_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping])) == "numeric") {
-            if(input$upgma_tippoint_scale == "magma") {
-              scale_color_viridis(option = "A")
-            } else if(input$upgma_tippoint_scale == "inferno") {
-              scale_color_viridis(option = "B")
-            } else if(input$upgma_tippoint_scale == "plasma") {
-              scale_color_viridis(option = "C")
-            } else if(input$upgma_tippoint_scale == "viridis") {
-              scale_color_viridis(option = "D")
-            } else if(input$upgma_tippoint_scale == "cividis") {
-              scale_color_viridis(option = "E")
-            } else if(input$upgma_tippoint_scale == "rocket") {
-              scale_color_viridis(option = "F")
-            } else if(input$upgma_tippoint_scale == "mako") {
-              scale_color_viridis(option = "G")
-            } else if(input$upgma_tippoint_scale == "turbo") {
-              scale_color_viridis(option = "H")
-            } 
-          } else {
-            if(input$upgma_tippoint_scale == "magma") {
-              scale_color_viridis(discrete = TRUE, option = "A")
-            } else if(input$upgma_tippoint_scale == "inferno") {
-              scale_color_viridis(discrete = TRUE, option = "B")
-            } else if(input$upgma_tippoint_scale == "plasma") {
-              scale_color_viridis(discrete = TRUE, option = "C")
-            } else if(input$upgma_tippoint_scale == "viridis") {
-              scale_color_viridis(discrete = TRUE, option = "D")
-            } else if(input$upgma_tippoint_scale == "cividis") {
-              scale_color_viridis(discrete = TRUE, option = "E")
-            } else if(input$upgma_tippoint_scale == "rocket") {
-              scale_color_viridis(discrete = TRUE, option = "F")
-            } else if(input$upgma_tippoint_scale == "mako") {
-              scale_color_viridis(discrete = TRUE, option = "G")
-            } else if(input$upgma_tippoint_scale == "turbo") {
-              scale_color_viridis(discrete = TRUE, option = "H")
-            } 
-          }
-        } else {
-          scale_color_brewer(palette = input$upgma_tippoint_scale)
-        }
-      }
-    }
-  })
-  
-  # Tiplab Scale
-  upgma_tiplab_scale <- reactive({
-    if(!is.null(input$upgma_tiplab_scale) & !is.null(input$upgma_color_mapping_div_mid)) {
-      if(input$upgma_tiplab_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$upgma_color_mapping_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$upgma_color_mapping_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_color_mapping]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_color_mapping]), na.rm = TRUE)
-        }
-        scale_color_gradient2(low = brewer.pal(3, input$upgma_tiplab_scale)[1],
-                              mid = brewer.pal(3, input$upgma_tiplab_scale)[2],
-                              high = brewer.pal(3, input$upgma_tiplab_scale)[3],
-                              midpoint = midpoint)
-      } else {
-        if(input$upgma_tiplab_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_upgma[input$upgma_color_mapping])) == "numeric") {
-            if(input$upgma_tiplab_scale == "magma") {
-              scale_color_viridis(option = "A")
-            } else if(input$upgma_tiplab_scale == "inferno") {
-              scale_color_viridis(option = "B")
-            } else if(input$upgma_tiplab_scale == "plasma") {
-              scale_color_viridis(option = "C")
-            } else if(input$upgma_tiplab_scale == "viridis") {
-              scale_color_viridis(option = "D")
-            } else if(input$upgma_tiplab_scale == "cividis") {
-              scale_color_viridis(option = "E")
-            } else if(input$upgma_tiplab_scale == "rocket") {
-              scale_color_viridis(option = "F")
-            } else if(input$upgma_tiplab_scale == "mako") {
-              scale_color_viridis(option = "G")
-            } else if(input$upgma_tiplab_scale == "turbo") {
-              scale_color_viridis(option = "H")
-            } 
-          } else {
-            if(input$upgma_tiplab_scale == "magma") {
-              scale_color_viridis(discrete = TRUE, option = "A")
-            } else if(input$upgma_tiplab_scale == "inferno") {
-              scale_color_viridis(discrete = TRUE, option = "B")
-            } else if(input$upgma_tiplab_scale == "plasma") {
-              scale_color_viridis(discrete = TRUE, option = "C")
-            } else if(input$upgma_tiplab_scale == "viridis") {
-              scale_color_viridis(discrete = TRUE, option = "D")
-            } else if(input$upgma_tiplab_scale == "cividis") {
-              scale_color_viridis(discrete = TRUE, option = "E")
-            } else if(input$upgma_tiplab_scale == "rocket") {
-              scale_color_viridis(discrete = TRUE, option = "F")
-            } else if(input$upgma_tiplab_scale == "mako") {
-              scale_color_viridis(discrete = TRUE, option = "G")
-            } else if(input$upgma_tiplab_scale == "turbo") {
-              scale_color_viridis(discrete = TRUE, option = "H")
-            } 
-          }
-        } else {
-          scale_color_brewer(palette = input$upgma_tiplab_scale)
-        }
-      }
-    }
-  })
-  
-  # Clade Highlight
-  upgma_clades <- reactive({
-    if(!is.null(input$upgma_parentnode)) {
-      if(!length(input$upgma_parentnode) == 0) {
-        if(length(input$upgma_parentnode) == 1) {
-          fill <- input$upgma_clade_scale
-        } else if (length(input$upgma_parentnode) == 2) {
-          if(startsWith(input$upgma_clade_scale, "#")) {
-            fill <- brewer.pal(3, "Set1")[1:2]
-          } else {
-            fill <- brewer.pal(3, input$upgma_clade_scale)[1:2]
-          }
-        } else {
-          fill <- brewer.pal(length(input$upgma_parentnode), input$upgma_clade_scale)
-        }
-        geom_hilight(node = as.numeric(input$upgma_parentnode),
-                     fill = fill,
-                     type = input$upgma_clade_type,
-                     to.bottom = TRUE)
-      } else {NULL}
-    }
-  })
-  
-  # Legend Position
-  upgma_legend_pos <- reactive({
-    if(!is.null(input$upgma_legend_x) & !is.null(input$upgma_legend_y)) {
-      c(input$upgma_legend_x, input$upgma_legend_y)
-    } else {
-      c(0.1, 1)
-    }
-  })
-  
-  # Heatmap offset
-  upgma_heatmap_offset <- reactive({
-    if(is.null(input$upgma_heatmap_offset)) {
-      0
-    } else {input$upgma_heatmap_offset}
-  })
-  
-  # Tiles fill color gradient
-  upgma_gradient <- reactive({
-    if(!is.null(input$upgma_tiles_show_1) & 
-       !is.null(input$upgma_fruit_variable) & 
-       !is.null(input$upgma_tiles_scale_1) &
-       !is.null(input$upgma_tiles_mapping_div_mid_1)) {
-      if(input$upgma_tiles_show_1 == TRUE) {
-        if(input$upgma_tiles_scale_1 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$upgma_tiles_mapping_div_mid_1 == "Zero") {
-            midpoint <- 0
-          } else if(input$upgma_tiles_mapping_div_mid_1 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable]), na.rm = TRUE)
-          }
-          scale_fill_gradient2(low = brewer.pal(3, input$upgma_tiles_scale_1)[1],
-                               mid = brewer.pal(3, input$upgma_tiles_scale_1)[2],
-                               high = brewer.pal(3, input$upgma_tiles_scale_1)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$upgma_tiles_scale_1 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
-              if(input$upgma_tiles_scale_1 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$upgma_tiles_scale_1 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$upgma_tiles_scale_1 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$upgma_tiles_scale_1 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$upgma_tiles_scale_1 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$upgma_tiles_scale_1 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$upgma_tiles_scale_1 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$upgma_tiles_scale_1 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$upgma_tiles_scale_1 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$upgma_tiles_scale_1 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$upgma_tiles_scale_1 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$upgma_tiles_scale_1 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$upgma_tiles_scale_1 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$upgma_tiles_scale_1 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$upgma_tiles_scale_1 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$upgma_tiles_scale_1 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$upgma_tiles_scale_1)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_gradient2 <- reactive({
-    if(!is.null(input$upgma_tiles_show_2) & 
-       !is.null(input$upgma_fruit_variable_2) & 
-       !is.null(input$upgma_tiles_scale_2) &
-       !is.null(input$upgma_tiles_mapping_div_mid_2)) {
-      if(input$upgma_tiles_show_2 == TRUE) {
-        if(input$upgma_tiles_scale_2 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$upgma_tiles_mapping_div_mid_2 == "Zero") {
-            midpoint <- 0
-          } else if(input$upgma_tiles_mapping_div_mid_2 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_2]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_2]), na.rm = TRUE)
-          }
-          scale_fill_gradient2(low = brewer.pal(3, input$upgma_tiles_scale_2)[1],
-                               mid = brewer.pal(3, input$upgma_tiles_scale_2)[2],
-                               high = brewer.pal(3, input$upgma_tiles_scale_2)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$upgma_tiles_scale_2 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2])) == "numeric") {
-              if(input$upgma_tiles_scale_2 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$upgma_tiles_scale_2 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$upgma_tiles_scale_2 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$upgma_tiles_scale_2 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$upgma_tiles_scale_2 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$upgma_tiles_scale_2 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$upgma_tiles_scale_2 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$upgma_tiles_scale_2 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$upgma_tiles_scale_2 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$upgma_tiles_scale_2 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$upgma_tiles_scale_2 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$upgma_tiles_scale_2 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$upgma_tiles_scale_2 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$upgma_tiles_scale_2 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$upgma_tiles_scale_2 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$upgma_tiles_scale_2 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$upgma_tiles_scale_2)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_gradient3 <- reactive({
-    if(!is.null(input$upgma_tiles_show_3) & 
-       !is.null(input$upgma_fruit_variable_3) & 
-       !is.null(input$upgma_tiles_scale_3) &
-       !is.null(input$upgma_tiles_mapping_div_mid_3)) {
-      if(input$upgma_tiles_show_3 == TRUE) {
-        if(input$upgma_tiles_scale_3 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$upgma_tiles_mapping_div_mid_3 == "Zero") {
-            midpoint <- 0
-          } else if(input$upgma_tiles_mapping_div_mid_3 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_3]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_3]), na.rm = TRUE)
-          }
-          scale_fill_gradient3(low = brewer.pal(3, input$upgma_tiles_scale_3)[1],
-                               mid = brewer.pal(3, input$upgma_tiles_scale_3)[2],
-                               high = brewer.pal(3, input$upgma_tiles_scale_3)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$upgma_tiles_scale_3 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3])) == "numeric") {
-              if(input$upgma_tiles_scale_3 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$upgma_tiles_scale_3 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$upgma_tiles_scale_3 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$upgma_tiles_scale_3 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$upgma_tiles_scale_3 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$upgma_tiles_scale_3 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$upgma_tiles_scale_3 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$upgma_tiles_scale_3 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$upgma_tiles_scale_3 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$upgma_tiles_scale_3 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$upgma_tiles_scale_3 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$upgma_tiles_scale_3 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$upgma_tiles_scale_3 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$upgma_tiles_scale_3 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$upgma_tiles_scale_3 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$upgma_tiles_scale_3 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$upgma_tiles_scale_3)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_gradient4 <- reactive({
-    if(!is.null(input$upgma_tiles_show_4) & 
-       !is.null(input$upgma_fruit_variable_4) & 
-       !is.null(input$upgma_tiles_scale_4) &
-       !is.null(input$upgma_tiles_mapping_div_mid_4)) {
-      if(input$upgma_tiles_show_4 == TRUE) {
-        if(input$upgma_tiles_scale_4 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$upgma_tiles_mapping_div_mid_4 == "Zero") {
-            midpoint <- 0
-          } else if(input$upgma_tiles_mapping_div_mid_4 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_4]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_4]), na.rm = TRUE)
-          }
-          scale_fill_gradient4(low = brewer.pal(3, input$upgma_tiles_scale_4)[1],
-                               mid = brewer.pal(3, input$upgma_tiles_scale_4)[2],
-                               high = brewer.pal(3, input$upgma_tiles_scale_4)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$upgma_tiles_scale_4 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
-              if(input$upgma_tiles_scale_4 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$upgma_tiles_scale_4 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$upgma_tiles_scale_4 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$upgma_tiles_scale_4 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$upgma_tiles_scale_4 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$upgma_tiles_scale_4 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$upgma_tiles_scale_4 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$upgma_tiles_scale_4 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$upgma_tiles_scale_4 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$upgma_tiles_scale_4 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$upgma_tiles_scale_4 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$upgma_tiles_scale_4 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$upgma_tiles_scale_4 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$upgma_tiles_scale_4 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$upgma_tiles_scale_4 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$upgma_tiles_scale_4 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$upgma_tiles_scale_4)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_gradient5 <- reactive({
-    if(!is.null(input$upgma_tiles_show_5) & 
-       !is.null(input$upgma_fruit_variable_5) & 
-       !is.null(input$upgma_tiles_scale_5) &
-       !is.null(input$upgma_tiles_mapping_div_mid_5)) {
-      if(input$upgma_tiles_show_5 == TRUE) {
-        if(input$upgma_tiles_scale_5 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$upgma_tiles_mapping_div_mid_5 == "Zero") {
-            midpoint <- 0
-          } else if(input$upgma_tiles_mapping_div_mid_5 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_5]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_5]), na.rm = TRUE)
-          }
-          scale_fill_gradient5(low = brewer.pal(3, input$upgma_tiles_scale_5)[1],
-                               mid = brewer.pal(3, input$upgma_tiles_scale_5)[2],
-                               high = brewer.pal(3, input$upgma_tiles_scale_5)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$upgma_tiles_scale_5 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5])) == "numeric") {
-              if(input$upgma_tiles_scale_5 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$upgma_tiles_scale_5 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$upgma_tiles_scale_5 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$upgma_tiles_scale_5 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$upgma_tiles_scale_5 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$upgma_tiles_scale_5 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$upgma_tiles_scale_5 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$upgma_tiles_scale_5 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$upgma_tiles_scale_5 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$upgma_tiles_scale_5 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$upgma_tiles_scale_5 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$upgma_tiles_scale_5 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$upgma_tiles_scale_5 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$upgma_tiles_scale_5 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$upgma_tiles_scale_5 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$upgma_tiles_scale_5 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$upgma_tiles_scale_5)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  # No label clip off for linear upgma tree
-  upgma_clip_label <- reactive({
-    if(!(input$upgma_layout == "circular" | input$upgma_layout == "inward")) {
-      coord_cartesian(clip = "off")
-    } else {NULL}
-  })
-  
-  # Geom Fruit
-  upgma_fruit <- reactive({
-    if((!is.null(input$upgma_tiles_show_1)) & 
-       (!is.null(input$upgma_fruit_variable)) & 
-       (!is.null(input$upgma_layout)) & 
-       (!is.null(input$upgma_fruit_offset_circ)) & 
-       (!is.null(input$upgma_fruit_width_circ)) & 
-       (!is.null(input$upgma_fruit_alpha))) {
-      if(input$upgma_tiles_show_1 == TRUE) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
-            offset = input$upgma_fruit_offset_circ,
-            width = input$upgma_fruit_width_circ,
-            alpha = input$upgma_fruit_alpha
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
-            offset = input$upgma_fruit_offset_circ,
-            width = input$upgma_fruit_width_circ,
-            alpha = input$upgma_fruit_alpha
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$upgma_tiles_show_1 == TRUE) {
-        if(!is.null(Vis$upgma_max_x)) {
-          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
-            offset = 0,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
-            offset = 0,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  # Geom Fruit
-  upgma_fruit2 <- reactive({
-    if((!is.null(input$upgma_tiles_show_2)) & 
-       (!is.null(input$upgma_fruit_variable_2)) & 
-       (!is.null(input$upgma_layout)) & 
-       (!is.null(input$upgma_fruit_offset_circ_2)) & 
-       (!is.null(input$upgma_fruit_width_circ_2)) & 
-       (!is.null(input$upgma_fruit_alpha_2))) {
-      if(input$upgma_tiles_show_2 == TRUE) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_2)),
-            offset = input$upgma_fruit_offset_circ_2,
-            width = input$upgma_fruit_width_circ_2,
-            alpha = input$upgma_fruit_alpha_2
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_2)),
-            offset = input$upgma_fruit_offset_circ_2,
-            width = input$upgma_fruit_width_circ_2,
-            alpha = input$upgma_fruit_alpha_2
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$upgma_tiles_show_2 == TRUE) {
-        if(!is.null(Vis$upgma_max_x)) {
-          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_2)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_2)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_fruit3 <- reactive({
-    if((!is.null(input$upgma_tiles_show_3)) & 
-       (!is.null(input$upgma_fruit_variable_3)) & 
-       (!is.null(input$upgma_layout)) & 
-       (!is.null(input$upgma_fruit_offset_circ_3)) & 
-       (!is.null(input$upgma_fruit_width_circ_3)) & 
-       (!is.null(input$upgma_fruit_alpha_3))) {
-      if(input$upgma_tiles_show_3 == TRUE) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_3)),
-            offset = input$upgma_fruit_offset_circ_3,
-            width = input$upgma_fruit_width_circ_3,
-            alpha = input$upgma_fruit_alpha_3
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_3)),
-            offset = input$upgma_fruit_offset_circ_3,
-            width = input$upgma_fruit_width_circ_3,
-            alpha = input$upgma_fruit_alpha_3
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$upgma_tiles_show_3 == TRUE) {
-        if(!is.null(Vis$upgma_max_x)) {
-          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_3)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_3)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_fruit4 <- reactive({
-    if((!is.null(input$upgma_tiles_show_4)) & 
-       (!is.null(input$upgma_fruit_variable_4)) & 
-       (!is.null(input$upgma_layout)) & 
-       (!is.null(input$upgma_fruit_offset_circ_4)) & 
-       (!is.null(input$upgma_fruit_width_circ_4)) & 
-       (!is.null(input$upgma_fruit_alpha_4))) {
-      if(input$upgma_tiles_show_4 == TRUE) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_4)),
-            offset = input$upgma_fruit_offset_circ_4,
-            width = input$upgma_fruit_width_circ_4,
-            alpha = input$upgma_fruit_alpha_4
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_4)),
-            offset = input$upgma_fruit_offset_circ_4,
-            width = input$upgma_fruit_width_circ_4,
-            alpha = input$upgma_fruit_alpha_4
-          )
-        }
-      } else {
-        if(input$upgma_tiles_show_4 == TRUE) {
-          if(!is.null(Vis$upgma_max_x)) {
-            if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-              width <- 1
-            } else {
-              width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-            }
-          } else {
-            width <- 2
-          }
-          if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-            geom_fruit(
-              geom = geom_tile,
-              mapping = aes(fill= !!sym(input$upgma_fruit_variable_4)),
-              offset = 0.15,
-              width = width * 3,
-              alpha = 1
-            )
-          } else {
-            geom_fruit(
-              geom = geom_tile,
-              mapping = aes(fill= !!sym(input$upgma_fruit_variable_4)),
-              offset = 0.05,
-              width = width,
-              alpha = 1
-            )
-          }
-        } else {NULL}
-      }
-    }
-  })
-  
-  upgma_fruit5 <- reactive({
-    if((!is.null(input$upgma_tiles_show_5)) & 
-       (!is.null(input$upgma_fruit_variable_5)) & 
-       (!is.null(input$upgma_layout)) & 
-       (!is.null(input$upgma_fruit_offset_circ_5)) & 
-       (!is.null(input$upgma_fruit_width_circ_5)) & 
-       (!is.null(input$upgma_fruit_alpha_5))) {
-      if(input$upgma_tiles_show_5 == TRUE) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_5)),
-            offset = input$upgma_fruit_offset_circ_5,
-            width = input$upgma_fruit_width_circ_5,
-            alpha = input$upgma_fruit_alpha_5
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_5)),
-            offset = input$upgma_fruit_offset_circ_5,
-            width = input$upgma_fruit_width_circ_5,
-            alpha = input$upgma_fruit_alpha_5
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$upgma_tiles_show_5 == TRUE) {
-        if(!is.null(Vis$upgma_max_x)) {
-          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_5)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_5)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  # Xlim
-  upgma_limit <- reactive({
-    if(input$upgma_layout == "circular") {
-      xlim(input$upgma_xlim, NA)
-    } else {NULL}
-  })
-  
-  # Treescale
-  upgma_treescale <- reactive({
-    if(!input$upgma_layout == "circular") {
-      if(input$upgma_treescale_show == TRUE) {
-        geom_treescale(x = upgma_treescale_x(),
-                       y = upgma_treescale_y(),
-                       width = upgma_treescale_width(),
-                       color = input$upgma_color,
-                       fontsize = 4)
-      } else {NULL}
-    } else {NULL}
-  }) 
-  
-  # Treescale Y Position
-  upgma_treescale_y <- reactive({
-    if(is.null(input$upgma_treescale_y)) {
-      0
-    } else {input$upgma_treescale_y}
-  })
-  
-  # Treescale X Position
-  upgma_treescale_x <- reactive({
-    if(is.null(input$upgma_treescale_x)) {
-      round(ceiling(Vis$upgma_max_x) * 0.2, 0)
-    } else {input$upgma_treescale_x}
-  })
-  
-  # Treescale width
-  upgma_treescale_width <- reactive({
-    if(!is.null(input$upgma_treescale_width)) {
-      input$upgma_treescale_width
-    } else {
-      round(ceiling(Vis$upgma_max_x) * 0.1, 0)
-    }
-  })
-  
-  # Label branches
-  upgma_label_branch <- reactive({
-    if(!input$upgma_layout == "circular" | !input$upgma_layout == "inward") {
-      if(input$upgma_show_branch_label == TRUE) {
-        geom_label(
-          aes(
-            x=!!sym("branch"), 
-            label= !!sym(input$upgma_branch_label)),
-          fill = input$upgma_branch_label_color,
-          size = upgma_branch_size(),
-          label.r = unit(input$upgma_branch_labelradius, "lines"),
-          nudge_x = input$upgma_branch_x,
-          nudge_y = input$upgma_branch_y,
-          fontface = input$upgma_branchlab_fontface,
-          alpha = input$upgma_branchlab_alpha
-        )
-      } else {NULL}
-    } else {NULL}
-  })
-  
-  # Branch label size
-  upgma_branch_size <- reactive({
-    if(!is.null(input$upgma_branch_size)) {
-      input$upgma_branch_size
-    } else {
-      Vis$branch_size_upgma
-    }
-  })
-  
-  # Rootedge
-  upgma_rootedge <- reactive({
-    if(input$upgma_rootedge_show == TRUE) {
-      if(is.null(input$upgma_rootedge_length)) {
-        geom_rootedge(rootedge = round(ceiling(Vis$upgma_max_x) * 0.05, 0),
-                      linetype = input$upgma_rootedge_line)
-      } else {
-        geom_rootedge(rootedge = input$upgma_rootedge_length,
-                      linetype = input$upgma_rootedge_line)
-      }
-    } else {NULL}
-  })
-  
-  # Tippoints
-  upgma_tippoint <- reactive({
-    if(input$upgma_tippoint_show == TRUE | input$upgma_tipcolor_mapping_show == TRUE | input$upgma_tipshape_mapping_show == TRUE) {
-      if(input$upgma_tipcolor_mapping_show == TRUE & input$upgma_tipshape_mapping_show == FALSE) {
-        geom_tippoint(
-          aes(color = !!sym(input$upgma_tipcolor_mapping)),
-          alpha = input$upgma_tippoint_alpha,
-          shape = input$upgma_tippoint_shape,
-          size = upgma_tippoint_size()
-        )
-      } else if (input$upgma_tipcolor_mapping_show == FALSE & input$upgma_tipshape_mapping_show == TRUE) {
-        geom_tippoint(
-          aes(shape = !!sym(input$upgma_tipshape_mapping)),
-          alpha = input$upgma_tippoint_alpha,
-          color = input$upgma_tippoint_color,
-          size = upgma_tippoint_size()
-        )
-      } else if (input$upgma_tipcolor_mapping_show == TRUE & input$upgma_tipshape_mapping_show == TRUE) {
-        geom_tippoint(
-          aes(shape = !!sym(input$upgma_tipshape_mapping),
-              color = !!sym(input$upgma_tipcolor_mapping)),
-          alpha = input$upgma_tippoint_alpha,
-          size = upgma_tippoint_size()
-        )
-      } else {
-        geom_tippoint(
-          alpha = input$upgma_tippoint_alpha,
-          colour = input$upgma_tippoint_color,
-          fill = input$upgma_tippoint_color,
-          shape = input$upgma_tippoint_shape,
-          size = upgma_tippoint_size()
-        )
-      } 
-    } else {NULL}
-  })
-  
-  # Nodepoints
-  upgma_nodepoint <- reactive({
-    if(input$upgma_nodepoint_show == TRUE) {
-      geom_nodepoint(
-        alpha = input$upgma_nodepoint_alpha,
-        color = input$upgma_nodepoint_color,
-        shape = input$upgma_nodepoint_shape,
-        size = upgma_nodepoint_size()
-      )
-    } else {NULL}
-  })
-  
-  # Nodepoint size
-  upgma_nodepoint_size <- reactive({
-    if(!is.null(input$upgma_nodepoint_size)) {
-      input$upgma_nodepoint_size
-    } else {
-      Vis$nodepointsize_upgma
-    }
-  })
-  
-  # upgma circular or not
-  upgma_tiplab <- reactive({
-    if(input$upgma_tiplab_show == TRUE) {
-      if(input$upgma_layout == "circular") {
-        if(input$upgma_mapping_show == TRUE) {
-          geom_tiplab(
-            upgma_mapping_tiplab(), 
-            geom = "text",
-            size = upgma_tiplab_size(),
-            alpha = input$upgma_tiplab_alpha,
-            fontface = input$upgma_tiplab_fontface,
-            align = as.logical(input$upgma_align),
-            hjust = as.numeric(input$upgma_tiplab_position),
-            check.overlap = input$upgma_tiplab_overlap
-          )
-        } else {
-          geom_tiplab(
-            upgma_mapping_tiplab(),
-            color = input$upgma_tiplab_color,
-            geom = "text",
-            size = upgma_tiplab_size(),
-            alpha = input$upgma_tiplab_alpha,
-            fontface = input$upgma_tiplab_fontface,
-            align = as.logical(input$upgma_align),
-            hjust = as.numeric(input$upgma_tiplab_position),
-            check.overlap = input$upgma_tiplab_overlap
-          )
-        }
-      } else if (input$upgma_layout == "inward") {
-        if(input$upgma_mapping_show == TRUE) {
-          geom_tiplab(
-            upgma_mapping_tiplab(), 
-            geom = "text",
-            size = upgma_tiplab_size(),
-            alpha = input$upgma_tiplab_alpha,
-            fontface = input$upgma_tiplab_fontface,
-            align = as.logical(input$upgma_align),
-            hjust = as.numeric(input$upgma_tiplab_position_inw),
-            check.overlap = input$upgma_tiplab_overlap
-          )
-        } else {
-          geom_tiplab(
-            upgma_mapping_tiplab(),
-            color = input$upgma_tiplab_color,
-            geom = "text",
-            size = upgma_tiplab_size(),
-            alpha = input$upgma_tiplab_alpha,
-            fontface = input$upgma_tiplab_fontface,
-            align = as.logical(input$upgma_align),
-            hjust = as.numeric(input$upgma_tiplab_position_inw),
-            check.overlap = input$upgma_tiplab_overlap
-          )
-        }
-      } else {
-        if(input$upgma_mapping_show == TRUE) {
-          if(input$upgma_geom == TRUE) {
-            geom_tiplab(
-              upgma_mapping_tiplab(), 
-              geom = upgma_geom(),
-              angle = input$upgma_tiplab_angle,
-              size = upgma_tiplab_size(),
-              alpha = input$upgma_tiplab_alpha,
-              fontface = input$upgma_tiplab_fontface,
-              align = as.logical(input$upgma_align),
-              nudge_x = input$upgma_tiplab_nudge_x,
-              check.overlap = input$upgma_tiplab_overlap,
-              label.padding = unit(upgma_tiplab_padding(), "lines"),
-              label.r = unit(input$upgma_tiplab_labelradius, "lines"), 
-              fill = input$upgma_tiplab_fill
-            )
-          } else {
-            geom_tiplab(
-              upgma_mapping_tiplab(), 
-              geom = upgma_geom(),
-              angle = input$upgma_tiplab_angle,
-              size = upgma_tiplab_size(),
-              alpha = input$upgma_tiplab_alpha,
-              fontface = input$upgma_tiplab_fontface,
-              align = as.logical(input$upgma_align),
-              nudge_x = input$upgma_tiplab_nudge_x,
-              check.overlap = input$upgma_tiplab_overlap
-            )
-          }
-        } else {
-          if(input$upgma_geom == TRUE) {
-            geom_tiplab(
-              upgma_mapping_tiplab(), 
-              geom = upgma_geom(),
-              color = input$upgma_tiplab_color,
-              angle = input$upgma_tiplab_angle,
-              size = upgma_tiplab_size(),
-              alpha = input$upgma_tiplab_alpha,
-              fontface = input$upgma_tiplab_fontface,
-              align = as.logical(input$upgma_align),
-              nudge_x = input$upgma_tiplab_nudge_x,
-              check.overlap = input$upgma_tiplab_overlap,
-              label.padding = unit(upgma_tiplab_padding(), "lines"),
-              label.r = unit(input$upgma_tiplab_labelradius, "lines"), 
-              fill = input$upgma_tiplab_fill
-            )
-          } else {
-            geom_tiplab(
-              upgma_mapping_tiplab(), 
-              geom = upgma_geom(),
-              color = input$upgma_tiplab_color,
-              angle = input$upgma_tiplab_angle,
-              size = upgma_tiplab_size(),
-              alpha = input$upgma_tiplab_alpha,
-              fontface = input$upgma_tiplab_fontface,
-              align = as.logical(input$upgma_align),
-              nudge_x = input$upgma_tiplab_nudge_x,
-              check.overlap = input$upgma_tiplab_overlap
-            )
-          }
-        }
-      }
-    } else {NULL}
-  })
-  
-  # Tip panel size
-  upgma_tiplab_padding <- reactive({
-    if(!is.null(input$upgma_tiplab_padding)) {
-      input$upgma_tiplab_padding
-    } else {
-      Vis$tiplab_padding_upgma
-    }
-  })
-  
-  # Tiplab size
-  upgma_tiplab_size <- reactive({
-    if(!is.null(input$upgma_tiplab_size)) {
-      input$upgma_tiplab_size
-    } else {
-      Vis$labelsize_upgma
-    }
-  })
-  
-  # Tippoint size
-  upgma_tippoint_size <- reactive({
-    if(!is.null(input$upgma_tippoint_size)) {
-      input$upgma_tippoint_size
-    } else {
-      Vis$tippointsize_upgma
-    }
-  })
-  
-  # Show Label Panels?
-  upgma_geom <- reactive({
-    if(input$upgma_geom == TRUE) {
-      "label"
-    } else {"text"}
-  })
-  
-  # upgma Tiplab color
-  upgma_mapping_tiplab <- reactive({
-    if(input$upgma_mapping_show == TRUE) {
-      if(!is.null(input$upgma_tiplab)) {
-        aes(label = !!sym(input$upgma_tiplab),
-            color = !!sym(input$upgma_color_mapping))
-      } else {
-        aes(label = !!sym("Assembly Name"),
-            color = !!sym(input$upgma_color_mapping))
-      }
-    } else {
-      if(!is.null(input$upgma_tiplab)) {
-        aes(label = !!sym(input$upgma_tiplab))
-      } else {
-        aes(label = !!sym("Assembly Name"))
-      }
-    }
-  })
-  
-  # upgma Tree Layout
-  layout_upgma <- reactive({
-    if(input$upgma_layout == "inward") {
-      "circular"
-    } else {input$upgma_layout}
-  })
-  
-  # upgma inward circular
-  upgma_inward <- reactive({
-    if (input$upgma_layout == "inward") {
-      layout_inward_circular(xlim = input$upgma_inward_xlim)
-    } else {
-      NULL
-    }
-  })
-  
-  ### Save MST Plot ----
-  output$save_plot_html <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save MST;", paste0("MST_", Sys.Date(), ".html")))
-      paste0("MST_", Sys.Date(), ".html")
-    },
-    content = function(file) {
-      mst_tree() %>% visSave(file = file, background = mst_background_color())
-    }
-  )
-  
-  ### Save NJ Plot ----
-  
-  # Define download handler to save the plot
-  
-  output$download_nj <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save NJ;", paste0("NJ_", Sys.Date(), ".", input$filetype_nj)))
-      paste0("NJ_", Sys.Date(), ".", input$filetype_nj)
-    },
-    content = function(file) {
-      if (input$filetype_nj == "png") {
-        png(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale))
-        print(nj_tree())
-        dev.off()
-      } else if (input$filetype_nj == "jpeg") {
-        jpeg(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale), quality = 100)
-        print(nj_tree())
-        dev.off()
-      } else if (input$filetype_nj == "svg") {
-        plot <- print(nj_tree())
-        ggsave(file=file, plot=plot, device = svg(width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio))/96,
-                                                  height = as.numeric(input$nj_scale)/96))
-      } else if (input$filetype_nj == "bmp") {
-        bmp(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale))
-        print(nj_tree())
-        dev.off()
-      }
-    }
-  )
-  
-  ### Save UPGMA Plot ----
-  
-  # Define download handler to save the plot
-  
-  output$download_upgma <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save UPGMA;", paste0("UPGMA_", Sys.Date(), ".", input$filetype_upgma)))
-      paste0("UPGMA_", Sys.Date(), ".", input$filetype_upgma)
-    },
-    content = function(file) {
-      if (input$filetype_upgma == "png") {
-        png(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale))
-        print(upgma_tree())
-        dev.off()
-      } else if (input$filetype_upgma == "jpeg") {
-        jpeg(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale), quality = 100)
-        print(upgma_tree())
-        dev.off()
-      } else if (input$filetype_upgma == "svg") {
-        plot <- print(upgma_tree())
-        ggsave(file=file, plot=plot, device = svg(width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio))/96,
-                                                  height = as.numeric(input$upgma_scale)/96))
-      } else if (input$filetype_upgma == "bmp") {
-        bmp(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale))
-        print(upgma_tree())
-        dev.off()
-      }
-    }
-  )
-  
-  ### Reactive Events ----
-  
-  # MST cluster reset button
-  observeEvent(input$mst_cluster_reset, {
-    if(!is.null(DB$schemeinfo))
-    updateNumericInput(session, "mst_cluster_threshold", value = as.numeric(DB$schemeinfo[7, 2]))
-  })
-  
-  # Shut off "Align Labels" control for UPGMA trees
-  shinyjs::disable('upgma_align')
-  shinyjs::disable('upgma_tiplab_linesize')
-  shinyjs::disable('upgma_tiplab_linetype')
-  
-  # Conditional disabling of control elemenmts
-  observe({
-    
-    # Tiles for inward layout
-    if(input$nj_layout == "inward") {
-      shinyjs::disable('nj_tiles_show') 
-      shinyjs::disable('nj_tiles_show_2')
-      shinyjs::disable('nj_tiles_show_3') 
-      shinyjs::disable('nj_tiles_show_4')
-      shinyjs::disable('nj_tiles_show_5') 
-      shinyjs::disable('nj_fruit_variable')
-      shinyjs::disable('nj_fruit_variable_2')
-      shinyjs::disable('nj_fruit_variable_3')
-      shinyjs::disable('nj_fruit_variable_4')
-      shinyjs::disable('nj_fruit_variable_5')
-      shinyjs::disable('nj_fruit_width')
-      shinyjs::disable('nj_fruit_width_2')
-      shinyjs::disable('nj_fruit_width_3')
-      shinyjs::disable('nj_fruit_width_4')
-      shinyjs::disable('nj_fruit_width_5')
-      shinyjs::disable('nj_fruit_offset')
-      shinyjs::disable('nj_fruit_offset_2')
-      shinyjs::disable('nj_fruit_offset_3')
-      shinyjs::disable('nj_fruit_offset_4')
-      shinyjs::disable('nj_fruit_offset_5')
-    } else {
-      shinyjs::enable('nj_tiles_show') 
-      shinyjs::enable('nj_tiles_show_2')
-      shinyjs::enable('nj_tiles_show_3') 
-      shinyjs::enable('nj_tiles_show_4')
-      shinyjs::enable('nj_tiles_show_5') 
-      shinyjs::enable('nj_fruit_variable')
-      shinyjs::enable('nj_fruit_variable_2')
-      shinyjs::enable('nj_fruit_variable_3')
-      shinyjs::enable('nj_fruit_variable_4')
-      shinyjs::enable('nj_fruit_variable_5')
-      shinyjs::enable('nj_fruit_width')
-      shinyjs::enable('nj_fruit_width_2')
-      shinyjs::enable('nj_fruit_width_3')
-      shinyjs::enable('nj_fruit_width_4')
-      shinyjs::enable('nj_fruit_width_5')
-      shinyjs::enable('nj_fruit_offset')
-      shinyjs::enable('nj_fruit_offset_2')
-      shinyjs::enable('nj_fruit_offset_3')
-      shinyjs::enable('nj_fruit_offset_4')
-      shinyjs::enable('nj_fruit_offset_5')
-    }
-    
-    if(input$upgma_layout == "inward") {
-      shinyjs::disable('upgma_tiles_show') 
-      shinyjs::disable('upgma_tiles_show_2')
-      shinyjs::disable('upgma_tiles_show_3') 
-      shinyjs::disable('upgma_tiles_show_4')
-      shinyjs::disable('upgma_tiles_show_5') 
-      shinyjs::disable('upgma_fruit_variable')
-      shinyjs::disable('upgma_fruit_variable_2')
-      shinyjs::disable('upgma_fruit_variable_3')
-      shinyjs::disable('upgma_fruit_variable_4')
-      shinyjs::disable('upgma_fruit_variable_5')
-      shinyjs::disable('upgma_fruit_width')
-      shinyjs::disable('upgma_fruit_width_2')
-      shinyjs::disable('upgma_fruit_width_3')
-      shinyjs::disable('upgma_fruit_width_4')
-      shinyjs::disable('upgma_fruit_width_5')
-      shinyjs::disable('upgma_fruit_offset')
-      shinyjs::disable('upgma_fruit_offset_2')
-      shinyjs::disable('upgma_fruit_offset_3')
-      shinyjs::disable('upgma_fruit_offset_4')
-      shinyjs::disable('upgma_fruit_offset_5')
-    } else {
-      shinyjs::enable('upgma_tiles_show') 
-      shinyjs::enable('upgma_tiles_show_2')
-      shinyjs::enable('upgma_tiles_show_3') 
-      shinyjs::enable('upgma_tiles_show_4')
-      shinyjs::enable('upgma_tiles_show_5') 
-      shinyjs::enable('upgma_fruit_variable')
-      shinyjs::enable('upgma_fruit_variable_2')
-      shinyjs::enable('upgma_fruit_variable_3')
-      shinyjs::enable('upgma_fruit_variable_4')
-      shinyjs::enable('upgma_fruit_variable_5')
-      shinyjs::enable('upgma_fruit_width')
-      shinyjs::enable('upgma_fruit_width_2')
-      shinyjs::enable('upgma_fruit_width_3')
-      shinyjs::enable('upgma_fruit_width_4')
-      shinyjs::enable('upgma_fruit_width_5')
-      shinyjs::enable('upgma_fruit_offset')
-      shinyjs::enable('upgma_fruit_offset_2')
-      shinyjs::enable('upgma_fruit_offset_3')
-      shinyjs::enable('upgma_fruit_offset_4')
-      shinyjs::enable('upgma_fruit_offset_5')
-    }
-    
-    # Shut off branch labels for NJ and UPGMA plots for circular layout
-    if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-      shinyjs::disable('nj_show_branch_label')
-    } else {
-      shinyjs::enable('nj_show_branch_label')
-    }
-    
-    if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-      shinyjs::disable('upgma_show_branch_label')
-    } else {
-      shinyjs::enable('upgma_show_branch_label')
-    }
-  })
-  
-  #### Generate Plot ----
-  
-  hamming_nj <- reactive({
-    if(anyNA(DB$allelic_profile)) {
-      if(input$na_handling == "omit") {
-        allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
-        
-        allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
-        
-        compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
-        
-      } else if(input$na_handling == "ignore_na"){
-        compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
-        
-      } else {
-        compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
-      } 
-      
-    } else {compute.distMatrix(DB$allelic_profile_true, hamming.dist)}
-  })
-  
-  hamming_mst <- reactive({
-    if(anyNA(DB$allelic_profile)) {
-      if(input$na_handling == "omit") {
-        allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
-        
-        allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
-        
-        dist <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
-        
-      } else if (input$na_handling == "ignore_na") {
-        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
-      } else {
-        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
-      }
-    } else {
-      dist <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
-    }
-    
-    # Find indices of pairs with a distance of 0
-    zero_distance_pairs <- as.data.frame(which(as.matrix(dist) == 0, arr.ind = TRUE))
-    
-    zero_distance_pairs <- zero_distance_pairs[zero_distance_pairs$row != zero_distance_pairs$col, ]
-    
-    if(nrow(zero_distance_pairs) > 0) {
-      
-      # Sort each row so that x <= y
-      df_sorted <- t(apply(zero_distance_pairs, 1, function(row) sort(row)))
-      
-      # Remove duplicate rows
-      df_unique <- as.data.frame(unique(df_sorted))
-      
-      colnames(df_unique) <- c("col", "row")
-      
-      # get metadata in df
-      vector_col <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        vector_col[count] <- Vis$meta_mst$`Assembly Name`[i]
-        count <- count + 1
-      }
-      
-      vector_row <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        vector_row[count] <- Vis$meta_mst$`Assembly Name`[i]
-        count <- count + 1
-      }
-      
-      col_id <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_id[count] <- Vis$meta_mst$`Assembly ID`[i]
-        count <- count + 1
-      }
-      
-      row_id <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_id[count] <- Vis$meta_mst$`Assembly ID`[i]
-        count <- count + 1
-      }
-      
-      col_index <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_index[count] <- Vis$meta_mst$Index[i]
-        count <- count + 1
-      }
-      
-      row_index <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_index[count] <- Vis$meta_mst$Index[i]
-        count <- count + 1
-      }
-      
-      col_date <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_date[count] <- Vis$meta_mst$`Isolation Date`[i]
-        count <- count + 1
-      }
-      
-      row_date <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_date[count] <- Vis$meta_mst$`Isolation Date`[i]
-        count <- count + 1
-      }
-      
-      col_host <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_host[count] <- Vis$meta_mst$Host[i]
-        count <- count + 1
-      }
-      
-      row_host <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_host[count] <- Vis$meta_mst$Host[i]
-        count <- count + 1
-      }
-      
-      col_country <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_country[count] <- Vis$meta_mst$Country[i]
-        count <- count + 1
-      }
-      
-      row_country <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_country[count] <- Vis$meta_mst$Country[i]
-        count <- count + 1
-      }
-      
-      col_city <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_city[count] <- Vis$meta_mst$City[i]
-        count <- count + 1
-      }
-      
-      row_city <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_city[count] <- Vis$meta_mst$City[i]
-        count <- count + 1
-      }
-      
-      df_unique <- cbind(df_unique, col_name = vector_col, row_name = vector_row, 
-                         col_index = col_index, row_index = row_index, col_id = col_id,
-                         row_id = row_id, col_date = col_date, row_date = row_date,
-                         col_host = col_host, row_host = row_host, col_country = col_country,
-                         row_country = row_country, col_city = col_city, row_city = row_city)
-      
-      # Add groups
-      grouped_df <- df_unique %>%
-        group_by(col) %>%
-        mutate(group_id = cur_group_id())
-      
-      # Merge groups
-      name <- character(0)
-      index <- character(0)
-      id <- character(0)
-      count <- 1
-      for (i in grouped_df$group_id) {
-        name[count] <- paste(unique(append(grouped_df$col_name[which(grouped_df$group_id == i)], 
-                                           grouped_df$row_name[which(grouped_df$group_id == i)])), 
-                             collapse = "\n")
-        
-        id[count] <- paste(unique(append(grouped_df$col_id[which(grouped_df$group_id == i)], 
-                                         grouped_df$row_id[which(grouped_df$group_id == i)])), 
-                           collapse = "\n")
-        
-        index[count] <- paste(unique(append(grouped_df$col_index[which(grouped_df$group_id == i)], 
-                                            grouped_df$row_index[which(grouped_df$group_id == i)])), 
-                              collapse = "\n")
-        
-        count <- count + 1
-      }
-      
-      merged_names <- cbind(grouped_df, "Index" = index, "Assembly Name" = name, "Assembly ID" = id)
-      
-      # remove duplicate groups
-      
-      final <- merged_names[!duplicated(merged_names$group_id), ]
-      
-      final_cleaned <- final[!(final$col_name %in% final$row_name),]
-      
-      final_cleaned <- select(final_cleaned, 3, 17:20)
-      
-      # adapt metadata
-      Date_merged <- character(0)
-      for(j in 1:length(final_cleaned$Index)) {
-        Date <- character(0)
-        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
-          Date <- append(Date, Vis$meta_mst$`Isolation Date`[which(Vis$meta_mst$Index == i)])
-        }
-        Date_merged <- append(Date_merged, paste(Date, collapse = "\n"))
-      }
-      
-      Host_merged <- character(0)
-      for(j in 1:length(final_cleaned$Index)) {
-        Host <- character(0)
-        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
-          Host <- append(Host, Vis$meta_mst$Host[which(Vis$meta_mst$Index == i)])
-        }
-        Host_merged <- append(Host_merged, paste(Host, collapse = "\n"))
-      }
-      
-      Country_merged <- character(0)
-      for(j in 1:length(final_cleaned$Index)) {
-        Country <- character(0)
-        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
-          Country <- append(Country, Vis$meta_mst$Country[which(Vis$meta_mst$Index == i)])
-        }
-        Country_merged <- append(Country_merged, paste(Country, collapse = "\n"))
-      }
-      
-      City_merged <- character(0)
-      for(j in 1:length(final_cleaned$Index)) {
-        City <- character(0)
-        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
-          City <- append(City, Vis$meta_mst$City[which(Vis$meta_mst$Index == i)])
-        }
-        City_merged <- append(City_merged, paste(City, collapse = "\n"))
-      }
-      
-      final_meta <- cbind(final_cleaned, "Isolation Date" = Date_merged, 
-                          "Host" = Host_merged, "Country" = Country_merged, "City" = City_merged)
-      
-      
-      # Merging with original data frame / allelic profile
-      
-      allelic_profile_true <- DB$allelic_profile_true
-      meta_true <- Vis$meta_mst
-      
-      rownames(allelic_profile_true) <- Vis$meta_mst$`Assembly Name`
-      rownames(meta_true) <- Vis$meta_mst$`Assembly Name`
-      
-      omit <- unique(append(df_unique$col_name, df_unique$row_name)) %in% final_cleaned$col_name
-      
-      omit_id <- unique(append(df_unique$col_name, df_unique$row_name))[!omit]
-      
-      remove <- !(rownames(allelic_profile_true) %in% omit_id)
-      
-      allelic_profile_clean <- allelic_profile_true[remove, ]
-      
-      meta_clean <- meta_true[remove, ]
-      
-      # substitute meta assembly names with group names
-      
-      count <- 1
-      for(i in which(rownames(meta_clean) %in% final_meta$col_name)) {
-        meta_clean$Index[i] <- final_meta$Index[count]
-        meta_clean$`Assembly Name`[i] <- final_meta$`Assembly Name`[count]
-        meta_clean$`Assembly ID`[i] <- final_meta$`Assembly ID`[count]
-        meta_clean$`Isolation Date`[i] <- final_meta$`Isolation Date`[count]
-        meta_clean$Host[i] <- final_meta$Host[count]
-        meta_clean$Country[i] <- final_meta$Country[count]
-        meta_clean$City[i] <- final_meta$City[count]
-        count <- count + 1
-      }
-      
-      # Metadata completion
-      # get group size
-      
-      size_vector <- numeric(0)
-      for(i in 1:nrow(meta_clean)) {
-        if (str_count(meta_clean$`Assembly Name`[i], "\n") == 0) {
-          size_vector[i] <- 1
-        } else {
-          size_vector[i] <- str_count(meta_clean$`Assembly Name`[i], "\n") +1
-        }
-      }
-      
-      meta_clean <- mutate(meta_clean, size = size_vector)
-      
-      # get font size dependent on group size
-      
-      font_size <- numeric(nrow(meta_clean))
-      
-      for (i in 1:length(font_size)) {
-        if(meta_clean$size[i] < 3) {
-          font_size[i] <- 12
-        } else {
-          font_size[i] <- 11
-        }
-      }
-      
-      # get v-align dependent on group size
-      valign <- numeric(nrow(meta_clean))
-      
-      for (i in 1:length(valign)) {
-        if(meta_clean$size[i] == 1) {
-          valign[i] <- -30
-        } else if(meta_clean$size[i] == 2) {
-          valign[i] <- -38
-        } else if(meta_clean$size[i] == 3) {
-          valign[i] <- -46
-        } else if(meta_clean$size[i] == 4) {
-          valign[i] <- -54
-        } else if(meta_clean$size[i] == 5) {
-          valign[i] <- -62
-        } else if(meta_clean$size[i] > 5) {
-          valign[i] <- -70
-        }
-      }
-      
-      Vis$unique_meta <- meta_clean %>%
-        cbind(font_size = font_size, valign = valign)
-      
-      # final dist calculation
-      
-      if(anyNA(DB$allelic_profile)){
-        if(input$na_handling == "omit") {
-          allelic_profile_clean_noNA_names <- allelic_profile_clean[, colSums(is.na(allelic_profile_clean)) == 0]
-          compute.distMatrix(allelic_profile_clean_noNA_names, hamming.dist)
-        } else if (input$na_handling == "ignore_na") {
-          compute.distMatrix(allelic_profile_clean, hamming.distIgnore)
-        } else {
-          compute.distMatrix(allelic_profile_clean, hamming.distCategory)
-        }
-      } else {compute.distMatrix(allelic_profile_clean, hamming.dist)}
-      
-      
-    } else {
-      font_size <- rep(12, nrow(Vis$meta_mst))
-      valign <- rep(-30, nrow(Vis$meta_mst))
-      size <- rep(1, nrow(Vis$meta_mst))
-      Vis$unique_meta <- Vis$meta_mst %>%
-        cbind(size , font_size, valign)
-      
-      dist
-    }
-    
-  })
-  
-  observeEvent(input$create_tree, {
-    log_print("Input create_tree")
-    
-    if(is.null(DB$data)) {
-      log_print("Missing data")
-      
-      show_toast(
-        title = "Missing data",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if(nrow(DB$allelic_profile_true) < 3) {
-      log_print("Min. of 3 entries required for visualization")
-      
-      show_toast(
-        title = "Min. of 3 entries required for visualization",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      
-      if(any(duplicated(DB$meta$`Assembly Name`)) | any(duplicated(DB$meta$`Assembly ID`))) {
-        log_print("Duplicated assemblies")
-        
-        dup_name <- which(duplicated(DB$meta_true$`Assembly Name`))
-        dup_id <- which(duplicated(DB$meta_true$`Assembly ID`))
-        
-        showModal(
-          modalDialog(
-            if((length(dup_name) + length(dup_id)) == 1) {
-              if(length(dup_name) == 1) {
-                HTML(paste0("Entry #", dup_name,
-                            " contains a duplicated assembly name:", "<br><br>",
-                            DB$meta_true$`Assembly Name`[dup_name]))
-              } else {
-                HTML(paste0("Entry #", dup_id,
-                            " contains a duplicated assembly ID:", "<br><br>",
-                            DB$meta_true$`Assembly ID`[dup_id]))
-              }
-            } else {
-              if(length(dup_name) == 0) {
-                HTML(c("Entries contain duplicated IDs <br><br>",
-                       paste0(unique(DB$meta_true$`Assembly ID`[dup_id]), "<br>")))
-              } else if(length(dup_id) == 0) {
-                HTML(c("Entries contain duplicated names<br><br>",
-                       paste0(unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>")))
-              } else {
-                HTML(c("Entries contain duplicated names and IDs <br><br>",
-                       paste0("Name: ", unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>"),
-                       paste0("ID: ", unique(DB$meta_true$`Assembly ID`[dup_id]), "<br>")))
-              }
-            },
-            title = "Duplicate entries",
-            fade = TRUE,
-            easyClose = TRUE,
-            footer = tagList(
-              modalButton("Cancel"),
-              actionButton("change_entries", "Go to Entry Table", class = "btn btn-default")
-            )
-          )
-        )
-      } else {
-        
-        set.seed(1)
-        
-        if (input$tree_algo == "Neighbour-Joining") {
-          
-          log_print("Rendering NJ tree")
-          
-          output$nj_field <- renderUI({
-            addSpinner(
-              plotOutput("tree_nj", width = paste0(as.character(as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), "px"), height = paste0(as.character(input$nj_scale), "px")),
-              spin = "dots",
-              color = "#ffffff"
-            )
-          })
-          
-          Vis$meta_nj <- select(DB$meta_true, -2)
-          
-          if(length(unique(gsub(" ", "_", colnames(Vis$meta_nj)))) < length(gsub(" ", "_", colnames(Vis$meta_nj)))) {
-            show_toast(
-              title = "Conflicting Custom Variable Names",
-              type = "warning",
-              position = "bottom-end",
-              timer = 6000
-            )
-          } else {
-            
-            # Create phylogenetic tree data
-            Vis$nj <- ape::nj(hamming_nj())
-            
-            # Create phylogenetic tree meta data
-            Vis$meta_nj <- mutate(Vis$meta_nj, taxa = Index) %>%
-              relocate(taxa)
-            
-            # Get number of included entries calculate start values for tree 
-            if(!is.null(input$nj_layout)) {
-              if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-                if(sum(DB$data$Include) < 21) {
-                  Vis$labelsize_nj <- 5.5
-                  Vis$tippointsize_nj <- 5.5
-                  Vis$nodepointsize_nj <- 4
-                  Vis$tiplab_padding_nj <- 0.25
-                  Vis$branch_size_nj <- 4.5
-                } else if (between(sum(DB$data$Include), 21, 40)) {
-                  Vis$labelsize_nj <- 5
-                  Vis$tippointsize_nj <- 5
-                  Vis$nodepointsize_nj <- 3.5
-                  Vis$tiplab_padding_nj <- 0.2
-                  Vis$branch_size_nj <- 4
-                } else if (between(sum(DB$data$Include), 41, 60)) {
-                  Vis$labelsize_nj <- 4.5
-                  Vis$tippointsize_nj <- 4.5
-                  Vis$nodepointsize_nj <- 3
-                  Vis$tiplab_padding_nj <- 0.15
-                  Vis$branch_size_nj <- 3.5
-                } else if (between(sum(DB$data$Include), 61, 80)) {
-                  Vis$labelsize_nj <- 4
-                  Vis$tippointsize_nj <- 4
-                  Vis$nodepointsize_nj <- 2.5
-                  Vis$tiplab_padding_nj <- 0.1
-                  Vis$branch_size_nj <- 3
-                } else if (between(sum(DB$data$Include), 81, 100)) {
-                  Vis$labelsize_nj <- 3.5
-                  Vis$tippointsize_nj <- 3.5
-                  Vis$nodepointsize_nj <- 2
-                  Vis$tiplab_padding_nj <- 0.1
-                  Vis$branch_size_nj <- 2.5
-                } else {
-                  Vis$labelsize_nj <- 3
-                  Vis$tippointsize_nj <- 3
-                  Vis$nodepointsize_nj <- 1.5
-                  Vis$tiplab_padding_nj <- 0.05
-                  Vis$branch_size_nj <- 2
-                }
-              } else {
-                if(sum(DB$data$Include) < 21) {
-                  Vis$labelsize_nj <- 5
-                  Vis$tippointsize_nj <- 5
-                  Vis$nodepointsize_nj <- 4
-                  Vis$tiplab_padding_nj <- 0.25
-                  Vis$branch_size_nj <- 4.5
-                } else if (between(sum(DB$data$Include), 21, 40)) {
-                  Vis$labelsize_nj <- 4.5
-                  Vis$tippointsize_nj <- 4.5
-                  Vis$nodepointsize_nj <- 3.5
-                  Vis$tiplab_padding_nj <- 0.2
-                  Vis$branch_size_nj <- 4
-                } else if (between(sum(DB$data$Include), 41, 60)) {
-                  Vis$labelsize_nj <- 4
-                  Vis$tippointsize_nj <- 4
-                  Vis$nodepointsize_nj <- 3
-                  Vis$tiplab_padding_nj <- 0.15
-                  Vis$branch_size_nj <- 3.5
-                } else if (between(sum(DB$data$Include), 61, 80)) {
-                  Vis$labelsize_nj <- 3.5
-                  Vis$tippointsize_nj <- 3.5
-                  Vis$nodepointsize_nj <- 2.5
-                  Vis$tiplab_padding_nj <- 0.1
-                  Vis$branch_size_nj <- 3
-                } else if (between(sum(DB$data$Include), 81, 100)) {
-                  Vis$labelsize_nj <- 3
-                  Vis$tippointsize_nj <- 3
-                  Vis$nodepointsize_nj <- 2
-                  Vis$tiplab_padding_nj <- 0.1
-                  Vis$branch_size_nj <- 2.5
-                } else {
-                  Vis$labelsize_nj <- 2.5
-                  Vis$tippointsize_nj <- 2.5
-                  Vis$nodepointsize_nj <- 1.5
-                  Vis$tiplab_padding_nj <- 0.05
-                  Vis$branch_size_nj <- 2
-                }
-              }
-            } else {
-              Vis$labelsize_nj <- 4
-              Vis$tippointsize_nj <- 4
-              Vis$nodepointsize_nj <- 2.5
-              Vis$tiplab_padding_nj <- 0.2
-              Vis$branch_size_nj <- 3.5
-            }
-            
-            Vis$nj_tree <- ggtree(Vis$nj)
-            
-            # Get upper and lower end of x range
-            Vis$nj_max_x <- max(Vis$nj_tree$data$x)
-            Vis$nj_min_x <- min(Vis$nj_tree$data$x)
-            
-            # Get parent node numbers
-            Vis$nj_parentnodes <- Vis$nj_tree$data$parent
-            
-            # Update visualization control inputs
-            if(!is.null(input$nj_tiplab_size)) {
-              updateNumericInput(session, "nj_tiplab_size", value = Vis$labelsize_nj)
-            }
-            if(!is.null(input$nj_tippoint_size)) {
-              updateSliderInput(session, "nj_tippoint_size", value = Vis$tippointsize_nj)
-            }
-            if(!is.null(input$nj_nodepoint_size)) {
-              updateSliderInput(session, "nj_nodepoint_size", value = Vis$nodepointsize_nj)
-            }
-            if(!is.null(input$nj_tiplab_padding)) {
-              updateSliderInput(session, "nj_tiplab_padding", value = Vis$tiplab_padding_nj)
-            }
-            if(!is.null(input$nj_branch_size)) {
-              updateNumericInput(session, "nj_branch_size", value = Vis$branch_size_nj)
-            }
-            if(!is.null(input$nj_treescale_width)) {
-              updateNumericInput(session, "nj_treescale_width", value = round(ceiling(Vis$nj_max_x) * 0.1, 0))
-            }
-            if(!is.null(input$nj_rootedge_length)) {
-              updateSliderInput(session, "nj_rootedge_length", value = round(ceiling(Vis$nj_max_x) * 0.05, 0))
-            }
-            
-            output$tree_nj <- renderPlot({
-              nj_tree()
-            })
-            
-            Vis$nj_true <- TRUE
-          }
-        } else if (input$tree_algo == "UPGMA") {
-          
-          log_print("Rendering UPGMA tree")
-          
-          output$upgma_field <- renderUI({
-            addSpinner(
-              plotOutput("tree_upgma", width = paste0(as.character(as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), "px"), height = paste0(as.character(input$upgma_scale), "px")),
-              spin = "dots",
-              color = "#ffffff"
-            )
-          })
-          
-          Vis$meta_upgma <- select(DB$meta_true, -2)
-          
-          if(length(unique(gsub(" ", "_", colnames(Vis$meta_upgma)))) < length(gsub(" ", "_", colnames(Vis$meta_upgma)))) {
-            show_toast(
-              title = "Conflicting Custom Variable Names",
-              type = "warning",
-              position = "bottom-end",
-              timer = 6000
-            )
-          } else {
-            
-            # Create phylogenetic tree data
-            Vis$upgma <- phangorn::upgma(hamming_nj())
-            
-            # Create phylogenetic tree meta data
-            Vis$meta_upgma <- mutate(Vis$meta_upgma, taxa = Index) %>%
-              relocate(taxa)
-            
-            # Get number of included entries calculate start values for tree 
-            if(!is.null(input$upgma_layout)) {
-              if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-                if(sum(DB$data$Include) < 21) {
-                  Vis$labelsize_upgma <- 5.5
-                  Vis$tippointsize_upgma <- 5.5
-                  Vis$nodepointsize_upgma <- 4
-                  Vis$tiplab_padding_upgma <- 0.25
-                  Vis$branch_size_upgma <- 4.5
-                } else if (between(sum(DB$data$Include), 21, 40)) {
-                  Vis$labelsize_upgma <- 5
-                  Vis$tippointsize_upgma <- 5
-                  Vis$nodepointsize_upgma <- 3.5
-                  Vis$tiplab_padding_upgma <- 0.2
-                  Vis$branch_size_upgma <- 4
-                } else if (between(sum(DB$data$Include), 41, 60)) {
-                  Vis$labelsize_upgma <- 4.5
-                  Vis$tippointsize_upgma <- 4.5
-                  Vis$nodepointsize_upgma <- 3
-                  Vis$tiplab_padding_upgma <- 0.15
-                  Vis$branch_size_upgma <- 3.5
-                } else if (between(sum(DB$data$Include), 61, 80)) {
-                  Vis$labelsize_upgma <- 4
-                  Vis$tippointsize_upgma <- 4
-                  Vis$nodepointsize_upgma <- 2.5
-                  Vis$tiplab_padding_upgma <- 0.1
-                  Vis$branch_size_upgma <- 3
-                } else if (between(sum(DB$data$Include), 81, 100)) {
-                  Vis$labelsize_upgma <- 3.5
-                  Vis$tippointsize_upgma <- 3.5
-                  Vis$nodepointsize_upgma <- 2
-                  Vis$tiplab_padding_upgma <- 0.1
-                  Vis$branch_size_upgma <- 2.5
-                } else {
-                  Vis$labelsize_upgma <- 3
-                  Vis$tippointsize_upgma <- 3
-                  Vis$nodepointsize_upgma <- 1.5
-                  Vis$tiplab_padding_upgma <- 0.05
-                  Vis$branch_size_upgma <- 2
-                }
-              } else {
-                if(sum(DB$data$Include) < 21) {
-                  Vis$labelsize_upgma <- 5
-                  Vis$tippointsize_upgma <- 5
-                  Vis$nodepointsize_upgma <- 4
-                  Vis$tiplab_padding_upgma <- 0.25
-                  Vis$branch_size_upgma <- 4.5
-                } else if (between(sum(DB$data$Include), 21, 40)) {
-                  Vis$labelsize_upgma <- 4.5
-                  Vis$tippointsize_upgma <- 4.5
-                  Vis$nodepointsize_upgma <- 3.5
-                  Vis$tiplab_padding_upgma <- 0.2
-                  Vis$branch_size_upgma <- 4
-                } else if (between(sum(DB$data$Include), 41, 60)) {
-                  Vis$labelsize_upgma <- 4
-                  Vis$tippointsize_upgma <- 4
-                  Vis$nodepointsize_upgma <- 3
-                  Vis$tiplab_padding_upgma <- 0.15
-                  Vis$branch_size_upgma <- 3.5
-                } else if (between(sum(DB$data$Include), 61, 80)) {
-                  Vis$labelsize_upgma <- 3.5
-                  Vis$tippointsize_upgma <- 3.5
-                  Vis$nodepointsize_upgma <- 2.5
-                  Vis$tiplab_padding_upgma <- 0.1
-                  Vis$branch_size_upgma <- 3
-                } else if (between(sum(DB$data$Include), 81, 100)) {
-                  Vis$labelsize_upgma <- 3
-                  Vis$tippointsize_upgma <- 3
-                  Vis$nodepointsize_upgma <- 2
-                  Vis$tiplab_padding_upgma <- 0.1
-                  Vis$branch_size_upgma <- 2.5
-                } else {
-                  Vis$labelsize_upgma <- 2.5
-                  Vis$tippointsize_upgma <- 2.5
-                  Vis$nodepointsize_upgma <- 1.5
-                  Vis$tiplab_padding_upgma <- 0.05
-                  Vis$branch_size_upgma <- 2
-                }
-              }
-            } else {
-              Vis$labelsize_upgma <- 4
-              Vis$tippointsize_upgma <- 4
-              Vis$nodepointsize_upgma <- 2.5
-              Vis$tiplab_padding_upgma <- 0.2
-              Vis$branch_size_upgma <- 3.5
-            }
-            
-            Vis$upgma_tree <- ggtree(Vis$upgma)
-            
-            # Get upper and lower end of x range
-            Vis$upgma_max_x <- max(Vis$upgma_tree$data$x)
-            Vis$upgma_min_x <- min(Vis$upgma_tree$data$x)
-            
-            # Get parent node numbers
-            Vis$upgma_parentnodes <- Vis$upgma_tree$data$parent
-            
-            # Update visualization control inputs
-            if(!is.null(input$upgma_tiplab_size)) {
-              updateNumericInput(session, "upgma_tiplab_size", value = Vis$labelsize_upgma)
-            }
-            if(!is.null(input$upgma_tippoint_size)) {
-              updateSliderInput(session, "upgma_tippoint_size", value = Vis$tippointsize_upgma)
-            }
-            if(!is.null(input$upgma_nodepoint_size)) {
-              updateSliderInput(session, "upgma_nodepoint_size", value = Vis$nodepointsize_upgma)
-            }
-            if(!is.null(input$upgma_tiplab_padding)) {
-              updateSliderInput(session, "upgma_tiplab_padding", value = Vis$tiplab_padding_upgma)
-            }
-            if(!is.null(input$upgma_branch_size)) {
-              updateNumericInput(session, "upgma_branch_size", value = Vis$branch_size_upgma)
-            }
-            if(!is.null(input$upgma_treescale_width)) {
-              updateNumericInput(session, "upgma_treescale_width", value = round(ceiling(Vis$upgma_max_x) * 0.1, 0))
-            }
-            if(!is.null(input$upgma_rootedge_length)) {
-              updateSliderInput(session, "upgma_rootedge_length", value = round(ceiling(Vis$upgma_max_x) * 0.05, 0))
-            }
-            
-            output$tree_upgma <- renderPlot({
-              upgma_tree()
-            })
-            
-            Vis$upgma_true <- TRUE
-          }
-        } else {
-          
-          log_print("Rendering MST graph")
-          
-          output$mst_field <- renderUI({
-            if(input$mst_background_transparent == TRUE) {
-              visNetworkOutput("tree_mst", width = paste0(as.character(as.numeric(input$mst_scale) * as.numeric(input$mst_ratio)), "px"), height = paste0(as.character(input$mst_scale), "px"))
-            } else {
-              addSpinner(
-                visNetworkOutput("tree_mst", width = paste0(as.character(as.numeric(input$mst_scale) * as.numeric(input$mst_ratio)), "px"), height = paste0(as.character(input$mst_scale), "px")),
-                spin = "dots",
-                color = "#ffffff"
-              )
-            }
-          })
-          
-          if(nrow(DB$meta_true) > 100) {
-            
-            log_print("Over 100 isolates in MST graph")
-            
-            show_toast(
-              title = "Computation might take a while",
-              type = "warning",
-              position = "bottom-end",
-              timer = 10000
-            )
-          }
-          
-          meta_mst <- DB$meta_true
-          Vis$meta_mst <- meta_mst
-          
-          # prepare igraph object
-          Vis$ggraph_1 <- hamming_mst() |>
-            as.matrix() |>
-            graph.adjacency(weighted = TRUE) |>
-            igraph::mst() 
-          
-          output$tree_mst <- renderVisNetwork({
-            mst_tree()
-          })
-          
-          Vis$mst_true <- TRUE
-        }
-      }
-    }
-  })
-  
-  # _______________________ ####
-  
-  ## Report ----
-  
-  observe({
-    if(!is.null(DB$data)) {
-      if(!is.null(input$tree_algo)) {
-        if(input$tree_algo == "Minimum-Spanning") {
-          shinyjs::disable("rep_plot_report")
-          updateCheckboxInput(session, "rep_plot_report", value = FALSE)
-        } else {
-          shinyjs::enable("rep_plot_report")
-        }
-      }
-    }
-  })
-  
-  ### Report creation UI ----
-  
-  observeEvent(input$create_rep, {
-    
-    if((input$tree_algo == "Minimum-Spanning" & isTRUE(Vis$mst_true)) |
-       (input$tree_algo == "UPGMA" & isTRUE(Vis$upgma_true)) |
-       (input$tree_algo == "Neighbour-Joining" & isTRUE(Vis$nj_true))) {
-      # Get currently selected missing value handling option
-      if(input$na_handling == "ignore_na") {
-        na_handling <- "Ignore missing values for pairwise comparison"
-      } else if(input$na_handling == "omit") {
-        na_handling <- "Omit loci with missing values for all assemblies"
-      } else if(input$na_handling == "category") {
-        na_handling <- "Treat missing values as allele variant"
-      }
-      
-      extra_var <- character()
-      if(input$tree_algo == "Minimum-Spanning") {
-        shinyjs::runjs("mstReport();")
-        if(isTRUE(input$mst_color_var)) {
-          extra_var <- c(extra_var, input$mst_col_var)
-        }
-      } else if(input$tree_algo == "Neighbour-Joining") {
-        if(isTRUE(input$nj_mapping_show)) {
-          extra_var <- c(extra_var, input$nj_color_mapping)
-        }
-        if(isTRUE(input$nj_tipcolor_mapping_show)) {
-          extra_var <- c(extra_var, input$nj_tipcolor_mapping)
-        }
-        if(isTRUE(input$nj_tipshape_mapping_show)) {
-          extra_var <- c(extra_var, input$nj_tipshape_mapping)
-        }
-        if(isTRUE(input$nj_tiles_show_1)) {
-          extra_var <- c(extra_var, input$nj_fruit_variable)
-        }
-        if(isTRUE(input$nj_tiles_show_2)) {
-          extra_var <- c(extra_var, input$nj_fruit_variable_2)
-        }
-        if(isTRUE(input$nj_tiles_show_3)) {
-          extra_var <- c(extra_var, input$nj_fruit_variable_3)
-        }
-        if(isTRUE(input$nj_tiles_show_4)) {
-          extra_var <- c(extra_var, input$nj_fruit_variable_4)
-        }
-        if(isTRUE(input$nj_tiles_show_5)) {
-          extra_var <- c(extra_var, input$nj_fruit_variable_5)
-        }
-        if(isTRUE(input$nj_heatmap_show)) {
-          extra_var <- c(extra_var, input$nj_heatmap_select)
-        }
-      } else if(input$tree_algo == "UPGMA") {
-        if(isTRUE(input$UPGMA_mapping_show)) {
-          extra_var <- c(extra_var, input$UPGMA_color_mapping)
-        }
-        if(isTRUE(input$UPGMA_tipcolor_mapping_show)) {
-          extra_var <- c(extra_var, input$UPGMA_tipcolor_mapping)
-        }
-        if(isTRUE(input$UPGMA_tipshape_mapping_show)) {
-          extra_var <- c(extra_var, input$UPGMA_tipshape_mapping)
-        }
-        if(isTRUE(input$UPGMA_tiles_show_1)) {
-          extra_var <- c(extra_var, input$UPGMA_fruit_variable)
-        }
-        if(isTRUE(input$UPGMA_tiles_show_2)) {
-          extra_var <- c(extra_var, input$UPGMA_fruit_variable_2)
-        }
-        if(isTRUE(input$UPGMA_tiles_show_3)) {
-          extra_var <- c(extra_var, input$UPGMA_fruit_variable_3)
-        }
-        if(isTRUE(input$UPGMA_tiles_show_4)) {
-          extra_var <- c(extra_var, input$UPGMA_fruit_variable_4)
-        }
-        if(isTRUE(input$UPGMA_tiles_show_5)) {
-          extra_var <- c(extra_var, input$UPGMA_fruit_variable_5)
-        }
-        if(isTRUE(input$UPGMA_heatmap_show)) {
-          extra_var <- c(extra_var, input$UPGMA_heatmap_select)
-        }
-      }
-      
-      showModal(
-        modalDialog(
-          fluidRow(
-            column(
-              width = 12,
-              fluidRow(
-                column(
-                  width = 4,
-                  align = "left",
-                  HTML(
-                    paste(
-                      tags$span(style='color:black; font-size: 15px; font-weight: 900', 'General')
-                    )
-                  )
-                ),
-                column(
-                  width = 3,
-                  align = "left",
-                  checkboxInput(
-                    "rep_general",
-                    label = "",
-                    value = TRUE
-                  )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 12,
-                  align = "left",
-                  fluidRow(
-                    column(
-                      width = 3,
-                      checkboxInput(
-                        "rep_date_general", 
-                        label = h5("Date", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 7,
-                      dateInput(
-                        "mst_date_general_select",
-                        "",
-                        max = Sys.Date()
-                      )
-                    )
-                  ),
-                  fluidRow(
-                    column(
-                      width = 3,
-                      checkboxInput(
-                        "rep_operator_general", 
-                        label = h5("Operator", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 8,
-                      textInput(
-                        "mst_operator_general_select",
-                        ""
-                      ) 
-                    )
-                  ),
-                  fluidRow(
-                    column(
-                      width = 3,
-                      checkboxInput(
-                        "rep_institute_general", 
-                        label = h5("Institute", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 8,
-                      textInput(
-                        "mst_institute_general_select",
-                        ""
-                      ) 
-                    )
-                  ),
-                  fluidRow(
-                    column(
-                      width = 3,
-                      checkboxInput(
-                        "rep_comm_general", 
-                        label = h5("Comment", style = "color:black;")
-                      )
-                    ),
-                    column(
-                      width = 8,
-                      textAreaInput(
-                        inputId = "mst_comm_general_select",
-                        label = "",
-                        width = "100%",
-                        height = "60px",
-                        cols = NULL,
-                        rows = NULL,
-                        placeholder = NULL,
-                        resize = "vertical"
-                      ) 
-                    )
-                  )
-                )
-              ),
-              hr(),
-              fluidRow(
-                column(
-                  width = 4,
-                  align = "left",
-                  HTML(
-                    paste(
-                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Isolate Table')
-                    )
-                  )
-                ),
-                column(
-                  width = 3,
-                  align = "left",
-                  checkboxInput(
-                    "rep_entrytable",
-                    label = "",
-                    value = TRUE
-                  )
-                ),
-                column(
-                  width = 4,
-                  align = "left",
-                  HTML(
-                    paste(
-                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Include Plot')
-                    )
-                  )
-                ),
-                column(
-                  width = 1,
-                  align = "left",
-                  checkboxInput(
-                    "rep_plot_report",
-                    label = "",
-                    value = TRUE
-                  )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 6,
-                  align = "left",
-                  div(
-                    class = "rep_tab_sel",
-                    pickerInput("select_rep_tab",
-                                label = "",
-                                choices = names(DB$meta)[-2],
-                                selected = c("Assembly Name", "Scheme", "Isolation Date",
-                                             "Host", "Country", "City", extra_var),
-                                options = list(
-                                  size = 10,
-                                  `actions-box` = TRUE,
-                                  style = "background-color: white; border-radius: 5px;"
-                                ),
-                                multiple = TRUE)
-                  )
-                )
-              ),
-              hr(),
-              fluidRow(
-                column(
-                  width = 4,
-                  align = "left",
-                  HTML(
-                    paste(
-                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Analysis Parameter')
-                    )
-                  )
-                ),
-                column(
-                  width = 3,
-                  align = "left",
-                  checkboxInput(
-                    "rep_analysis",
-                    label = "",
-                    value = TRUE
-                  )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 6,
-                  align = "left",
-                  fluidRow(
-                    column(
-                      width = 4,
-                      checkboxInput(
-                        "rep_cgmlst_analysis",
-                        label = h5("Scheme", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 8,
-                      align = "right",
-                      HTML(
-                        paste(
-                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', DB$scheme)
-                        )
-                      )
-                    )
-                  ),
-                  fluidRow(
-                    column(
-                      width = 4,
-                      checkboxInput(
-                        "rep_tree_analysis",
-                        label = h5("Tree", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 8,
-                      align = "right",
-                      HTML(
-                        paste(
-                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', input$tree_algo)
-                        )
-                      )
-                    )
-                  )
-                ),
-                column(
-                  width = 6,
-                  align = "left",
-                  fluidRow(
-                    column(2),
-                    column(
-                      width = 4,
-                      checkboxInput(
-                        "rep_distance",
-                        label = h5("Distance", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 5,
-                      align = "right",
-                      HTML(
-                        paste(
-                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', 'Hamming')
-                        )
-                      )
-                    )
-                  ),
-                  fluidRow(
-                    column(2),
-                    column(
-                      width = 4,
-                      checkboxInput(
-                        "rep_version",
-                        label = h5("Version", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 5,
-                      align = "right",
-                      HTML(
-                        paste(
-                          tags$span(style='color:black; position: relative; top: 17px; font-style: italic', phylotraceVersion)
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 3,
-                  align = "left",
-                  checkboxInput(
-                    "rep_missval",
-                    label = h5("NA handling", style = "color:black;"),
-                    value = TRUE
-                  )
-                ),
-                column(
-                  width = 7,
-                  align = "right",
-                  HTML(
-                    paste(
-                      tags$span(style='color: black; position: relative; top: 17px; font-style: italic; right: 35px;', na_handling)
-                    )
-                  )
-                )
-              )
-            )
-          ),
-          title = "cgMLST Report Generation",
-          easyClose = TRUE,
-          footer = tagList(
-            modalButton("Cancel"),
-            downloadBttn(
-              "download_report",
-              style = "simple",
-              label = "Save",
-              size = "sm",
-              icon = icon("download")
-            )
-          )
-        )
-      )
-    } else {
-      show_toast(
-        title = "No tree created",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    }
-  })
-  
-  observe({
-    if(!is.null(input$rep_general)) {
-      if(isFALSE(input$rep_general)) {
-        shinyjs::disable('rep_date_general') 
-        shinyjs::disable('rep_operator_general') 
-        shinyjs::disable('rep_institute_general') 
-        shinyjs::disable('rep_comm_general') 
-        shinyjs::disable('mst_date_general_select') 
-        shinyjs::disable('mst_operator_general_select') 
-        shinyjs::disable('mst_institute_general_select') 
-        shinyjs::disable('mst_comm_general_select') 
-      } else {
-        shinyjs::enable('rep_date_general') 
-        shinyjs::enable('rep_operator_general') 
-        shinyjs::enable('rep_institute_general') 
-        shinyjs::enable('rep_comm_general')
-        shinyjs::enable('mst_date_general_select') 
-        shinyjs::enable('mst_operator_general_select') 
-        shinyjs::enable('mst_institute_general_select') 
-        shinyjs::enable('mst_comm_general_select') 
-      }
-    }
-    
-    if(!is.null(input$rep_analysis)) {
-      if(isFALSE(input$rep_analysis)) {
-        shinyjs::disable('rep_cgmlst_analysis') 
-        shinyjs::disable('rep_tree_analysis') 
-        shinyjs::disable('rep_distance') 
-        shinyjs::disable('rep_missval') 
-        shinyjs::disable('rep_version') 
-      } else {
-        shinyjs::enable('rep_cgmlst_analysis') 
-        shinyjs::enable('rep_tree_analysis') 
-        shinyjs::enable('rep_distance') 
-        shinyjs::enable('rep_missval') 
-        shinyjs::enable('rep_version') 
-      }
-    }
-    
-    if(length(input$select_rep_tab) > 0) {
-      updateCheckboxInput(session, "rep_entrytable", value = TRUE)
-    } else {
-      updateCheckboxInput(session, "rep_entrytable", value = FALSE)
-    }
-  })
-  
-  ### Save Report ----
-  
-  #### Get Report elements ----
-  
-  observe({
-    if(!is.null(DB$data)){
-      if(!is.null(input$tree_algo)) {
-        req(c(input$rep_entrytable, input$rep_general,
-              input$rep_date_general, input$rep_operator_general,
-              input$rep_institute_general, input$rep_comm_general,
-              input$rep_analysis, input$rep_cgmlst_analysis,
-              input$rep_tree_analysis, input$rep_distance,
-              input$rep_missval, input$rep_version,
-              input$rep_plot_report, input$select_rep_tab))
-        Report$report_df <- data.frame(Element = c("entry_table", "general_show",
-                                                   "general_date", "operator",
-                                                   "institute", "comment",
-                                                   "analysis_show", "scheme",
-                                                   "tree", "distance", "na_handling", "version",
-                                                   "plot"),
-                                       Include = c(input$rep_entrytable, input$rep_general,
-                                                   input$rep_date_general, input$rep_operator_general,
-                                                   input$rep_institute_general, input$rep_comm_general,
-                                                   input$rep_analysis, input$rep_cgmlst_analysis,
-                                                   input$rep_tree_analysis, input$rep_distance,
-                                                   input$rep_missval, input$rep_version,
-                                                   input$rep_plot_report))
-      }
-    }
-  })
-  
-  #### Get Report values ----
-  
-  observeEvent(input$create_tree, {
-    if(input$tree_algo == "Minimum-Spanning") {
-      Report$report_list_mst <- list(entry_table = DB$meta_true,
-                                     scheme = DB$schemeinfo, 
-                                     tree = input$tree_algo,
-                                     na_handling = if(anyNA(DB$allelic_profile_true)){input$na_handling} else {NULL},
-                                     distance = "Hamming Distances",
-                                     version = c(phylotraceVersion, "2.5.1"),
-                                     plot = "MST")
-    } else if(input$tree_algo == "Neighbour-Joining") {
-      Report$report_list_nj <- list(entry_table = DB$meta_true,
-                                    scheme = DB$schemeinfo, 
-                                    tree = input$tree_algo,
-                                    na_handling = input$na_handling,
-                                    distance = "Hamming Distances",
-                                    version = c(phylotraceVersion, "2.5.1"),
-                                    plot = "NJ")
-    } else {
-      Report$report_list_upgma <- list(entry_table = DB$meta_true,
-                                       scheme = DB$schemeinfo, 
-                                       tree = input$tree_algo,
-                                       na_handling = input$na_handling,
-                                       distance = "Hamming Distances",
-                                       version = c(phylotraceVersion, "2.5.1"),
-                                       plot = "UPGMA")
-    }
-  })
-  
-  # Save plot for Report
-  plot.report <- reactive({
-    if(input$tree_algo == "Neighbour-Joining") {
-      jpeg(paste0(getwd(), "/Report/NJ.jpeg"), width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale), quality = 100)
-      print(nj_tree())
-      dev.off()
-    } else if(input$tree_algo == "UPGMA") {
-      jpeg(paste0(getwd(), "/Report/UPGMA.jpeg"), width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale), quality = 100)
-      print(upgma_tree())
-      dev.off()
-    } else if (input$tree_algo == "Minimum-Spanning") {
-      shinyjs::runjs("mstReport();")
-      decoded_data <- base64enc::base64decode(input$canvas_data)
-      writeBin(decoded_data, paste0(getwd(), "/Report/MST.jpg"))
-    }
-  })
-  
-  #### Event Save Report ----
-  output$download_report <- downloadHandler(
-    filename = function() {
-      if(input$tree_algo == "Minimum-Spanning") {
-        paste0("MST_Report_", Sys.Date(), ".html")
-      } else if(input$tree_algo == "Neighbour-Joining") {
-        paste0("NJ_Report_", Sys.Date(), ".html")
-      } else {paste0("UPGMA_Report_", Sys.Date(), ".html")}
-    },
-    content = function(file) {
-      if(input$tree_algo == "Minimum-Spanning") {
-        plot.report()
-        
-        report <- c(Report$report_list_mst, 
-                    "general_date" = as.character(input$mst_date_general_select),
-                    "operator" = input$mst_operator_general_select,
-                    "institute" = input$mst_institute_general_select,
-                    "comment" = input$mst_comm_general_select,
-                    "report_df" = Report$report_df)
-        
-        report[["table_columns"]] <- input$select_rep_tab
-        
-        # Save data to an RDS file if any elements were selected
-        if (!is.null(report)) {
-          
-          log_print("Creating MST report")
-          
-          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
-          
-          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
-          
-          file.copy(paste0(getwd(), "/Report/Report.html"), file)
-        } else {
-          log_print("Creating MST report failed (report is null)")
-        }
-      } else if(input$tree_algo == "Neighbour-Joining") {
-        plot.report()
-        report <- c(Report$report_list_nj, 
-                    "general_date" = as.character(input$mst_date_general_select),
-                    "operator" = input$mst_operator_general_select,
-                    "institute" = input$mst_institute_general_select,
-                    "comment" = input$mst_comm_general_select,
-                    "report_df" = Report$report_df)
-        
-        report[["table_columns"]] <- input$select_rep_tab
-        
-        # Save data to an RDS file if any elements were selected
-        if (!is.null(report)) {
-          log_print("Creating NJ report")
-          
-          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
-          
-          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
-          
-          file.copy(paste0(getwd(), "/Report/Report.html"), file)
-        } else {
-          log_print("Creating NJ report failed (report is null)")
-        }
-        
-      } else {
-        plot.report()
-        report <- c(Report$report_list_upgma, 
-                    "general_date" = as.character(input$mst_date_general_select),
-                    "operator" = input$mst_operator_general_select,
-                    "institute" = input$mst_institute_general_select,
-                    "comment" = input$mst_comm_general_select,
-                    "report_df" = Report$report_df)
-        
-        report[["table_columns"]] <- input$select_rep_tab
-        
-        # Save data to an RDS file if any elements were selected
-        if (!is.null(report)) {
-          log_print("Creating UPGMA report")
-          
-          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
-          
-          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
-          
-          file.copy(paste0(getwd(), "/Report/Report.html"), file)
-        } else {
-          log_print("Creating UPGMA report failed (report is null)")
-        }
-        
-      }
-      removeModal()
-    }
-  )
-  
-  
-  # _______________________ ####
-  
-  ## Gene Screening  ----
-  
-  ### Render UI Elements ----
-  
-  # Rendering results table
-  output$gs_results_table <- renderUI({
-    req(DB$data)
-    if(!is.null(Screening$selected_isolate)) {
-      if(length(Screening$selected_isolate) > 0) {
-        fluidRow(
-          div(class = "loci_table",
-              DT::dataTableOutput("gs_profile_table")),
-          br(),
-          HTML(
-            paste0("<span style='color: white; font-size: 12px'>", 
-                   '<strong>RSL</strong> = <em>Reference Sequence Length</em>&nbsp&nbsp|&nbsp&nbsp',
-                   '<strong>%CRS</strong> = <em>% Coverage of Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
-                   '<strong>%IRS</strong> = <em>% Identity to Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
-                   '<strong>ACS</strong> = <em>Accession of Closest Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
-                   '<strong>NCS</strong> = <em>Name of Closest Sequence</em>')
-            
-          )
-        )
-      } else {
-        fluidRow(
-          br(), br(),
-          p(
-            HTML(
-              paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
-                     'Select entry from the table to display resistance profile')
-              
-            )
-          )
-        )
-      }
-    } else {
-      fluidRow(
-        br(), br(),
-        p(
-          HTML(
-            paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
-                   'Select entry from the table to display resistance profile')
-            
-          )
-        )
-      )
-    }
-  })
-  
-  # Gene screening download button
-  output$gs_download <- renderUI({
-    req(DB$data)
-    if(!is.null(Screening$selected_isolate)) {
-      if(length(Screening$selected_isolate) > 0) {
-        fluidRow(
-          downloadBttn(
-            "download_resistance_profile",
-            style = "simple",
-            label = "Profile Table",
-            size = "sm",
-            icon = icon("download"),
-            color = "primary"
-          ),
-          bsTooltip("download_resistance_profile_bttn", 
-                    HTML(paste0("Save resistance profile table for</br>",
-                                Screening$selected_isolate)), 
-                    placement = "bottom", trigger = "hover")
-        )
-      } else {NULL}
-    } else {NULL}
-  })
-  
-  # Conditionally render table selectiom interface
-  output$gs_table_selection <- renderUI({
-    req(DB$data, input$gs_view)
-    if(input$gs_view == "Table") {
-      fluidRow(
-        column(1),
-        column(
-          width = 10,
-          div(class = "loci_table",
-              dataTableOutput("gs_isolate_table"))
-        )
-      )
-    } else {NULL}
-  })
-  
-  # Resistance profile table output display
-  output$gs_profile_display <- renderUI({
-    req(DB$data)
-    if(!is.null(DB$meta_gs) & !is.null(input$gs_view)) {
-      if(input$gs_view == "Table") {
-        column(
-          width = 10,
-          hr(), 
-          fluidRow(
-            column(
-              width = 4,
-              p(
-                HTML(
-                  paste0("<span style='color: white; font-size: 18px'>", 
-                         "Gene Screening Results</br>",
-                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
-                         "Comprising genes for resistance, virulence, stress, etc.")
-                )
-              )
-            ),
-            column(
-              width = 4,
-              uiOutput("gs_download")
-            )
-          ),
-          br(),
-          uiOutput("gs_results_table")
-        )
-      } else {
-        column(
-          width = 10,
-          fluidRow(
-            column(
-              width = 4,
-              p(
-                HTML(
-                  paste0("<span style='color: white; font-size: 18px'>", 
-                         "Gene Screening Results</br>",
-                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
-                         "Comprising genes for resistance, virulence, stress, etc.")
-                )
-              )
-            ),
-            column(
-              width = 4,
-              div(
-                class = "gs-picker",
-                pickerInput(
-                  "gs_profile_select",
-                  "",
-                  choices = list(
-                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
-                    },
-                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
-                    },
-                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
-                    }
-                  ),
-                  choicesOpt = list(
-                    disabled = c(
-                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
-                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
-                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
-                    )
-                  ),
-                  options = list(
-                    `live-search` = TRUE,
-                    size = 10,
-                    style = "background-color: white; border-radius: 5px;"
-                  )
-                )
-              )
-            ),
-            column(
-              width = 3,
-              uiOutput("gs_download")
-            )
-          ),
-          br(),
-          uiOutput("gs_results_table")
-        )
-      }
-    } else {NULL}
-  })
-  
-  # Screening sidebar
-  output$screening_sidebar <- renderUI({
-    req(DB$data)
-    if(!is.null(DB$meta_gs)) {
-      column(
-        width = 12,
-        align = "center",
-        br(), br(),
-        p(
-          HTML(
-            paste(
-              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Toggle View')
-            )
-          )
-        ),
-        radioGroupButtons(
-          inputId = "gs_view",
-          choices = c("Picker", "Table"),
-          selected = "Picker",
-          checkIcon = list(
-            yes = icon("square-check"),
-            no = icon("square")
-          )
-        ),
-        br()
-      )
-    } else {NULL}
-  })
-  
-  # Resistance profile table
-  observe({
-    req(DB$meta_gs, Screening$selected_isolate, DB$database, DB$scheme, DB$data)
-    
-    if(length(Screening$selected_isolate) > 0 & any(Screening$selected_isolate %in% DB$data$`Assembly ID`)) {
-      iso_select <- Screening$selected_isolate
-      iso_path <- file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
-                            iso_select, "resProfile.tsv")
-      
-      res_profile <- read.delim(iso_path)
-      
-      colnames(res_profile) <- c(
-        "Protein Identifier",	"Contig ID", "Start", "Stop", "Strand", "Gene Symbol", 
-        "Sequence Name", "Scope", "Element Type",  "Element Subtype", "Class", 
-        "Subclass", "Method", "Target Length", "RSL",	"%CRS", "%IRS", 
-        "Alignment Length", "ACS", "Name of Closest Sequence", "HMM ID", "HMM Description")
-      
-      Screening$res_profile <- res_profile %>%
-        relocate(c("Gene Symbol", "Sequence Name", "Element Subtype", "Class", 
-                   "Subclass", "Scope", "Contig ID", "Target Length", "Alignment Length",
-                   "Start", "Stop", "Strand"))
-      
-      # Generate gene profile table
-      output$gs_profile_table <- DT::renderDataTable(
-        Screening$res_profile,
-        selection = "single",
-        rownames= FALSE,
-        options = list(pageLength = 10, scrollX = TRUE,
-                       autoWidth = TRUE,
-                       columnDefs = list(list(width = '400px', targets = c("Sequence Name",
-                                                                           "Name of Closest Sequence"))),
-                       columnDefs = list(list(width = 'auto', targets = "_all")),
-                       columnDefs = list(list(searchable = TRUE,
-                                              targets = "_all")),
-                       initComplete = DT::JS(
-                         "function(settings, json) {",
-                         "$('th:first-child').css({'border-top-left-radius': '5px'});",
-                         "$('th:last-child').css({'border-top-right-radius': '5px'});",
-                         # "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                         # "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                         "}"
-                       ),
-                       drawCallback = DT::JS(
-                         "function(settings) {",
-                         # "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                         # "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                         "}"
-                       ))
-      )
-    } else {
-      output$gs_profile_table <- NULL
-    }
-  })
-
-  #Resistance profile selection table
-  observe({
-    req(DB$meta, DB$data)
-    output$gs_isolate_table <- renderDataTable(
-      select(DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ], -c(3, 4, 10, 11, 12)),
-      selection = "single",
-      rownames= FALSE,
-      options = list(pageLength = 10,
-                     columnDefs = list(list(searchable = TRUE,
-                                            targets = "_all")),
-                     initComplete = DT::JS(
-                       "function(settings, json) {",
-                       "$('th:first-child').css({'border-top-left-radius': '5px'});",
-                       "$('th:last-child').css({'border-top-right-radius': '5px'});",
-                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                       "}"
-                     ),
-                     drawCallback = DT::JS(
-                       "function(settings) {",
-                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                       "}"
-                     ))
-    )
-  })
-  
-  observe({
-    req(input$screening_res_sel, DB$database, DB$scheme, DB$data)
-    if(!is.null(Screening$status_df) &
-       !is.null(input$screening_res_sel) & 
-       !is.null(Screening$status_df$status) & 
-       !is.null(Screening$status_df$isolate)) {
-      if(length(input$screening_res_sel) > 0) {
-        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
-          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
-            results <- read.delim(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
-                                            input$screening_res_sel, "resProfile.tsv"))
-            
-            output$screening_table <- renderDataTable(
-              select(results, c(6, 7, 8, 9, 11)),
-              selection = "single",
-              options = list(pageLength = 10,
-                             columnDefs = list(list(searchable = TRUE,
-                                                    targets = "_all")),
-                             initComplete = DT::JS(
-                               "function(settings, json) {",
-                               "$('th:first-child').css({'border-top-left-radius': '5px'});",
-                               "$('th:last-child').css({'border-top-right-radius': '5px'});",
-                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                               "}"
-                             ),
-                             drawCallback = DT::JS(
-                               "function(settings) {",
-                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                               "}"
-                             )))
-          } else {output$screening_table <- NULL}
-        }
-      } else {
-        output$screening_table <- NULL
-      }
-    } else {
-      output$screening_table <- NULL
-    }
-      
-  })
-  
-  # Availablity feedback
-  output$gene_screening_info <- renderUI({
-    req(DB$data)
-    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
-      p(
-        HTML(
-          paste(
-            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
-          )
-        )
-      )
-    } else {
-      p(
-        HTML(
-          paste(
-            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
-          )
-        )
-      )
-    }
-  })
-  
-  output$gene_resistance_info <- renderUI({
-    req(DB$data)
-    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
-      p(
-        HTML(
-          paste(
-            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
-          )
-        )
-      )
-    } else {
-      p(
-        HTML(
-          paste(
-            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
-          )
-        )
-      )
-    }
-  })
-  
-  # Screening Interface
-  
-  output$screening_interface <- renderUI({
-    req(DB$data)
-    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
-      column(
-        width = 12,
-        fluidRow(
-          column(1),
-          column(
-            width = 3,
-            align = "center",
-            br(), br(),
-            p(
-              HTML(
-                paste(
-                  tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Isolates for Screening')
-                )
-              )
-            ),
-            if(Screening$picker_status) {
-              div(
-                class = "screening_div",
-                pickerInput(
-                  "screening_select",
-                  "",
-                  choices = list(
-                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
-                    },
-                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
-                    },
-                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
-                    }
-                  ),
-                  choicesOpt = list(
-                    disabled = c(
-                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
-                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
-                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
-                    )
-                  ),
-                  options = list(
-                    `live-search` = TRUE,
-                    `actions-box` = TRUE,
-                    size = 10,
-                    style = "background-color: white; border-radius: 5px;"
-                  ),
-                  multiple = TRUE
-                )
-              )
-            } else {
-              div(
-                class = "screening_div",
-                pickerInput(
-                  "screening_select",
-                  "",
-                  choices = Screening$picker_choices,
-                  selected = Screening$picker_selected,
-                  options = list(
-                    `live-search` = TRUE,
-                    `actions-box` = TRUE,
-                    size = 10,
-                    style = "background-color: white; border-radius: 5px;"
-                  ),
-                  multiple = TRUE
-                ) 
-              )
-            },
-            br(), br(),
-            uiOutput("genome_path_gs")
-          ),
-          column(
-            width = 3,
-            uiOutput("screening_start")
-          ),
-          column(
-            width = 3,
-            align = "center",
-            br(), br(),
-            uiOutput("screening_result_sel")
-          ),
-          column(1)
-        ),
-        fluidRow(
-          column(1),
-          column(
-            width = 10,
-            br(), br(), 
-            uiOutput("screening_result"),
-            br(), br(), br(), br()
-          )
-        )
-      )
-    }
-  })
-  
-  ### Screening Events ----
-  
-  observe({
-    req(DB$data, input$gs_view)
-    if(input$gs_view == "Table") {
-      meta_gs <- DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ]
-      Screening$selected_isolate <- meta_gs$`Assembly ID`[input$gs_isolate_table_rows_selected]
-    } else if(input$gs_view == "Picker") {
-      Screening$selected_isolate <- input$gs_profile_select
-    }
-  })
-  
-  output$download_resistance_profile <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save resistance profile table ", Screening$selected_isolate, "_Profile.csv"))
-      
-      paste0(format(Sys.Date()), "_", Screening$selected_isolate, "_Profile.csv")
-    },
-    content = function(file) {
-      write.table(
-        Screening$res_profile,
-        file, 
-        sep = ";",
-        row.names = FALSE, 
-        quote = FALSE
-      ) 
-    }
-  )
-  
-  # Reset screening 
-  observeEvent(input$screening_reset_bttn, {
-    log_print("Reset gene screening")
-    
-    # reset status file
-    sapply(Screening$status_df$isolate, remove.screening.status)
-    
-    # set feedback variables
-    Screening$status <- "idle"
-    Screening$status_df <- NULL
-    Screening$choices <- NULL
-    Screening$picker_status <- TRUE
-    Screening$first_result <- NULL
-    
-    # change reactive UI
-    output$screening_table <- NULL
-    output$screening_result <- NULL
-    output$screening_fail <- NULL
-    
-    updatePickerInput(session, "screening_select", selected = character(0))
-    
-    # disable isolate picker
-    shinyjs::runjs("$('#screening_select').prop('disabled', false);")
-    shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
-  })
-  
-  # Cancel screening
-  observeEvent(input$screening_cancel, {
-    showModal(
-      modalDialog(
-        paste0(
-          "Gene screening is still pending. Stopping this process will cancel the screening."
-        ),
-        title = "Reset Multi Typing",
-        fade = TRUE,
-        easyClose = TRUE,
-        footer = tagList(
-          modalButton("Cancel"),
-          actionButton("conf_screening_cancel", "Stop", class = "btn btn-danger")
-        )
-      )
-    )
-  })
-  
-  observeEvent(input$conf_screening_cancel, {
-    log_print("Cancelled gene screening")
-    removeModal()
-    
-    show_toast(
-      title = "Gene Screening Terminated",
-      type = "warning",
-      position = "bottom-end",
-      timer = 6000
-    )
-    
-    # terminate screening
-    system(paste("kill $(pgrep -f 'execute/screening.sh')"), wait = FALSE)
-    system(paste("killall -TERM tblastn"), wait = FALSE)
-    
-    # reset status file
-    sapply(Screening$status_df$isolate, remove.screening.status)
-    
-    # set feedback variables
-    Screening$status <- "idle"
-    Screening$status_df <- NULL
-    Screening$choices <- NULL
-    Screening$picker_status <- TRUE
-    Screening$first_result <- NULL
-    
-    # change reactive UI
-    output$screening_table <- NULL
-    output$screening_result <- NULL
-    
-    updatePickerInput(session, "screening_select", selected = character(0))
-    
-    # disable isolate picker
-    shinyjs::runjs("$('#screening_select').prop('disabled', false);")
-    shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
-  })
-  
-  # Get selected assembly
-  observe({
-    req(DB$data, Screening$status)
-    if (length(input$screening_select) < 1) {
-      output$genome_path_gs <- renderUI(HTML(
-        paste("<span style='color: white; font-style:italic'>", length(input$screening_select), " isolate(s) queried for screening")
-      ))
-      
-      output$screening_start <- NULL
-      
-    } else if (length(input$screening_select) > 0) {
-      
-      output$screening_start <- renderUI({
-        
-        fluidRow(
-          column(
-            width = 12,
-            br(), br(), 
-            if(length(input$screening_select) < 1) {
-              column(
-                width = 12,
-                align = "center",
-                p(
-                  HTML(paste(
-                    '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-                    paste("<span style='color: white; font-style:italic'>", 
-                          "&nbsp Select Isolate(s) for Screening")))
-                )
-              )
-            } else if(Screening$status == "finished") {
-              column(
-                width = 12,
-                align = "center",
-                p(
-                  HTML(paste(
-                    '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:white"></i>',
-                    paste("<span style='color: white; font-style:italic'>", 
-                          "&nbsp Reset to Perform Screening Again")))
-                ),
-                actionButton(
-                  "screening_reset_bttn",
-                  "Reset",
-                  icon = icon("arrows-rotate")
-                ),
-                if(!is.null(Screening$status_df)) {
-                  p(
-                    HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
-                               sum(Screening$status_df$status != "unfinished"), "/",
-                               nrow(Screening$status_df), " Isolate(s) screened"))
-                  )
-                }
-              )
-            } else if(Screening$status == "idle") {
-              column(
-                width = 12,
-                align = "center",
-                p(
-                  HTML(paste(
-                    '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
-                    paste("<span style='color: white;'>",
-                          "&nbsp Screening Ready")))
-                ),
-                actionButton(
-                  inputId = "screening_start_button",
-                  label = "Start",
-                  icon = icon("circle-play")
-                )
-              )
-            } else if(Screening$status == "started") {
-              column(
-                width = 12,
-                align = "center",
-                p(
-                  HTML(paste(
-                    '<i class="fa-solid fa-clock" style="font-size:15px;color:white"></i>',
-                    paste("<span style='color: white;'>",
-                          "&nbsp Running Screening ...")))
-                ),
-                fluidRow(
-                  column(3),
-                  column(
-                    width = 3,
-                    actionButton(
-                      inputId = "screening_cancel",
-                      label = "Terminate",
-                      icon = icon("ban")
-                    )
-                  ),
-                  column(
-                    width = 3,
-                    HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:22px;color:white;margin-top:27px;position:relative;left:20px"></i>'))
-                  )
-                ),
-                if(!is.null(Screening$status_df)) {
-                  p(
-                    HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
-                               sum(Screening$status_df$status != "unfinished"), "/",
-                               nrow(Screening$status_df), " isolate(s) screened"))
-                  )
-                }
-              )
-            }
-          )
-        )
-      })
-    } else {NULL}
-  })
-  
-  #### Running Screening ----
-  
-  observeEvent(input$screening_start_button, {
-    
-    if(tail(readLogFile(), 1) != "0") {
-      show_toast(
-        title = "Pending Multi Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
-      show_toast(
-        title = "Pending Single Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      
-      log_print("Started gene screening")
-      
-      Screening$status <- "started"
-      Screening$picker_choices <- list(
-        Unscreened = if (sum(DB$data$Screened == "No") == 1) {
-          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
-        } else {
-          DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
-        },
-        Screened =  if (sum(DB$data$Screened == "Yes") == 1) {
-          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
-        } else {
-          DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
-        },
-        `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
-          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
-        } else {
-          DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
-        }
-      )
-      Screening$picker_selected <- input$screening_select
-      Screening$picker_status <- FALSE
-      
-      show_toast(
-        title = "Gene screening started",
-        type = "success",
-        position = "bottom-end",
-        timer = 6000
-      )
-      
-      Screening$meta_df <- data.frame(wd = getwd(),
-                                 selected = paste(
-                                   file.path(DB$database, gsub(" ", "_", DB$scheme),
-                                             "Isolates", input$screening_select,
-                                             paste0(input$screening_select, ".zip")), 
-                                   collapse = " "),
-                                 species = gsub(" ", "_", DB$scheme))
-      
-      Screening$status_df <- data.frame(isolate = basename(gsub(".zip", "", str_split_1(Screening$meta_df$selected, " "))), 
-                                        status = "unfinished")
-      
-       # Reset screening status
-      sapply(Screening$status_df$isolate, remove.screening.status)
-      
-      saveRDS(Screening$meta_df, paste0(getwd(), "/execute/screening_meta.rds"))
-      
-      # Disable pickerInput
-      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').prop('disabled', true);"))
-      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').selectpicker('refresh');"))
-    
-      # System execution screening.sh
-      system(paste("bash", paste0(getwd(), "/execute/screening.sh")), wait = FALSE)
-    }
-  })
-  
-  observe({
-    req(DB$data, Screening$status, input$screening_res_sel, Screening$status_df)
-    if(!is.null(Screening$status_df) &
-       !is.null(Screening$status_df$status) & 
-       !is.null(Screening$status_df$isolate) &
-       !is.null(input$screening_res_sel)) {
-      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
-        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
-          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
-            output$screening_result <- renderUI(
-              column(
-                width = 12,
-                hr(), br(),
-                dataTableOutput("screening_table") 
-              )
-            )
-          } else {
-            output$screening_result <- renderUI(
-              column(
-                width = 12,
-                hr(), br(),
-                verbatimTextOutput("screening_fail")
-              )
-            )
-          }
-        }
-      } else {
-        output$screening_result <- NULL
-      }
-    } else {
-      output$screening_result <- NULL
-    }
-  })
-  
-  observe({
-    req(DB$data, Screening$status, input$screening_res_sel)
-    if(!is.null(Screening$status_df) &
-       !is.null(Screening$status_df$status) & 
-       !is.null(Screening$status_df$isolate) &
-       !is.null(input$screening_res_sel)) {
-      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
-        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
-          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "fail") {
-            output$screening_fail <- renderPrint({
-              cat(paste(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
-                                            "Isolates", input$screening_res_sel, "status.txt")),"\n"))
-            })
-          }
-        }
-      } else {
-        output$screening_fail <- NULL
-      }
-    } else {
-      output$screening_fail <- NULL
-    }
-  })
-  
-  observe({
-    req(DB$data)
-    if(!is.null(Screening$status)) {
-      if(Screening$status != "idle") {
-        
-        # start status screening for user feedback
-        check_screening()
-        
-        if(isTRUE(Screening$first_result)) {
-          output$screening_result_sel <- renderUI(
-            column(
-              width = 12,
-              align = "center",
-              selectInput(
-                "screening_res_sel",
-                label = h5("Select Result", style = "color:white; margin-bottom: 28px; margin-top: -10px;"),
-                choices = ""
-              ),
-              if(!is.null(Screening$status_df)) {
-                p(HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
-                             if(sum(Screening$status_df$status == "success") == 1) {
-                               "1 success &nbsp / &nbsp"
-                             } else {
-                               paste0(sum(Screening$status_df$status == "success"), " successes &nbsp / &nbsp")
-                             },
-                             if(sum(Screening$status_df$status == "fail") == 1) {
-                               "1 failure"
-                             } else {
-                               paste0(sum(Screening$status_df$status == "fail"), " failures")
-                             })))
-              }
-            )
-          )
-          
-          Screening$first_result <- FALSE
-        }
-      } else if(Screening$status == "idle") {
-        output$screening_result_sel <- NULL
-      }
-    }
-  }) 
-    
-  check_screening <- reactive({
-    invalidateLater(500, session)
-    
-    req(Screening$status_df)
-    
-    if(Screening$status == "started") {
-      
-      Screening$status_df$status <- sapply(Screening$status_df$isolate, check_status)
-      
-      if(any("unfinished" != Screening$status_df$status) &
-         !identical(Screening$choices, Screening$status_df$isolate[which(Screening$status_df$status != "unfinished")])) {
-        
-        status_df <- Screening$status_df[which(Screening$status_df$status != "unfinished"),]
-        
-        Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
-                                                                 Screening$status_df$status == "fail")]
-        
-        if(sum(Screening$status_df$status != "unfinished") > 0) {
-          if(is.null(Screening$first_result)) {
-            Screening$first_result <- TRUE
-          }
-        }
-        
-        if(tail(status_df$status, 1) == "success") {
-          
-          # Changing "Screened" metadata variable in database
-          Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
-          
-          Database[["Typing"]]$Screened[which(Database[["Typing"]]["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
-
-          saveRDS(Database, file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
-
-          DB$data$Screened[which(DB$data["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
-          
-          DB$meta_gs <- select(DB$data, c(1, 3:13))
-          DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-          DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-          
-          show_toast(
-            title = paste("Successful screening of", tail(Screening$choices, 1)),
-            type = "success",
-            position = "bottom-end",
-            timer = 6000)
-          
-          updateSelectInput(session = session,
-                            inputId = "screening_res_sel",
-                            choices = Screening$choices,
-                            selected = tail(Screening$choices, 1))
-          
-        } else if(tail(status_df$status, 1) == "fail") {
-          
-          show_toast(
-            title = paste("Failed screening of", tail(status_df$isolate, 1)),
-            type = "error",
-            position = "bottom-end",
-            timer = 6000)
-          
-          updateSelectInput(session = session,
-                            inputId = "screening_res_sel",
-                            choices = Screening$choices,
-                            selected = tail(Screening$choices, 1))
-        }
-        
-        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
-          Screening$status <- "finished"
-        }
-      } else {
-        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
-          Screening$status <- "finished"
-        }
-      }
-      
-      if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
-        Screening$status <- "finished"
-      }
-    }
-  }) 
-  
-  
-  # _______________________ ####
-  
-  ## Typing  ----
-  
-  # Render Single/Multi Switch
-  
-  readLogFile <- reactive({
-    invalidateLater(5000, session)
-    readLines(paste0(getwd(), "/logs/script_log.txt"))
-  })
-  
-  # Render sidebar dependent on data presence
-  # No sidebar
-  output$typing_sidebar <- renderUI({
-    if(!is.null(DB$exist)) {
-      if(DB$exist) {
-        NULL
-      } else {
-        column(
-          width = 12,
-          align = "center",
-          br(), br(),
-          p(
-            HTML(
-              paste(
-                tags$span(style='color: white; font-size: 18px; margin-bottom: 0px', 'Typing Mode')
-              )
-            )
-          ),
-          radioGroupButtons(
-            inputId = "typing_mode",
-            choices = c("Single", "Multi"),
-            selected = "Single",
-            checkIcon = list(
-              yes = icon("square-check"),
-              no = icon("square")
-            )
-          ),
-          br()
-        )
-      }
-    }
-    
-  })
-  
-  # No db typing message
-  output$typing_no_db <- renderUI({
-    if(!is.null(DB$exist)) {
-      if(DB$exist) {
-        column(
-          width = 4,
-          align = "left",
-          br(),
-          br(),
-          br(),
-          br(),
-          p(
-            HTML(
-              paste0(
-                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 50px', 'To initiate allelic typing, a cgMLST scheme must be downloaded first.'
-                )
-              )
-            )
-          )
-        )
-      } else {NULL}
-    } else {NULL}
-  })
-  
-  ### Single Typing ----
-  
-  #### Render UI Elements ----
-  
-  # Render single typing naming issues
-  output$single_select_issues <- renderUI({
-    req(input$assembly_id)
-    
-    if(nchar(trimws(input$assembly_id)) < 1) {
-      ass_id <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
-    } else {
-      ass_id <- trimws(input$assembly_id)
-    }
-    
-    if(ass_id %in% unlist(DB$data["Assembly ID"])) {
-      HTML(paste(
-        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-        paste("<span style='color: white; font-style:italic'>", 
-              "&nbsp Assembly ID already present in database.")))
-    } else if (ass_id == "") {
-      HTML(paste(
-        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-        paste("<span style='color: white; font-style:italic'>", 
-              "&nbsp Empty Assembly ID.")))
-    } else if (grepl("[()/\\:*?\"<>|]", ass_id)) {
-      HTML(paste(
-        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-        paste("<span style='color: white; font-style:italic'>", 
-              "&nbsp Invalid Assembly ID. Avoid special characters.")))
-    } else if(grepl(" ", ass_id)) {
-      HTML(paste(
-        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-        paste("<span style='color: white; font-style:italic'>", 
-              "&nbsp Invalid Assembly ID. Avoid empty spaces.")))
-    } else {HTML(paste(
-      '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
-      paste("<span style='color: white; font-style:italic'>",
-            "&nbsp Assembly ID compatible with local database.")))}
-  })
-  
-  # Render Typing Results if finished
-  observe({
-    if(Typing$progress_format_end == 999999) {
-      if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
-        if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
-          output$typing_result_table <- renderRHandsontable({
-            Typing$typing_result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
-            Typing$typing_result_table <- mutate_all(Typing$typing_result_table, as.character)
-            if(nrow(Typing$typing_result_table) > 0) {
-              if(nrow(Typing$typing_result_table) > 15) {
-                rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
-                              stretchH = "all", height = 500, readOnly = TRUE,
-                              contextMenu = FALSE) %>%
-                  hot_cols(columnSorting = TRUE) %>%
-                  hot_rows(rowHeights = 25) %>%
-                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter",
-                          cellWidths = list(100, 160, NULL)) %>%
-                  hot_col("Value", renderer=htmlwidgets::JS(
-                    "function(instance, td, row, col, prop, value, cellProperties) {
-                      if (value.length > 8) {
-                        value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                      }
-                      td.innerHTML = value;
-                      td.style.textAlign = 'center';
-                      return td;
-                     }"
-                  ))
-              } else {
-                rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
-                              stretchH = "all", readOnly = TRUE,
-                              contextMenu = FALSE,) %>%
-                  hot_cols(columnSorting = TRUE) %>%
-                  hot_rows(rowHeights = 25) %>%
-                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter",
-                          cellWidths = list(100, 160, NULL)) %>%
-                  hot_col("Value", renderer=htmlwidgets::JS(
-                    "function(instance, td, row, col, prop, value, cellProperties) {
-                      if (value.length > 8) {
-                        value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                      }
-                      td.innerHTML = value;
-                      td.style.textAlign = 'center';
-                      return td;
-                     }"
-                  ))
-              }
-            }
-          })
-          
-          output$single_typing_results <- renderUI({
-            result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
-            number_events <- nrow(result_table)
-            
-            n_new <- length(grep("New Variant", result_table$Event))
-            
-            n_missing <- number_events - n_new
-            
-            # Show results table only if successful typing 
-            if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
-              if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
-                if(number_events > 0) {
-                  column(
-                    width = 12,
-                    HTML(paste("<span style='color: white;'>", 
-                               length(Typing$scheme_loci_f) - number_events,
-                               "loci were assigned a variant from local scheme.")),
-                    br(), 
-                    HTML(paste("<span style='color: white;'>", 
-                               n_missing,
-                               if(n_missing == 1) " locus not assigned (<i>NA</i>)." else " loci not assigned (<i>NA</i>).")),
-                    br(),
-                    HTML(paste("<span style='color: white;'>", 
-                               n_new,
-                               if(n_new == 1) " locus with new variant."  else " loci with new variants.")),
-                    br(), br(),
-                    rHandsontableOutput("typing_result_table")
-                  )
-                } else {
-                  column(
-                    width = 12,
-                    HTML(paste("<span style='color: white;'>", 
-                               length(Typing$scheme_loci_f),
-                               "successfully assigned from local scheme."))
-                  )
-                }
-              }
-            }
-          })
-          
-        } else {
-          
-          output$single_typing_results <- NULL
-          
-        }
-      } else {
-        output$single_typing_results <- NULL
-      }
-    }
-    
-  })
-  
-  # Render Initiate Typing UI
-  output$initiate_typing_ui <- renderUI({
-    column(
-      width = 4,
-      align = "center",
-      br(),
-      br(),
-      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-      br(),
-      br(),
-      p(
-        HTML(
-          paste(
-            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File (FASTA)')
-          )
-        )
-      ),
-      fluidRow(
-        column(1),
-        column(
-          width = 11,
-          align = "center",
-          shinyFilesButton(
-            "genome_file",
-            "Browse" ,
-            icon = icon("file"),
-            title = "Select the assembly in .fasta/.fna/.fa format:",
-            multiple = FALSE,
-            buttonType = "default",
-            class = NULL,
-            root = path_home()
-          ),
-          br(),
-          br(),
-          uiOutput("genome_path"),
-          br()
-        )
-      )
-    )
-  })
-  
-  # Render Declare Metadata UI
-  
-  observe({
-    if (nrow(Typing$single_path) < 1) {
-      output$genome_path <- renderUI(HTML(
-        paste("<span style='color: white; margin-left:-30px'>", "No file selected.")
-      ))
-      
-      # dont show subsequent metadata declaration and typing start UI
-      output$metadata_single_box <- NULL
-      output$start_typing_ui <- NULL
-      
-    } else if (nrow(Typing$single_path) > 0) {
-      
-      if (str_detect(str_sub(Typing$single_path$name, start = -6), ".fasta") | 
-          str_detect(str_sub(Typing$single_path$name, start = -6), ".fna") | 
-          str_detect(str_sub(Typing$single_path$name, start = -6), ".fa")) {
-        
-        # Render selected assembly path
-        output$genome_path <- renderUI({
-          HTML(
-            paste(
-              "<span style='color: white; margin-left:-30px; font-weight: bolder'>",
-              as.character(Typing$single_path$name)
-            )
-          )
-        })
-        
-        # Render metadata declaration box
-        output$metadata_single_box <- renderUI({
-          
-          # Render placeholder 
-          updateTextInput(session, "assembly_id", value = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
-          updateTextInput(session, "assembly_name", value = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
-          
-          column(
-            width = 3,
-            align = "center",
-            br(), br(),
-            h3(p("Declare Metadata"), style = "color:white; margin-left:-40px"),
-            br(), br(),
-            div(
-              class = "multi_meta_box",
-              box(
-                solidHeader = TRUE,
-                status = "primary",
-                width = "90%",
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput("assembly_id",
-                                value = "",
-                                label = "",
-                                width = "80%")
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 12,
-                    uiOutput("single_select_issues")
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput("assembly_name",
-                                label = "",
-                                width = "80%")
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      dateInput("append_isodate",
-                                label = "",
-                                width = "80%",
-                                max = Sys.Date())
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput("append_host",
-                                label = "",
-                                width = "80%")
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table_country",
-                      pickerInput(
-                        "append_country",
-                        label = "",
-                        choices = list("Common" = sel_countries,
-                                       "All Countries" = country_names),
-                        options = list(
-                          `live-search` = TRUE,
-                          `actions-box` = TRUE,
-                          size = 10,
-                          style = "background-color: white; border-radius: 5px;"
-                        ),
-                        width = "90%"
-                      )
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput(
-                        "append_city",
-                        label = "",
-                        width = "80%"
-                      )
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 12,
-                    align = "center",
-                    br(), br(),
-                    actionButton(
-                      inputId = "conf_meta_single",
-                      label = "Confirm"
-                    ),
-                    br()
-                  )
-                ),
-                br()
-              )
-            )
-          )
-        })
-      } else {
-        show_toast(
-          title = "Wrong file type (only fasta/fna/fa)",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-      }
-    }
-  })
-  
-  # Get genome datapath
-  
-  observe({
-    # Get selected Genome in Single Mode
-    shinyFileChoose(input,
-                    "genome_file",
-                    roots = c(Home = path_home(), Root = "/"),
-                    defaultRoot = "Home",
-                    session = session,
-                    filetypes = c('', 'fasta', 'fna', 'fa'))
-    Typing$single_path <- parseFilePaths(roots = c(Home = path_home(), Root = "/"), input$genome_file)
-    
-  })
-  
-  #### Run blat ----
-  
-  observeEvent(input$typing_start, {
-    
-    log_print("Input typing_start")
-    
-    if(tail(readLogFile(), 1) != "0") {
-      show_toast(
-        title = "Pending Multi Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if (Screening$status == "started") {
-      show_toast(
-        title = "Pending Gene Screening",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      
-      if(!is.null(DB$data)) {
-        if(sum(apply(DB$data, 1, anyNA)) >= 1) {
-          DB$no_na_switch <- TRUE
-        } else {
-          DB$no_na_switch <- FALSE
-        }
-      }
-      
-      # Activate entry detection
-      DB$check_new_entries <- TRUE
-      
-      Typing$single_end <- FALSE
-      
-      Typing$progress_format_start <- 0
-      Typing$progress_format_end <- 0
-      
-      # Remove Initiate Typing UI 
-      output$initiate_typing_ui <- NULL
-      output$metadata_single_box <- NULL
-      output$start_typing_ui <- NULL
-      
-      # status feedback
-      Typing$status <- "Processing"
-      
-      # Locate folder containing cgMLST scheme
-      search_string <- paste0(gsub(" ", "_", DB$scheme), "_alleles")
-      
-      scheme_folders <- dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme)))
-      
-      if (any(grepl(search_string, scheme_folders))) {
-        
-        # reset results file 
-        if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
-          unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
-        }
-        
-        # blat initiate index
-        scheme_select <- as.character(scheme_folders[which(grepl(search_string, scheme_folders))])
-        
-        show_toast(
-          title = "Typing Initiated",
-          type = "success",
-          position = "bottom-end",
-          timer = 6000
-        )
-        
-        log_print("Initiated single typing")
-        
-        ### Run blat Typing
-        
-        single_typing_df <- data.frame(
-          db_path = DB$database,
-          wd = getwd(),
-          save = input$save_assembly_st,
-          scheme = paste0(gsub(" ", "_", DB$scheme)),
-          genome = Typing$single_path$datapath,
-          alleles = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", search_string)
-        )
-        
-        saveRDS(single_typing_df, "execute/single_typing_df.rds")
-        
-        # Execute single typing script
-        system(paste("bash", paste0(getwd(), "/execute/single_typing.sh")), 
-               wait = FALSE)
-        
-        scheme_loci <- list.files(path = scheme_select, full.names = TRUE)
-        
-        # Filter the files that have FASTA extensions
-        Typing$scheme_loci_f <-
-          scheme_loci[grep("\\.(fasta|fa|fna)$", scheme_loci, ignore.case = TRUE)]
-        
-        output$single_typing_progress <- renderUI({
-          fluidRow(
-            br(), br(), 
-            column(width = 1),
-            column(
-              width = 3,
-              h3(p("Pending Single Typing ..."), style = "color:white")
-            ),
-            br(), br(), br(), 
-            fluidRow(
-              column(width = 1),
-              column(
-                width = 4,
-                br(), br(), br(),
-                fluidRow(
-                  column(
-                    width = 12,
-                    uiOutput("reset_single_typing"),
-                    HTML(
-                      paste(
-                        "<span style='color: white; font-weight: bolder'>",
-                        as.character(Typing$single_path$name)
-                      )
-                    ),
-                    br(), br(),
-                    progressBar(
-                      "progress_bar",
-                      value = 0,
-                      display_pct = TRUE,
-                      title = ""
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 12,
-                    uiOutput("typing_formatting"),
-                    uiOutput("typing_fin")
-                  )
-                )
-              ),
-              column(1),
-              column(
-                width = 5,
-                br(), br(), br(),
-                uiOutput("single_typing_results")
-              )
-            )
-          )
-        })
-      } else {
-        log_print("Folder containing cgMLST alleles not in working directory")
-        
-        show_alert(
-          title = "Error",
-          text = paste0(
-            "Folder containing cgMLST alleles not in working directory.",
-            "\n",
-            "Download cgMLST Scheme for selected Organism first."
-          ),
-          type = "error"
-        )
-      }
-    }
-  })
-  
-  # Function to update Progress Bar
-  update <- reactive({
-    invalidateLater(3000, session)
-    
-    # write progress in process tracker
-    cat(
-      c(length(list.files(paste0(getwd(), "/execute/blat_single/results"))),
-        readLines(paste0(getwd(), "/logs/progress.txt"))[-1]), 
-      file = paste0(getwd(), "/logs/progress.txt"),
-      sep = "\n"
-    )
-    
-    progress <- readLines(paste0(getwd(), "/logs/progress.txt"))
-    
-    # if typing with blat is finished -> "attaching" phase started
-    if(!is.na(progress[1])) {
-      if(!is.na(progress[2])) {
-        if(progress[2] == "888888") {
-          Typing$progress_format_start <- progress[2]
-          Typing$pending_format <- progress[2]
-          Typing$status <- "Attaching"
-        }
-      }
-      # "attaching" phase completed
-      if(!is.na(progress[3])) {
-        if(progress[3] == "999999") {
-          Typing$progress_format_end <- progress[3]
-          Typing$entry_added <- progress[3]
-          Typing$status <- "Finalized"
-        }
-      }
-      Typing$progress <- as.numeric(progress[1])
-      floor((Typing$progress / length(Typing$scheme_loci_f)) * 100)
-    } else {
-      floor((Typing$progress / length(Typing$scheme_loci_f)) * 100)
-    }
-  })
-  
-  # Observe Typing Progress
-  observe({
-    
-    if(readLogFile()[1] == "0") {
-      # Update Progress Bar
-      updateProgressBar(
-        session = session,
-        id = "progress_bar",
-        value = update(),
-        total = 100,
-        title = paste0(as.character(Typing$progress), "/", length(Typing$scheme_loci_f), " loci screened")
-      )
-    }
-    
-    if (Typing$progress_format_start == 888888) {
-      output$typing_formatting <- renderUI({
-        column(
-          width = 12,
-          align = "center",
-          br(),
-          fluidRow(
-            column(
-              width = 6,
-              HTML(paste("<span style='color: white;'>", "Transforming data ..."))
-            ),
-            column(
-              width = 3,
-              align = "left",
-              HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px;color:white"></i>'))
-            )
-          )
-        )
-      })
-    } else {
-      output$typing_formatting <- NULL
-    }
-    
-    # Render when finalized  
-    if (Typing$progress_format_end == 999999) {
-      
-      output$typing_formatting <- NULL
-      
-      output$typing_fin <- renderUI({
-        fluidRow(
-          column(
-            width = 12,
-            align = "center",
-            br(), br(),
-            if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
-              if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
-                req(Typing$scheme_loci_f, Typing$typing_result_table)
-                if(sum(Typing$typing_result_table$Event != "New Variant") >  (0.5 * length(Typing$scheme_loci_f))){
-                  HTML(
-                    paste("<span style='color: white;'>", 
-                          sub(".*Successful", "Finished", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
-                          paste("<span style='color: orange;'>", "Warning: Isolate contains large number of failed allele assignments."),
-                          paste("<span style='color: white;'>", "Reset to start another typing process."),
-                          sep = '<br/>\n'))                    
-                } else {
-                  HTML(paste("<span style='color: white;'>", 
-                             sub(".*Successful", "Successful", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
-                             "Reset to start another typing process.", sep = '<br/>'))
-                }
-              } else {
-                HTML(paste("<span style='color: white;'>", 
-                           sub(".*typing", "Typing", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
-                           "Reset to start another typing process.", sep = '<br/>'))
-              }
-            },
-            br(), br(),
-            actionButton(
-              "reset_single_typing",
-              "Reset",
-              icon = icon("arrows-rotate")
-            )
-          )
-        )
-      })
-    } else {
-      output$typing_fin <- NULL
-      output$single_typing_results <- NULL
-    }
-    
-  })
-  
-  #### Declare Metadata  ----
-  
-  observeEvent(input$conf_meta_single, {
-    
-    if(nchar(trimws(input$assembly_id)) < 1) {
-      ass_id <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
-    } else {
-      ass_id <- trimws(input$assembly_id)
-    }
-    
-    if(nchar(trimws(input$assembly_name)) < 1) {
-      ass_name <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
-    } else {
-      ass_name <- trimws(input$assembly_name)
-    }
-    
-    if(ass_id %in% unlist(DB$data["Assembly ID"])) {
-      show_toast(
-        title = "Assembly ID already present",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (isFALSE(Typing$reload)) {
-      show_toast(
-        title = "Reload Database first",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if (ass_id == "") {
-    show_toast(
-      title = "Empty Assembly ID",
-      type = "error",
-      position = "bottom-end",
-      timer = 3000
-      )
-    } else if (grepl("[()/\\:*?\"<>|]", ass_id)) {
-      show_toast(
-        title = "Invalid Assembly ID. No special characters allowed: ()/\\:*?\"<>|",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if(grepl(" ", ass_id)) {
-      show_toast(
-        title = "Empty spaces in Assembly ID not allowed",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if(Screening$status == "started") {
-      show_toast(
-        title = "Pending Single Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      
-      log_print("Single typing metadata confirmed")
-      
-      meta_info <- data.frame(assembly_id = ass_id,
-                              assembly_name = ass_name,
-                              cgmlst_typing = DB$scheme,
-                              append_isodate = input$append_isodate,
-                              append_host = trimws(input$append_host),
-                              append_country = trimws(input$append_country),
-                              append_city = trimws(input$append_city),
-                              append_analysisdate = Sys.Date(),
-                              db_directory = getwd()) 
-      
-      saveRDS(meta_info, paste0(
-        getwd(),
-        "/execute/meta_info_single.rds"
-      ))
-      
-      show_toast(
-        title = "Metadata declared",
-        type = "success",
-        position = "bottom-end",
-        timer = 3000
-      )
-      
-      # Render Start Typing UI
-      output$start_typing_ui <- renderUI({
-        div(
-          class = "multi_start_col",
-          column(
-            width = 3,
-            align = "center",
-            br(),
-            br(),
-            h3(p("Start Typing"), style = "color:white"),
-            br(),
-            br(),
-            HTML(
-              paste(
-                "<span style='color: white;'>",
-                "Typing by <strong>",
-                DB$scheme,
-                "</strong> scheme."
-              )
-            ),
-            br(), br(), br(), br(),
-            div(
-              class = "save-assembly",
-              materialSwitch(
-                "save_assembly_st",
-                h5(p("Save Assemblies in Local Database"), style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
-                value = TRUE,
-                right = TRUE)
-            ),
-            HTML(
-              paste(
-                "<span style='color: orange;'>",
-                "Isolates with unsaved assembly files can NOT be applied to screening for resistance genes."
-              )
-            ),
-            br(), br(), br(), br(),
-            actionButton(
-              inputId = "typing_start",
-              label = "Start",
-              icon = icon("circle-play")
-            )
-          )
-        )
-      })
-    }
-  })
-  
-  ####  Events Single Typing ----
-  
-  observeEvent(input$reset_single_typing, {
-    log_print("Reset single typing")
-    
-    Typing$status <- "Inactive"
-    
-    Typing$progress <- 0
-    
-    Typing$progress_format <- 900000
-    
-    output$single_typing_progress <- NULL
-    
-    output$typing_fin <- NULL
-    
-    output$single_typing_results <- NULL
-    
-    output$typing_formatting <- NULL
-    
-    Typing$single_path <- data.frame()
-    
-    # reset results file 
-    if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
-      unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
-      # Resetting single typing progress logfile bar 
-      con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
-      
-      cat("0\n", file = con)   
-      
-      close(con)
-    }
-    
-    output$initiate_typing_ui <- renderUI({
-      column(
-        width = 4,
-        align = "center",
-        br(),
-        br(),
-        h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-        br(),
-        br(),
-        p(
-          HTML(
-            paste(
-              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File (FASTA)')
-            )
-          )
-        ),
-        fluidRow(
-          column(1),
-          column(
-            width = 11,
-            align = "center",
-            shinyFilesButton(
-              "genome_file",
-              "Browse" ,
-              icon = icon("file"),
-              title = "Select the assembly in .fasta/.fna/.fa format:",
-              multiple = FALSE,
-              buttonType = "default",
-              class = NULL,
-              root = path_home()
-            ),
-            br(),
-            br(),
-            uiOutput("genome_path"),
-            br()
-          )
-        )
-      )
-    })
-  })
-  
-  # Notification for finalized Single typing
-  Typing$single_end <- TRUE
-  Typing$progress_format_end <- 0
-  
-  observe({
-    if(Typing$single_end == FALSE) {
-      if (Typing$progress_format_end == 999999) {
-        show_toast(
-          title = "Single Typing finalized",
-          type = "success",
-          position = "bottom-end",
-          timer = 8000
-        )
-        Typing$single_end <- TRUE
-      }
-    }
-  })
-  
-  ### Multi Typing ----
-  
-  #### Render Multi Typing UI Elements ----
-  output$initiate_multi_typing_ui <- renderUI({
-    column(
-      width = 4,
-      align = "center",
-      br(),
-      br(),
-      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-      br(), br(),
-      p(
-        HTML(
-          paste(
-            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
-          )
-        )
-      ),
-      fluidRow(
-        column(1),
-        column(
-          width = 11,
-          align = "center",
-          shinyDirButton(
-            "genome_file_multi",
-            "Browse",
-            icon = icon("folder-open"),
-            title = "Select the folder containing the genome assemblies (FASTA)",
-            buttonType = "default",
-            root = path_home()
-          ),
-          br(),
-          br(),
-          uiOutput("multi_select_info"),
-          br()
-        )
-      ),
-      uiOutput("multi_select_tab_ctrls"),
-      br(),
-      fluidRow(
-        column(1),
-        column(
-          width = 11,
-          align = "left",
-          rHandsontableOutput("multi_select_table")
-        )
-      )
-    )
-  })
-  
-  # Render selection info
-  output$multi_select_info <- renderUI({
-    
-    if(!is.null(Typing$multi_path)) {
-      if(length(Typing$multi_path) < 1) {
-        HTML(paste("<span style='color: white; margin-left:-30px'>", 
-                   "No files selected."))
-      } else {
-        HTML(paste("<span style='color: white; margin-left:-30px'>",
-                   sum(hot_to_r(input$multi_select_table)$Include == TRUE),
-                   " files selected."))
-      }
-    }
-  })
-  
-  # Render multi selection table issues
-  output$multi_select_issues <- renderUI({
-    req(Typing$multi_sel_table, input$multi_select_table)
-    if(any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
-       any(duplicated(hot_to_r(input$multi_select_table)$Files))){
-      HTML(
-        paste(
-          paste("<span style='color: orange;'>",
-                "Some name(s) are already present in local database.<br/>"),
-          paste("<span style='color: #ff7334;'>",
-                "Duplicated name(s). <br/>")
-        )
-      )
-    } else if (any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
-               !any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
-      HTML(
-        paste("<span style='color: #e0b300;'>",
-              "Some name(s) are already present in local database.<br/>")
-      )
-    } else if (!any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
-               any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
-      HTML(
-        paste("<span style='color: #ff7334;'>",
-              "Duplicated name(s). <br/>")
-      )
-    }
-  })
-  
-  output$multi_select_issue_info <- renderUI({
-    req(Typing$multi_sel_table, input$multi_select_table)
-    
-    multi_select_table <- hot_to_r(input$multi_select_table)
-    
-    if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
-       any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)])) |
-       any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
-      
-      if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)])))  {
-        
-        if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
-           any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
-          HTML(paste(
-            paste(
-              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-              paste("<span style='color: white; font-style:italic'>",
-                  "&nbspRename highlighted isolates or deselect them.</br>")),
-            paste(
-              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-              paste("<span style='color: white; font-style:italic'>",
-                  "&nbspFilename(s) contain(s) empty spaces."))
-          ))
-        } else {
-          HTML(paste(
-            '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-            paste("<span style='color: white; font-style:italic'>",
-                     "&nbspFilename(s) contain(s) empty spaces.")))
-        }
-      } else {
-        HTML(paste(
-          '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-          paste("<span style='color: white; font-style:italic'>", 
-                   "&nbspRename highlighted isolates or deselect them.")))
-      }
-    } else {
-      HTML(paste(
-        '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
-        paste("<span style='color: white; font-style:italic'>",
-              "&nbspFiles ready for allelic typing.")))
-    }
-  })
-  
-  # Render Metadata Select Box after Folder selection
-  observe({
-    if(!is.null(Typing$multi_sel_table)) {
-      if (nrow(Typing$multi_sel_table) > 0) {
-        
-        output$multi_select_tab_ctrls <- renderUI(
-          fluidRow(
-            column(1),
-            column(
-              width = 2,
-              align = "left",
-              actionButton(
-                "sel_all_mt",
-                "All",
-                icon = icon("check")
-              )
-            ),
-            column(
-              width = 2,
-              align = "left",
-              actionButton(
-                "desel_all_mt",
-                "None",
-                icon = icon("xmark")
-              )
-            ),
-            column(2),
-            column(
-              width = 5,
-              align = "right",
-              br(),
-              uiOutput("multi_select_issues")
-            )
-          )
-        )
-        
-        output$metadata_multi_box <- renderUI({
-          column(
-            width = 3,
-            align = "center",
-            br(),
-            br(),
-            h3(p("Declare Metadata"), style = "color:white;margin-left:-40px"),
-            br(), br(),
-            div(
-              class = "multi_meta_box",
-              box(
-                solidHeader = TRUE,
-                status = "primary",
-                width = "90%",
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      dateInput("append_isodate_multi",
-                                label = "",
-                                width = "80%",
-                                max = Sys.Date())
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput("append_host_multi",
-                                label = "",
-                                width = "80%")
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table_country",
-                      pickerInput(
-                        "append_country_multi",
-                        label = "",
-                        choices = list("Common" = sel_countries,
-                                       "All Countries" = country_names),
-                        options = list(
-                          `live-search` = TRUE,
-                          `actions-box` = TRUE,
-                          size = 10,
-                          style = "background-color: white; border-radius: 5px;"
-                        ),
-                        width = "90%"
-                      )
-                    )  
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput("append_city_multi",
-                                label = "",
-                                width = "80%")
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 12,
-                    align = "center",
-                    br(), br(),
-                    actionButton(
-                      inputId = "conf_meta_multi",
-                      label = "Confirm"
-                    ),
-                    br(), br(),
-                    uiOutput("multi_select_issue_info")
-                  )
-                )
-              )    
-            )
-          )
-        }) 
-      } else {
-        output$metadata_multi_box <- NULL
-      }
-    }
-  })
-  
-  # Check if ongoing Multi Typing - Render accordingly
-  observe({
-    # Get selected Genome in Multi Mode
-    shinyDirChoose(input,
-                   "genome_file_multi",
-                   roots = c(Home = path_home(), Root = "/"),
-                   defaultRoot = "Home",
-                   session = session,
-                   filetypes = c('', 'fasta', 'fna', 'fa'))
-    
-    Typing$multi_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)
-    
-    files_selected <- list.files(as.character(Typing$multi_path))
-    Typing$files_filtered <- files_selected[which(!endsWith(files_selected, ".gz") &
-                                                    grepl("\\.fasta|\\.fna|\\.fa", files_selected))]
-    
-    Typing$multi_sel_table <- data.frame(
-      Include = rep(TRUE, length(Typing$files_filtered)),
-      Files = gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", 
-                   Typing$files_filtered),
-      Type = sub(".*(\\.fasta|\\.fasta\\.gz|\\.fna|\\.fna\\.gz|\\.fa|\\.fa\\.gz)$",
-                 "\\1", Typing$files_filtered, perl = F))
-    
-    if(nrow(Typing$multi_sel_table) > 0) {
-      output$multi_select_tab_ctrls <- renderUI(
-        fluidRow(
-          column(1),
-          column(
-            width = 2,
-            align = "left",
-            actionButton(
-              "sel_all_mt",
-              "All",
-              icon = icon("check")
-            )
-          ),
-          column(
-            width = 2,
-            align = "left",
-            actionButton(
-              "desel_all_mt",
-              "None",
-              icon = icon("xmark")
-            )
-          ),
-          column(2),
-          column(
-            width = 5,
-            align = "right",
-            br(),
-            uiOutput("multi_select_issues")
-          )
-        )
-      )
-    } else {
-      output$multi_select_tab_ctrls <- NULL
-    }
-    
-    if(between(nrow(Typing$multi_sel_table), 1, 15)) {
-      output$multi_select_table <- renderRHandsontable({
-        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
-                             stretchH = "all", contextMenu = FALSE
-        ) %>%
-          hot_cols(columnSorting = FALSE) %>%
-          hot_rows(rowHeights = 25) %>%
-          hot_col(2, readOnly = FALSE,
-                  valign = "htBottom") %>%
-          hot_col(3, readOnly = TRUE) %>%
-          hot_col(1,
-                  halign = "htCenter",
-                  valign = "htTop", 
-                  colWidths = 60)
-        
-        htmlwidgets::onRender(rht, sprintf(
-          "function(el, x) {
-        var hot = this.hot;
-        
-        var columnData = hot.getDataAtCol(1); // Change column index if needed
-        var duplicates = {};
-          
-        var highlightInvalidAndDuplicates = function(invalidValues) {
-          
-          var columnData = hot.getDataAtCol(1); // Change column index if needed
-          var duplicates = {};
-
-          // Find all duplicate values
-          for (var i = 0; i < columnData.length; i++) {
-            var value = columnData[i];
-            if (value !== null && value !== undefined) {
-              if (duplicates[value]) {
-                duplicates[value].push(i);
-              } else {
-                duplicates[value] = [i];
-              }
-            }
-          }
-
-          // Reset all cell backgrounds in the column
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            if (cell) {
-              cell.style.background = 'white';
-            }
-          }
-
-          // Highlight duplicates and invalid values
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            var value = columnData[i];
-            if (cell) {
-              if (invalidValues.includes(value)) {
-                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
-              } else if (duplicates[value] && duplicates[value].length > 1) {
-                cell.style.background = '#FF7334'; // Highlight color for duplicates
-              }
-            }
-          }
-        };
-
-        var changefn = function(changes, source) {
-          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
-            highlightInvalidAndDuplicates(%s);
-          }
-        };
-
-        hot.addHook('afterChange', changefn);
-        hot.addHook('afterLoadData', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-        hot.addHook('afterRender', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-
-        highlightInvalidAndDuplicates(%s); // Initial highlight on load
-        
-        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
-          var colData = hot.getDataAtCol(0);
-          for (var i = 0; i < colData.length; i++) {
-            hot.setDataAtCell(i, 0, message.value);
-          }
-          hot.render(); // Re-render the table
-        });
-      }", 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id())))
-      })
-      
-    } else if(nrow(Typing$multi_sel_table) > 15) {
-      output$multi_select_table <- renderRHandsontable({
-        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
-                             stretchH = "all", height = 500,
-                             contextMenu = FALSE
-        ) %>%
-          hot_cols(columnSorting = FALSE) %>%
-          hot_rows(rowHeights = 25) %>%
-          hot_col(2,
-                  readOnly = FALSE,
-                  valign = "htBottom") %>%
-          hot_col(3, readOnly = TRUE) %>%
-          hot_col(1,
-                  halign = "htCenter",
-                  valign = "htTop", 
-                  colWidths = 60)
-        
-        htmlwidgets::onRender(rht, sprintf(
-          "function(el, x) {
-        var hot = this.hot;
-        
-        var columnData = hot.getDataAtCol(1); // Change column index if needed
-        var duplicates = {};
-          
-        var highlightInvalidAndDuplicates = function(invalidValues) {
-          
-          var columnData = hot.getDataAtCol(1); // Change column index if needed
-          var duplicates = {};
-
-          // Find all duplicate values
-          for (var i = 0; i < columnData.length; i++) {
-            var value = columnData[i];
-            if (value !== null && value !== undefined) {
-              if (duplicates[value]) {
-                duplicates[value].push(i);
-              } else {
-                duplicates[value] = [i];
-              }
-            }
-          }
-
-          // Reset all cell backgrounds in the column
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            if (cell) {
-              cell.style.background = 'white';
-            }
-          }
-
-          // Highlight duplicates and invalid values
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            var value = columnData[i];
-            if (cell) {
-              if (invalidValues.includes(value)) {
-                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
-              } else if (duplicates[value] && duplicates[value].length > 1) {
-                cell.style.background = '#FF7334'; // Highlight color for duplicates
-              }
-            }
-          }
-        };
-
-        var changefn = function(changes, source) {
-          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
-            highlightInvalidAndDuplicates(%s);
-          }
-        };
-
-        hot.addHook('afterChange', changefn);
-        hot.addHook('afterLoadData', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-        hot.addHook('afterRender', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-
-        highlightInvalidAndDuplicates(%s); // Initial highlight on load
-        
-        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
-          var colData = hot.getDataAtCol(0);
-          for (var i = 0; i < colData.length; i++) {
-            hot.setDataAtCell(i, 0, message.value);
-          }
-          hot.render(); // Re-render the table
-        });
-      }", 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id())))
-        
-      })
-      
-    } else {
-      output$multi_select_table <- NULL
-    } 
-  })
-  
-  observeEvent(input$conf_meta_multi, {
-    
-    multi_select_table <- hot_to_r(input$multi_select_table)[hot_to_r(input$multi_select_table)$Include == TRUE,]
-    
-    if(any(unlist(gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", multi_select_table$Files)) %in% unlist(DB$data["Assembly ID"]))) {
-      show_toast(
-        title = "Assembly ID(s) already present",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (any(duplicated(multi_select_table$Files))) {
-      show_toast(
-        title = "Duplicated filename(s)",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (any(multi_select_table$Files == "")) {
-      show_toast(
-        title = "Empty filename(s)",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (any(grepl("[()/\\:*?\"<>|]", multi_select_table$Files))) {
-      show_toast(
-        title = "Invalid filename(s). No special characters allowed: ()/\\:*?\"<>|",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (!any(multi_select_table$Include == TRUE)) {
-      show_toast(
-        title = "No files selected",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
-      show_toast(
-        title = "Empty spaces in filename(s) not allowed",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (isFALSE(Typing$reload)) {
-      show_toast(
-        title = "Reload Database first",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if(Screening$status == "started") {
-      show_toast(
-        title = "Pending Single Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      
-      log_print("Multi typing metadata confirmed")
-      
-      meta_info <- data.frame(cgmlst_typing = DB$scheme,
-                              append_isodate = trimws(input$append_isodate_multi),
-                              append_host = trimws(input$append_host_multi),
-                              append_country = trimws(input$append_country_multi),
-                              append_city = trimws(input$append_city_multi),
-                              append_analysisdate = Sys.Date(),
-                              db_directory = getwd())
-      
-      saveRDS(meta_info, paste0(getwd(), "/execute/meta_info.rds"))
-      
-      show_toast(
-        title = "Metadata declared",
-        type = "success",
-        position = "bottom-end",
-        timer = 3000
-      )
-      
-      output$start_multi_typing_ui <- renderUI({
-        div(
-          class = "multi_start_col",
-          column(
-            width = 3,
-            align = "center",
-            br(),
-            br(),
-            h3(p("Start Typing"), style = "color:white"),
-            br(),
-            br(),
-            HTML(
-              paste(
-                "<span style='color: white;'>",
-                "Typing by <strong>",
-                DB$scheme,
-                "</strong> scheme."
-              )
-            ),
-            br(), br(), br(), br(),
-            div(
-              class = "save-assembly",
-              materialSwitch(
-                "save_assembly_mt",
-                h5(p("Save Assemblies in Local Database"), style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
-                value = TRUE,
-                right = TRUE)
-            ),
-            HTML(
-              paste(
-                "<span style='color: orange;font-style:italic'>",
-                "Isolates with unsaved assembly files can NOT be applied to screening for resistance genes."
-              )
-            ),
-            br(), br(), br(), br(),
-            actionButton(
-              "start_typ_multi",
-              "Start",
-              icon = icon("circle-play")
-            )
-          )
-        )
-      })
-    }
-  })
-  
-  #### Events Multi Typing ----
-  
-  observeEvent(input$sel_all_mt, {
-    session$sendCustomMessage(type = "setColumnValue", message = list(value = TRUE))
-  })
-  
-  observeEvent(input$desel_all_mt, {
-    session$sendCustomMessage(type = "setColumnValue", message = list(value = FALSE))
-  })
-  
-  # Print Log
-  output$print_log <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save multi typing log ", paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")))
-      paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")
-    },
-    content = function(file) {
-      writeLines(readLines(paste0(getwd(), "/logs/script_log.txt")), file)
-    }
-  )
-  
-  # Reset Multi Typing
-  observeEvent(input$reset_multi, {
-    if(!grepl("Multi Typing", tail(readLines(paste0(getwd(),"/logs/script_log.txt")), n = 1))) {
-      showModal(
-        modalDialog(
-          paste0(
-            "A Multi Typing process is still pending. Stopping this process will cancel the processing."
-          ),
-          title = "Reset Multi Typing",
-          fade = TRUE,
-          easyClose = TRUE,
-          footer = tagList(
-            modalButton("Cancel"),
-            actionButton("conf_multi_kill", "Stop", class = "btn btn-danger")
-          )
-        )
-      )
-    } else {
-      
-      log_print("Reset multi typing")
-      
-      # Reset multi typing result list
-      saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
-      multi_help <- FALSE
-      Typing$result_list <- NULL
-      
-      # Null logfile
-      writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
-      
-      # Reset User Feedback variable
-      Typing$pending_format <- 0
-      Typing$multi_started <- FALSE
-      
-      output$initiate_multi_typing_ui <- renderUI({
-        column(
-          width = 4,
-          align = "center",
-          br(),
-          br(),
-          h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-          br(), br(),
-          p(
-            HTML(
-              paste(
-                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
-              )
-            )
-          ),
-          fluidRow(
-            column(1),
-            column(
-              width = 11,
-              align = "center",
-              shinyDirButton(
-                "genome_file_multi",
-                "Browse",
-                icon = icon("folder-open"),
-                title = "Select the folder containing the genome assemblies (FASTA)",
-                buttonType = "default",
-                root = path_home()
-              ),
-              br(),
-              br(),
-              uiOutput("multi_select_info"),
-              br()
-            )
-          ),
-          uiOutput("multi_select_tab_ctrls"),
-          br(),
-          fluidRow(
-            column(1),
-            column(
-              width = 11,
-              align = "left",
-              rHandsontableOutput("multi_select_table")
-            )
-          )
-        )
-      })
-      
-      output$pending_typing <- NULL
-      output$multi_typing_results <- NULL
-    }
-  })
-  
-  # Confirm Reset after 
-  observeEvent(input$conf_multi_kill, {
-    removeModal()
-    
-    log_print("Kill multi typing")
-    
-    # Kill multi typing and reset logfile  
-    system(paste("bash", paste0(getwd(), "/execute/kill_multi.sh")), 
-           wait = TRUE)
-    
-    show_toast(
-      title = "Execution cancelled",
-      type = "warning",
-      position = "bottom-end",
-      timer = 6000
-    )
-    
-    # Kill multi typing and reset logfile  
-    writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
-    
-    #Reset multi typing result list
-    saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
-    multi_help <- FALSE
-    Typing$result_list <- NULL
-    
-    # Reset User Feedback variable
-    Typing$pending_format <- 0
-    output$pending_typing <- NULL
-    output$multi_typing_results <- NULL
-    Typing$failures <- 0
-    Typing$successes <- 0
-    Typing$multi_started <- FALSE
-    
-    output$initiate_multi_typing_ui <- renderUI({
-      column(
-        width = 4,
-        align = "center",
-        br(),
-        br(),
-        h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-        br(), br(),
-        p(
-          HTML(
-            paste(
-              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
-            )
-          )
-        ),
-        fluidRow(
-          column(1),
-          column(
-            width = 11,
-            align = "center",
-            shinyDirButton(
-              "genome_file_multi",
-              "Browse",
-              icon = icon("folder-open"),
-              title = "Select the folder containing the genome assemblies (FASTA)",
-              buttonType = "default",
-              root = path_home()
-            ),
-            br(),
-            br(),
-            uiOutput("multi_select_info"),
-            br()
-          )
-        ),
-        uiOutput("multi_select_tab_ctrls"),
-        br(),
-        fluidRow(
-          column(1),
-          column(
-            width = 11,
-            align = "left",
-            rHandsontableOutput("multi_select_table")
-          )
-        )
-      )
-    })
-    
-  })
-  
-  observeEvent(input$start_typ_multi, {
-    log_print("Initiate multi typing")
-    
-    if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
-      show_toast(
-        title = "Pending Single Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if (Screening$status == "started") {
-      show_toast(
-        title = "Pending Gene Screening",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      removeModal()
-      
-      show_toast(
-        title = "Multi Typing started",
-        type = "success",
-        position = "bottom-end",
-        timer = 10000
-      )
-      
-      Typing$new_table <- NULL
-      
-      # Remove Allelic Typing Controls
-      output$initiate_multi_typing_ui <- NULL
-      output$metadata_multi_box <- NULL
-      output$start_multi_typing_ui <- NULL
-      
-      # Activate entry detection
-      DB$check_new_entries <- TRUE
-      
-      # Initiate Feedback variables
-      Typing$multi_started <- TRUE
-      Typing$pending <- TRUE
-      Typing$failures <- 0
-      Typing$successes <- 0
-      
-      # get selected file table
-      multi_select_table <- hot_to_r(input$multi_select_table)
-      
-      filenames <- paste(multi_select_table$Files[which(multi_select_table$Include == TRUE)], collapse = " ")
-      
-      files <- Typing$multi_sel_table$Files[which(multi_select_table$Include == TRUE)]
-      type <- Typing$multi_sel_table$Type[which(multi_select_table$Include == TRUE)]
-      genome_names <- paste(paste0(gsub(" ", "~", files), type), collapse = " ")
-      
-      # Start Multi Typing Script
-      multi_typing_df <- data.frame(
-        db_path = DB$database,
-        wd = getwd(),
-        save = input$save_assembly_mt,
-        scheme = paste0(gsub(" ", "_", DB$scheme)),
-        genome_folder = as.character(parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)),
-        filenames = paste0(filenames, collapse= " "),
-        genome_names = genome_names,
-        alleles = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")
-      )
-      
-      saveRDS(multi_typing_df, "execute/multi_typing_df.rds")
-      
-      # Execute multi blat script  
-      system(paste("bash", paste0(getwd(), "/execute/multi_typing.sh")), wait = FALSE)
-    }
-  })
-  
-  
-  #### User Feedback ----
-  
-  observe({
-    if(file.exists(paste0(getwd(), "/logs/script_log.txt"))) {
-      if(Typing$multi_started == TRUE) {
-        check_multi_status()
-      } else {
-        Typing$status <- "Inactive"
-      }
-    }
-  })
-  
-  check_multi_status <- reactive({
-    
-    invalidateLater(3000, session)
-    
-    log <- readLines(paste0(getwd(), "/logs/script_log.txt"))
-    
-    # Determine if Single or Multi Typing
-    if(str_detect(log[1], "Multi")) {
-      Typing$pending_mode <- "Multi"
-    } else {
-      Typing$pending_mode <- "Single"
-    }
-    
-    # Check typing status
-    if(str_detect(tail(log, 1), "Attaching")) {
-      Typing$status <- "Attaching"
-    } else if(str_detect(tail(log, 1), "Successful")) {
-      Typing$multi_help <- TRUE
-      Typing$status <- "Successful"
-      show_toast(
-        title = paste0("Successful", sub(".*Successful", "", tail(log, 1))),
-        type = "success",
-        position = "bottom-end",
-        timer = 8000
-      )
-    } else if(str_detect(tail(log, 1), "failed")) {
-      Typing$status <- "Failed"
-      show_toast(
-        title = sub(".* - ", "", tail(log, 1)),
-        type = "error",
-        position = "bottom-end",
-        timer = 8000
-      )
-    } else if(str_detect(tail(log, 1), "Processing")) {
-      Typing$status <- "Processing"
-      
-      if(any(str_detect(tail(log, 2), "Successful"))) {
-        
-        if(!identical(Typing$last_success, tail(log, 2)[1])) {
-          Typing$multi_help <- TRUE
-          show_toast(
-            title = paste0("Successful", sub(".*Successful", "", tail(log, 2)[1])),
-            type = "success",
-            position = "bottom-end",
-            timer = 8000
-          )
-          
-          Typing$last_success <- tail(log, 2)[1]
-        }
-      } else if(any(str_detect(tail(log, 2), "failed"))) {
-        
-        if(!identical(Typing$last_failure, tail(log, 2)[1])) {
-          
-          show_toast(
-            title = sub(".* - ", "", tail(log, 2)[1]),
-            type = "error",
-            position = "bottom-end",
-            timer = 8000
-          )
-          
-          Typing$last_failure <- tail(log, 2)[1]
-        }
-      }
-    } else if(str_detect(tail(log, 1), "finalized")) {
-      Typing$multi_help <- TRUE
-      Typing$status <- "Finalized"
-      
-      if(Typing$pending == TRUE) {
-        show_toast(
-          title = "Typing finalized",
-          type = "success",
-          position = "bottom-end",
-          timer = 8000
-        )
-        
-        Typing$pending <- FALSE
-      }
-    }
-  })
-  
-  ##### Render Multi Typing UI Feedback ----
-  
-  observe({
-    if(!is.null(input$multi_results_picker)) {
-      Typing$multi_table_length <- nrow(Typing$result_list[[input$multi_results_picker]])
-    } else {
-      Typing$multi_table_length <- NULL
-    }
-  })
-  
-  observe({
-    if(!is.null(Typing$result_list)) {
-      if(length(Typing$result_list) > 0) {
-        if(is.null(Typing$multi_table_length)) {
-          output$multi_typing_result_table <- renderRHandsontable({
-            rhandsontable(Typing$result_list[[input$multi_results_picker]], 
-                          rowHeaders = NULL, stretchH = "all",
-                          readOnly = TRUE, contextMenu = FALSE) %>%
-              hot_rows(rowHeights = 25) %>%
-              hot_col(1:3, valign = "htMiddle", halign = "htCenter",
-                      cellWidths = list(100, 160, NULL)) %>%
-              hot_col("Value", renderer=htmlwidgets::JS(
-                "function(instance, td, row, col, prop, value, cellProperties) {
-                  if (value.length > 8) {
-                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                  }
-                  td.innerHTML = value;
-                  td.style.textAlign = 'center';
-                  return td;
-                 }"
-              ))
-            })
-          
-        } else {
-          if(Typing$multi_table_length > 15) {
-            output$multi_typing_result_table <- renderRHandsontable({
-              rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
-                            stretchH = "all", height = 500,
-                            readOnly = TRUE, contextMenu = FALSE) %>%
-                hot_rows(rowHeights = 25) %>%
-                hot_col(1:3, valign = "htMiddle", halign = "htCenter",
-                        cellWidths = list(100, 160, NULL)) %>%
-                hot_col("Value", renderer=htmlwidgets::JS(
-                  "function(instance, td, row, col, prop, value, cellProperties) {
-                  if (value.length > 8) {
-                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                  }
-                  td.innerHTML = value;
-                  td.style.textAlign = 'center';
-                  return td;
-                 }"
-                ))
-              })
-          } else {
-            output$multi_typing_result_table <- renderRHandsontable({
-              rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
-                            stretchH = "all", readOnly = TRUE,
-                            contextMenu = FALSE) %>%
-                hot_rows(rowHeights = 25) %>%
-                hot_col(1:3, valign = "htMiddle", halign = "htCenter",
-                        cellWidths = list(100, 160, NULL)) %>%
-                hot_col("Value", renderer=htmlwidgets::JS(
-                  "function(instance, td, row, col, prop, value, cellProperties) {
-                  if (value.length > 8) {
-                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                  }
-                  td.innerHTML = value;
-                  td.style.textAlign = 'center';
-                  return td;
-                 }"
-                ))
-              })
-          }
-        }
-      } else {
-        output$multi_typing_result_table <- NULL
-      }
-    } else {
-      output$multi_typing_result_table <- NULL
-    }
-  })
-  
-  observe({
-    if(!is.null(Typing$multi_result_status)) {
-      if(Typing$multi_result_status == "start" | Typing$multi_result_status == "finalized"){
-        
-        if(Typing$multi_help == TRUE) {
-          Typing$result_list <- readRDS(paste0(getwd(), "/execute/event_list.rds"))
-          Typing$multi_help <- FALSE
-        }
-      } 
-    }
-  })
-  
-  
-  observe({
-    #Render multi typing result feedback table
-    
-    if(!is.null(Typing$result_list)) {
-      if(length(Typing$result_list) > 0) {
-        output$multi_typing_results <- renderUI({
-          column(
-            width = 12,
-            fluidRow(
-              column(1),
-              column(
-                width = 9,
-                br(), br(),
-                br(), br(),
-                br(), 
-                div(
-                  class = "mult_res_sel",
-                  selectInput(
-                    "multi_results_picker",
-                    label = h5("Select Typing Results", style = "color:white"),
-                    choices = names(Typing$result_list),
-                    selected = names(Typing$result_list)[length(names(Typing$result_list))],
-                  )
-                ),
-                br(), br()
-              )
-            ),
-            rHandsontableOutput("multi_typing_result_table")
-          )
-        })
-      }
-    }
-  })
-  
-  observe({
-    
-    # Render log content
-    output$logText <- renderPrint({
-      cat(rev(paste0(tail(readLogFile(), 50), "\n")))
-    })
-    
-    output$logTextFull <- renderPrint({
-      cat(rev(paste0(readLines(paste0(getwd(), "/logs/script_log.txt")), "\n")))
-    })
-    
-    # Render Pending UI
-    if(!grepl("Multi Typing", tail(readLogFile(), n = 1)) & grepl("Start Multi Typing", head(readLogFile(), n = 1))) {
-      
-      Typing$multi_result_status <- "start"
-      
-      output$initiate_multi_typing_ui <- NULL
-      
-      output$pending_typing <- renderUI({
-        fluidRow(
-          fluidRow(
-            br(), br(),
-            column(width = 2),
-            column(
-              width = 4,
-              h3(p("Pending Typing ..."), style = "color:white"),
-              br(), br(),
-              fluidRow(
-                column(
-                  width = 5,
-                  HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:24px;color:white;margin-top:5px"></i>'))
-                ),
-                column(
-                  width = 6,
-                  align = "left",
-                  actionButton(
-                    "reset_multi",
-                    "Terminate",
-                    icon = icon("ban")
-                  )
-                )
-              ),
-            )
-          ),
-          br(), br(),
-          fluidRow(
-            column(width = 2),
-            column(
-              width = 10,
-              verbatimTextOutput("logText")
-            )  
-          )
-        )
-      })
-    } else if(grepl("Multi Typing finalized", tail(readLogFile(), n = 1))) {
-      
-      Typing$multi_result_status <- "finalized"
-      
-      Typing$last_scheme <- NULL
-      
-      output$initiate_multi_typing_ui <- NULL
-      
-      output$pending_typing <- renderUI({
-        
-        fluidRow(
-          fluidRow(
-            br(), br(),
-            column(width = 2),
-            column(
-              width = 4,
-              h3(p("Pending Multi Typing ..."), style = "color:white"),
-              br(), br(),
-              HTML(paste("<span style='color: white;'>", 
-                         paste("Typing of", sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "Processing")), "assemblies finalized."),
-                         paste(sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "Successful")), "successes."),
-                         paste(sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "failed")), "failures."),
-                         "Reset to start another typing process.", 
-                         sep = '<br/>')),
-              br(), br(),
-              fluidRow(
-                column(
-                  width = 5,
-                  actionButton(
-                    "reset_multi",
-                    "Reset",
-                    icon = icon("arrows-rotate")
-                  )
-                ),
-                column(
-                  width = 5,
-                  downloadButton(
-                    "print_log",
-                    "Logfile",
-                    icon = icon("floppy-disk")
-                  )
-                )
-              )
-            )
-          ),
-          br(), br(),
-          fluidRow(
-            column(width = 2),
-            column(
-              width = 10,
-              verbatimTextOutput("logTextFull"),
-            )
-          )
-        )
-      })
-    } else if (!grepl("Start Multi Typing", head(readLogFile(), n = 1))){
-      output$pending_typing <- NULL
-      Typing$multi_result_status <- "idle"
-    }
-  })
-  
-  observe({
-    # Get selected Genome in Multi Mode
-    shinyDirChoose(input,
-                   "hash_dir",
-                   roots = c(Home = path_home(), Root = "/"),
-                   defaultRoot = "Home",
-                   session = session,
-                   filetypes = c('', 'fasta', 'fna', 'fa'))
-  })
-  
-  observeEvent(input$hash_start, {
-    dir_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$hash_dir)
-    if (!is_empty(list.files(dir_path)) && all(endsWith(list.files(dir_path), ".fasta"))) {
-      log_print("Hashing directory using utilities")
-      shinyjs::hide("hash_start")
-      shinyjs::show("hash_loading")
-      show_toast(
-        title = "Hashing started!",
-        type = "success",
-        position = "bottom-end",
-        timer = 6000
-      )
-      hash_database(dir_path)
-      shinyjs::hide("hash_loading")
-      shinyjs::show("hash_start")
-      show_toast(
-        title = "Hashing completed!",
-        type = "success",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      show_toast(
-        title = "Incorrect folder selected!",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    }
-  })
-  
-} # end server
-
-# _______________________ ####
-
-# Shiny ----
-
-shinyApp(ui = ui, server = server)
+######## PhyloTrace #########
+
+# _______________________ ####
+# CRAN Packages
+library(shiny)
+library(R.utils)
+library(igraph)
+library(shinyWidgets)
+library(shinydashboard)
+library(dashboardthemes)
+library(ggplot2)
+library(ggnewscale)
+library(ggplotify) 
+library(ape)
+library(tidyverse)
+library(rlang)
+library(tidytree)
+library(shinyFiles)
+library(dplyr)
+library(downloader)
+library(rvest)
+library(rmarkdown)
+library(knitr)
+library(kableExtra)
+library(fs)
+library(data.table)
+library(zoo)
+library(ggnetwork)
+library(rhandsontable)
+library(visNetwork)
+library(proxy)
+library(phangorn)
+library(cowplot)
+library(viridis)
+library(RColorBrewer)
+library(bslib)
+library(bsicons)
+library(DT)
+library(shinyBS)
+library(openssl)
+library(logr)
+# Bioconductor Packages
+library(treeio)
+library(ggtree)
+library(ggtreeExtra)
+
+source(paste0(getwd(), "/www/resources.R"))
+
+options(ignore.negative.edge=TRUE)
+
+# User Interface ----
+
+ui <- dashboardPage(
+  
+  title = "PhyloTrace 1.5.0",
+  
+  # Title
+  dashboardHeader(
+    
+    title = span(
+      div(
+        class = "img_logo",
+        img(
+          src = "PhyloTrace.jpg", width = 190
+        )
+      )
+    ),
+    uiOutput("loaded_scheme"),
+    uiOutput("databasetext"),
+    uiOutput("statustext"),
+    tags$li(class = "dropdown", 
+            tags$span(id = "currentTime", style = "color:white; font-weight:bold;")),
+    disable = FALSE
+  ),
+  
+  ## Sidebar ----
+  dashboardSidebar(
+    tags$head(includeCSS("www/head.css")),
+    tags$style(includeCSS("www/body.css")),
+    tags$style(HTML(
+      "@keyframes pulsate {
+          0% { transform: scale(1); }
+          50% { transform: scale(1.1); }
+          100% { transform: scale(1); }
+        }
+        .pulsating-button {
+          animation: pulsate 1s ease infinite;
+        }
+        .pulsating-button:hover {
+          animation: none;
+        }")),
+    br(), br(),
+    sidebarMenu(
+      id = "tabs",
+      sidebarMenuOutput("menu"),
+      uiOutput("menu_sep2"),
+      conditionalPanel(
+        "input.tabs==='db_browse_entries'",
+        uiOutput("entrytable_sidebar")
+      ),
+      conditionalPanel(
+        "input.tabs==='db_distmatrix'",
+        uiOutput("distmatrix_sidebar")
+      ),
+      conditionalPanel(
+        "input.tabs==='db_missing_values'",
+        uiOutput("missing_values_sidebar")
+      ),
+      conditionalPanel(
+        "input.tabs==='typing'",
+        uiOutput("typing_sidebar")
+      ),
+      conditionalPanel(
+        "input.tabs==='visualization'",
+        uiOutput("visualization_sidebar")
+      ),
+      conditionalPanel(
+        "input.tabs==='gs_profile'",
+        uiOutput("screening_sidebar")
+      )
+    )
+  ),
+  
+  dashboardBody(
+    tags$head(tags$link(rel = "shortcut icon", href = "favicon.ico")),
+    shinyjs::useShinyjs(),
+    
+    shinyDashboardThemeDIY(
+      ### general
+      appFontFamily = "Liberation Sans",
+      appFontColor = "#000000",
+      primaryFontColor = "#ffffff",
+      infoFontColor = "rgb(0,0,0)",
+      successFontColor = "rgb(0,0,0)",
+      warningFontColor = "rgb(0,0,0)",
+      dangerFontColor = "rgb(0,0,0)",
+      bodyBackColor = cssGradientThreeColors(
+        direction = "down",
+        colorStart = "#282f38",
+        colorMiddle = "#384454",
+        colorEnd = "#495d78",
+        colorStartPos = 0,
+        colorMiddlePos = 50,
+        colorEndPos = 100
+      ),
+      
+      ### header
+      logoBackColor = "#282f38",
+      headerButtonBackColor = "#282f38",
+      headerButtonIconColor = "#18ece1",
+      headerButtonBackColorHover = "#282f38",
+      headerButtonIconColorHover = "#ffffff",
+      headerBackColor = "#282f38",
+      headerBoxShadowColor = "#aaaaaa",
+      headerBoxShadowSize = "0px 0px 0px",
+      
+      ### sidebar
+      sidebarBackColor = cssGradientThreeColors(
+        direction = "down",
+        colorStart = "#282f38",
+        colorMiddle = "#384454",
+        colorEnd = "#495d78",
+        colorStartPos = 0,
+        colorMiddlePos = 50,
+        colorEndPos = 100),
+      
+      sidebarPadding = 0,
+      sidebarMenuBackColor = "transparent",
+      sidebarMenuPadding = 0,
+      sidebarMenuBorderRadius = 0,
+      sidebarShadowRadius = "5px 5px 5px",
+      sidebarShadowColor = "#282f38",
+      sidebarUserTextColor = "#ffffff",
+      sidebarSearchBackColor = "rgb(55,72,80)",
+      sidebarSearchIconColor = "rgb(153,153,153)",
+      sidebarSearchBorderColor = "rgb(55,72,80)",
+      sidebarTabTextColor = "rgb(255,255,255)",
+      sidebarTabTextSize = 15,
+      sidebarTabBorderStyle = "none none solid none",
+      sidebarTabBorderColor = "rgb(35,106,135)",
+      sidebarTabBorderWidth = 0,
+      sidebarTabBackColorSelected = cssGradientThreeColors(
+        direction = "right",
+        colorStart = "rgba(44,222,235,1)",
+        colorMiddle = "rgba(44,222,235,1)",
+        colorEnd = "rgba(0,255,213,1)",
+        colorStartPos = 0,
+        colorMiddlePos = 30,
+        colorEndPos = 100
+      ),
+      sidebarTabTextColorSelected = "rgb(0,0,0)",
+      sidebarTabRadiusSelected = "0px 0px 0px 0px",
+      sidebarTabBackColorHover = cssGradientThreeColors(
+        direction = "right",
+        colorStart = "rgba(44,222,235,1)",
+        colorMiddle = "rgba(44,222,235,1)",
+        colorEnd = "rgba(0,255,213,1)",
+        colorStartPos = 0,
+        colorMiddlePos = 30,
+        colorEndPos = 100
+      ),
+      sidebarTabTextColorHover = "rgb(50,50,50)",
+      sidebarTabBorderStyleHover = "none none solid none",
+      sidebarTabBorderColorHover = "rgb(75,126,151)",
+      sidebarTabBorderWidthHover = 0,
+      sidebarTabRadiusHover = "0px 0px 0px 0px",
+      
+      ### boxes
+      boxBackColor = "#ffffff",
+      boxBorderRadius = 7,
+      boxShadowSize = "0px 0px 0px",
+      boxShadowColor = "#ffffff",
+      boxTitleSize = 20,
+      boxDefaultColor = "#00a65a",
+      boxPrimaryColor = "#ffffff",
+      boxInfoColor = "#00a65a",
+      boxSuccessColor = "#00a65a",
+      boxWarningColor = "#ffffff",
+      boxDangerColor = "#ffffff",
+      tabBoxTabColor = "#ffffff",
+      tabBoxTabTextSize = 14,
+      tabBoxTabTextColor = "rgb(0,0,0)",
+      tabBoxTabTextColorSelected = "rgb(0,0,0)",
+      tabBoxBackColor = "#ffffff",
+      tabBoxHighlightColor = "#ffffff",
+      tabBoxBorderRadius = 5,
+      
+      ### inputs
+      buttonBackColor = "#282F38",
+      buttonTextColor = "#ffffff",
+      buttonBorderColor = "#282F38",
+      buttonBorderRadius = 5,
+      buttonBackColorHover = cssGradientThreeColors(
+        direction = "right",
+        colorStart = "rgba(44,222,235,1)",
+        colorMiddle = "rgba(44,222,235,1)",
+        colorEnd = "rgba(0,255,213,1)",
+        colorStartPos = 0,
+        colorMiddlePos = 30,
+        colorEndPos = 100
+      ),
+      buttonTextColorHover = "#000000",
+      buttonBorderColorHover = "transparent",
+      textboxBackColor = "#ffffff",
+      textboxBorderColor = "#ffffff",
+      textboxBorderRadius = 5,
+      textboxBackColorSelect = "#ffffff",
+      textboxBorderColorSelect = "#000000",
+      
+      ### tables
+      tableBackColor = "rgb(255,255,255)",
+      tableBorderColor = "rgb(240,240,240)",
+      tableBorderTopSize = 1,
+      tableBorderRowSize = 1
+    ),
+    
+    uiOutput("start_message"),
+    
+    tabItems(
+      
+      ## Tab Database ----
+      
+      ### Tab Browse Entries ----
+      
+      tabItem(
+        tabName = "db_browse_entries",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Browse Local Database"), style = "color:white")
+          )
+        ),
+        hr(), br(),
+        br(),
+        br(),
+        uiOutput("no_scheme_entries"),
+        uiOutput("db_no_entries"),
+        uiOutput("entry_table_controls"),
+        br(), br(),
+        fluidRow(
+          column(1),
+          column(
+            width = 8,
+            uiOutput("db_entries_table")
+          ),
+          column(
+            width = 3,
+            align = "left",
+            uiOutput("delete_box"),
+            uiOutput("compare_allele_box"),
+            uiOutput("download_entries"),
+            br(), br(), br(), br(), br(), br(), br(), br(),
+            br(), br(), br(), br(), br(), br(), br()
+          )
+        ),
+        br()
+      ),
+      
+      ### Tab Scheme Info  ----  
+      
+      tabItem(
+        tabName = "db_schemeinfo",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Scheme Info"), style = "color:white")
+          )
+        ),
+        hr(), br(), br(), br(),
+        uiOutput("no_scheme_info"),
+        fluidRow(
+          column(2),
+          column(
+            width = 7,
+            align = "center",
+            fluidRow(
+              column(
+                width = 7,
+                align = "right",
+                uiOutput("scheme_header")
+              ),
+              column(
+                width = 2,
+                align = "left",
+                uiOutput("download_scheme_info")
+              )
+            ),
+            br(),
+            br(),
+            uiOutput("scheme_info")
+          )
+        )
+      ),
+      
+      ### Tab Loci Info  ----  
+      
+      tabItem(
+        tabName = "db_loci_info",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Loci Info"), style = "color:white")
+          )
+        ),
+        hr(), br(), br(), br(),
+        fluidRow(
+          column(1),
+          column(
+            width = 10,
+            align = "center",
+            fluidRow(
+              column(
+                width = 6,
+                align = "right",
+                uiOutput("loci_header")
+              ),
+              column(
+                width = 2,
+                align = "left",
+                uiOutput("download_loci")
+              )
+            ),
+            br(),
+            div(class = "loci_table",
+                dataTableOutput("db_loci"))
+          )
+        ),
+        br(), br(),
+        fluidRow(
+          column(1),
+          uiOutput("sequence_selector"), 
+          column(1),
+          column(
+            width = 7,
+            br(),
+            uiOutput("loci_sequences")
+          )
+        )
+      ),
+      
+      ### Tab Distance Matrix  ----  
+      
+      tabItem(
+        tabName = "db_distmatrix",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Distance Matrix"), style = "color:white")
+          )
+        ),
+        hr(), br(), br(), br(),
+        uiOutput("no_scheme_distancematrix"),
+        uiOutput("distancematrix_no_entries"),
+        fluidRow(
+          column(1),
+          uiOutput("distmatrix_show")
+        ),
+        br(), br()
+      ),
+      
+      ### Tab Missing Values ----
+      
+      tabItem(
+        tabName = "db_missing_values",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Missing Values"), style = "color:white")
+          )
+        ),
+        hr(), br(), br(), br(),
+        fluidRow(
+          column(
+            width = 3,
+            uiOutput("missing_values"),
+            fluidRow(
+              column(
+                width = 2,
+                div(
+                  class = "rectangle-red-space" 
+                )
+              ),
+              column(
+                width = 10,
+                align = "left",
+                p(
+                  HTML(
+                    paste(
+                      tags$span(style="color: white; font-size: 15px; margin-left: 75px; position: relative; bottom: -12px", " =  ≥ 5% of loci missing")
+                    )
+                  )
+                )
+              )
+            )
+          ),
+          column(
+            width = 8,
+            rHandsontableOutput("table_missing_values")
+          )
+        )
+      ),
+      
+      ## Tab Manage Schemes  ----  
+      
+      tabItem(
+        tabName = "init",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Select cgMLST Scheme"), style = "color:white")
+          )
+        ),
+        hr(),
+        fluidRow(
+          column(1),
+          column(
+            width = 3,
+            br(),
+            br(),
+            br(),
+            pickerInput(
+              inputId = "select_cgmlst",
+              label = NULL,
+              choices = list(
+                "Acinetobacter baumanii",
+                "Bacillus anthracis",
+                "Bordetella pertussis",
+                "Brucella melitensis",
+                "Brucella spp.",
+                "Burkholderia mallei (FLI)",
+                "Burkholderia mallei (RKI)",
+                "Burkholderia pseudomallei",
+                "Campylobacter jejuni/coli",
+                "Clostridioides difficile",
+                "Clostridium perfringens",
+                "Corynebacterium diphtheriae",
+                "Cronobacter sakazakii/malonaticus",
+                "Enterococcus faecalis",
+                "Enterococcus faecium",
+                "Escherichia coli",
+                "Francisella tularensis",
+                "Klebsiella oxytoca sensu lato",
+                "Klebsiella pneumoniae sensu lato",
+                "Legionella pneumophila",
+                "Listeria monocytogenes",
+                "Mycobacterium tuberculosis complex",
+                "Mycobacteroides abscessus",
+                "Mycoplasma gallisepticum",
+                "Paenibacillus larvae",
+                "Pseudomonas aeruginosa",
+                "Salmonella enterica",
+                "Serratia marcescens",
+                "Staphylococcus aureus",
+                "Staphylococcus capitis",
+                "Streptococcus pyogenes"
+              ),
+              width = "300px",
+              options = list(
+                `live-search` = TRUE,
+                `actions-box` = TRUE,
+                size = 10,
+                style = "background-color: white; border-radius: 5px;"
+              ),
+              multiple = FALSE
+            )
+          ),
+          column(
+            width = 2,
+            br(),
+            br(),
+            br(),
+            h5(textOutput("scheme_update_info"), style = "color: white")
+          ),
+          column(
+            width = 2,
+            br(),
+            br(),
+            br(),
+            actionButton(
+              "download_cgMLST",
+              label = "Download",
+              icon = icon("download")
+            ),
+            shinyjs::hidden(
+              div(id = "loading",
+                  HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
+            )
+          )
+        ),
+        fluidRow(
+          column(1),
+          column(
+            width = 6,
+            align = "center",
+            br(),
+            br(),
+            br(),
+            addSpinner(
+              tableOutput("cgmlst_scheme"),
+              spin = "dots",
+              color = "#ffffff"
+            )
+          )
+        )
+      ),
+      
+      
+      
+      ## Tab Allelic Typing ----------------------------------------------
+      
+      
+      tabItem(
+        tabName = "typing",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Generate Allelic Profile"), style = "color:white")
+          )
+        ),
+        hr(),
+        uiOutput("typing_no_db"),
+        conditionalPanel(
+          "input.typing_mode == 'Single'",
+          fluidRow(
+            uiOutput("initiate_typing_ui"),
+            uiOutput("single_typing_progress"),
+            column(1),
+            uiOutput("metadata_single_box"),
+            column(1),
+            uiOutput("start_typing_ui")
+          )
+        ),
+        conditionalPanel(
+          "input.typing_mode == 'Multi'",
+          fluidRow(
+            uiOutput("initiate_multi_typing_ui"),
+            uiOutput("multi_stop"),
+            column(1),
+            uiOutput("metadata_multi_box"),
+            column(1),
+            uiOutput("start_multi_typing_ui")
+          ),
+          fluidRow(
+            column(
+              width = 6,
+              uiOutput("pending_typing")
+            ),
+            column(
+              width = 6,
+              uiOutput("multi_typing_results")
+            )
+          )
+        )
+      ),
+      
+      
+      ## Tab Visualization -------------------------------------------------------
+      
+      
+      tabItem(
+        tabName = "visualization",
+        fluidRow(
+          tags$script(src = "javascript_functions.js"),
+          column(
+            width = 12,
+            align = "center",
+            br(),
+            conditionalPanel(
+              "input.tree_algo=='Minimum-Spanning'",
+              uiOutput("mst_field")
+            ),
+            conditionalPanel(
+              "input.tree_algo=='Neighbour-Joining'",
+              uiOutput("nj_field")
+            ),
+            conditionalPanel(
+              "input.tree_algo=='UPGMA'",
+              uiOutput("upgma_field")
+            )
+          )
+        ),
+        br(),
+        hr(),
+        
+        ### Control panels MST ----
+        conditionalPanel(
+          "input.tree_algo=='Minimum-Spanning'",
+          fluidRow(
+            column(
+              width = 4,
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "100%",
+                height = "500px",
+                h3(p("Layout"), style = "color:white; position:relative; right:-15px"),
+                hr(),
+                fluidRow(
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Title"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          textInput(
+                            "mst_title",
+                            label = "",
+                            width = "100%",
+                            placeholder = "Plot Title"
+                          ),
+                          fluidRow(
+                            column(
+                              width = 7,
+                              colorPickr(
+                                inputId = "mst_title_color",
+                                selected = "#000000",
+                                label = "",
+                                update = "changestop",
+                                interaction = list(clear = FALSE,
+                                                   save = FALSE),
+                                position = "right-start",
+                                width = "100%"
+                              )
+                            ),
+                            column(
+                              width = 5,
+                              dropMenu(
+                                actionBttn(
+                                  "mst_title_menu",
+                                  label = "",
+                                  color = "default",
+                                  size = "sm",
+                                  style = "material-flat",
+                                  icon = icon("sliders")
+                                ),
+                                placement = "top-start",
+                                theme = "translucent",
+                                numericInput(
+                                  "mst_title_size",
+                                  label = h5("Size", style = "color:white; margin-bottom: 0px;"),
+                                  value = 40,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Subtitle"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          textInput(
+                            "mst_subtitle",
+                            label = "",
+                            width = "100%",
+                            placeholder = "Plot Subtitle"
+                          ),
+                          fluidRow(
+                            column(
+                              width = 7,
+                              colorPickr(
+                                inputId = "mst_subtitle_color",
+                                selected = "#000000",
+                                label = "",
+                                update = "changestop",
+                                interaction = list(clear = FALSE,
+                                                   save = FALSE),
+                                position = "right-start",
+                                width = "100%"
+                              )
+                            ),
+                            column(
+                              width = 5,
+                              dropMenu(
+                                actionBttn(
+                                  "mst_subtitle_menu",
+                                  label = "",
+                                  color = "default",
+                                  size = "sm",
+                                  style = "material-flat",
+                                  icon = icon("sliders")
+                                ),
+                                placement = "top-start",
+                                theme = "translucent",
+                                numericInput(
+                                  "mst_subtitle_size",
+                                  label = h5("Size", style = "color:white; margin-bottom: 0px;"),
+                                  value = 20,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                ),
+                hr(),
+                fluidRow(
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Legend"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 7,
+                              colorPickr(
+                                inputId = "mst_legend_color",
+                                selected = "#000000",
+                                label = "",
+                                update = "changestop",
+                                interaction = list(clear = FALSE,
+                                                   save = FALSE),
+                                position = "right-start",
+                                width = "100%"
+                              )
+                            ),
+                            column(
+                              width = 5,
+                              dropMenu(
+                                actionBttn(
+                                  "mst_legend_menu",
+                                  label = "",
+                                  color = "default",
+                                  size = "sm",
+                                  style = "material-flat",
+                                  icon = icon("sliders")
+                                ),
+                                placement = "top-start",
+                                theme = "translucent",
+                                fluidRow(
+                                  column(
+                                    width = 11,
+                                    sliderInput(
+                                      "mst_font_size",
+                                      label = h5("Font Size", style = "color:white; margin-bottom: 0px;"),
+                                      value = 18,
+                                      min = 15,
+                                      max = 30,
+                                      step = 1,
+                                      ticks = FALSE,
+                                      width = "180px"
+                                    )
+                                  ),
+                                  column(1)
+                                ),
+                                br(),
+                                fluidRow(
+                                  column(
+                                    width = 11,
+                                    sliderInput(
+                                      "mst_symbol_size",
+                                      label = h5("Key Size", style = "color:white; margin-bottom: 0px;"),
+                                      value = 20,
+                                      min = 10,
+                                      max = 30,
+                                      step = 1,
+                                      ticks = FALSE,
+                                      width = "180px"
+                                    )
+                                  ),
+                                  column(1)
+                                )
+                              )
+                            )
+                          ),
+                          fluidRow(
+                            column(
+                              width = 7,
+                              selectInput(
+                                "mst_legend_ori",
+                                label = "",
+                                width = "100%",
+                                choices = c("Left" = "left", "Right" = "right")
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Background"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "left",
+                              div(
+                                class = "mat-switch-mst-nodes",
+                                materialSwitch(
+                                  "mst_background_transparent",
+                                  h5(p("Transparent"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            )
+                          ),
+                          fluidRow(
+                            column(
+                              width = 7,
+                              colorPickr(
+                                inputId = "mst_background_color",
+                                width = "100%",
+                                selected = "#ffffff",
+                                label = "",
+                                update = "changestop",
+                                interaction = list(clear = FALSE,
+                                                   save = FALSE),
+                                position = "right-start"
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            column(
+              width = 4,
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "100%",
+                height = "500px",
+                h3(p("Nodes"), style = "color:white; position:relative; right:-15px"),
+                hr(),
+                fluidRow(
+                  column(
+                    width = 6,
+                    column(
+                      width = 12,
+                      align = "left",
+                      h4(p("Label"), style = "color:white;")
+                    ),
+                    column(
+                      width = 12,
+                      align = "center",
+                      div(
+                        class = "label_sel",
+                        uiOutput("mst_node_label")
+                      ),
+                      fluidRow(
+                        column(
+                          width = 7,
+                          colorPickr(
+                            inputId = "node_font_color",
+                            width = "100%",
+                            selected = "#000000",
+                            label = "",
+                            update = "changestop",
+                            interaction = list(clear = FALSE,
+                                               save = FALSE),
+                            position = "right-start"
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          dropMenu(
+                            actionBttn(
+                              "mst_label_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            numericInput(
+                              "node_label_fontsize",
+                              label = h5("Size", style = "color:white; margin-bottom: 0px;"),
+                              value = 14,
+                              min = 8,
+                              max = 30,
+                              step = 1,
+                              width = "80px"
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Color"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 10,
+                              align = "left",
+                              div(
+                                class = "mat-switch-mst-nodes",
+                                materialSwitch(
+                                  "mst_color_var",
+                                  h5(p("Add Variable"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            column(
+                              width = 2,
+                              bslib::tooltip(
+                                bsicons::bs_icon("info-circle", title = "Only categorical variables can \nbe mapped to the node color", color = "white", 
+                                                 height = "12px", width = "12px", position = "relative", top = "27px", right = "56px"),
+                                "Text shown in the tooltip.",
+                                show = FALSE,
+                                id = "mst_node_col_info"
+                              )
+                            )
+                          ),
+                          uiOutput("mst_color_mapping")
+                        )
+                      )
+                    ), br()
+                  )
+                ),
+                hr(),
+                fluidRow(
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Size"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "left",
+                              div(
+                                class = "mat-switch-mst-nodes",
+                                materialSwitch(
+                                  "scale_nodes",
+                                  h5(p("Scale by Duplicates"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                  value = TRUE,
+                                  right = TRUE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    column(
+                      width = 12,
+                      align = "left",
+                      fluidRow(
+                        column(
+                          width = 3,
+                          align = "left",
+                          conditionalPanel(
+                            "input.scale_nodes==true",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Range')
+                              )
+                            )
+                          ),
+                          conditionalPanel(
+                            "input.scale_nodes==false",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Size')
+                              )
+                            )
+                          )
+                        ),
+                        column(
+                          width = 9,
+                          align = "center",
+                          conditionalPanel(
+                            "input.scale_nodes==true",
+                            div(
+                              class = "mst_scale_slider",
+                              sliderInput(
+                                "mst_node_scale",
+                                label = "",
+                                min = 1,
+                                max = 80,
+                                value = c(20, 40),
+                                ticks = FALSE
+                              )
+                            )
+                          ),
+                          conditionalPanel(
+                            "input.scale_nodes==false",
+                            div(
+                              class = "mst_scale_slider",
+                              sliderInput(
+                                inputId = "mst_node_size",
+                                label = "",
+                                min = 1,
+                                max = 100,
+                                value = 30,
+                                ticks = FALSE
+                              ) 
+                            )
+                          )
+                        )
+                      ),
+                      br()
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Other Elements"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "left",
+                              div(
+                                class = "mat-switch-mst-nodes",
+                                materialSwitch(
+                                  "mst_shadow",
+                                  h5(p("Show Shadow"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                  value = TRUE,
+                                  right = TRUE
+                                )
+                              ),
+                              fluidRow(
+                                column(
+                                  width = 3,
+                                  align = "left",
+                                  HTML(
+                                    paste(
+                                      tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Shape')
+                                    )
+                                  )
+                                ),
+                                column(
+                                  width = 9,
+                                  align = "center",
+                                  div(
+                                    class = "mst_shape_sel",
+                                    selectInput(
+                                      "mst_node_shape",
+                                      "",
+                                      choices = list(`Label inside` = c("Circle" = "circle", "Box" = "box", "Text" = "text"),
+                                                     `Label outside` = c("Diamond" = "diamond", "Hexagon" = "hexagon","Dot" = "dot", "Square" = "square")),
+                                      selected = c("Dot" = "dot"),
+                                      width = "85%"
+                                    )
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            column(
+              width = 4,
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "100%",
+                height = "500px",
+                h3(p("Edges"), style = "color:white; position:relative; right:-15px"),
+                hr(),
+                fluidRow(
+                  column(
+                    width = 6,
+                    column(
+                      width = 12,
+                      align = "left",
+                      h4(p("Label"), style = "color:white;")
+                    ),
+                    column(
+                      width = 12,
+                      align = "center",
+                      div(
+                        class = "label_sel",
+                        selectInput(
+                          "mst_edge_label",
+                          label = "",
+                          choices = c(
+                            `Allelic Distance` = "weight",
+                            Index = "index",
+                            `Assembly ID` = "assembly_id",
+                            `Assembly Name` = "assembly_name",
+                            `Isolation Date` = "isolation_date",
+                            Host = "host",
+                            Country = "country",
+                            City = "city"
+                          ),
+                          selected = c(`Allelic Distance` = "weight"),
+                          width = "100%"
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 7,
+                          colorPickr(
+                            inputId = "mst_edge_font_color",
+                            width = "100%",
+                            selected = "#000000",
+                            label = "",
+                            update = "changestop",
+                            interaction = list(clear = FALSE,
+                                               save = FALSE),
+                            position = "right-start"
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          dropMenu(
+                            actionBttn(
+                              "mst_edgelabel_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            width = 5,
+                            numericInput(
+                              "mst_edge_font_size",
+                              label = h5("Size", style = "color:white; margin-bottom: 0px;"),
+                              value = 18,
+                              step = 1,
+                              min = 8,
+                              max = 30,
+                              width = "80px"
+                            )
+                          )
+                        )
+                      ),
+                      br()
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Color"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 7,
+                              div(
+                                class = "node_color",
+                                colorPickr(
+                                  inputId = "mst_color_edge",
+                                  width = "100%",
+                                  selected = "#000000",
+                                  label = "",
+                                  update = "changestop",
+                                  interaction = list(clear = FALSE,
+                                                     save = FALSE),
+                                  position = "right-start"
+                                )
+                              )
+                            ),
+                            column(
+                              width = 5,
+                              dropMenu(
+                                actionBttn(
+                                  "mst_edgecolor_menu",
+                                  label = "",
+                                  color = "default",
+                                  size = "sm",
+                                  style = "material-flat",
+                                  icon = icon("sliders")
+                                ),
+                                placement = "top-start",
+                                theme = "translucent",
+                                width = 5,
+                                sliderInput(
+                                  "mst_edge_opacity",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px;"),
+                                  value = 0.7,
+                                  step = 0.1,
+                                  min = 0,
+                                  max = 1,
+                                  ticks = FALSE,
+                                  width = "150px"
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                ),
+                hr(style = "margin-top: 3px !important"),
+                fluidRow(
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Length multiplier"), style = "color:white; position: relative; right: -15px; margin-bottom: -5px")
+                      )
+                    ),
+                    column(
+                      width = 12,
+                      align = "left",
+                      br(),
+                      div(
+                        class = "switch-mst-edges",
+                        materialSwitch(
+                          "mst_scale_edges",
+                          h5(p("Scale Allelic Distance"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                          value = FALSE,
+                          right = TRUE
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          align = "left",
+                          conditionalPanel(
+                            "input.mst_scale_edges==true",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Multiplier')
+                              )
+                            )
+                          ),
+                          conditionalPanel(
+                            "input.mst_scale_edges==false",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Length')
+                              )
+                            )
+                          )
+                        ),
+                        column(
+                          width = 9,
+                          align = "center",
+                          conditionalPanel(
+                            "input.mst_scale_edges==true",
+                            div(
+                              class = "slider_edge",
+                              sliderInput(
+                                inputId = "mst_edge_length_scale",
+                                label = NULL,
+                                min = 1,
+                                max = 40,
+                                value = 15,
+                                ticks = FALSE
+                              ) 
+                            )
+                          ),
+                          conditionalPanel(
+                            "input.mst_scale_edges==false",
+                            div(
+                              class = "slider_edge",
+                              sliderTextInput(
+                                inputId = "mst_edge_length",
+                                label = NULL,
+                                choices = append(seq(0.1, 1, 0.1), 2:100),
+                                selected = 35,
+                                hide_min_max = FALSE
+                              ) 
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 6,
+                        align = "left",
+                        h4(p("Clustering"), style = "color:white; text-align: left; position: relative; right: -15px")
+                      ),
+                      column(
+                        width = 2,
+                        bslib::tooltip(
+                          bsicons::bs_icon("info-circle", 
+                                           title = "Cluster threshold according to species-specific\nComplex Type Distance (cgMLST.org)", 
+                                           color = "white", height = "14px", width = "14px", 
+                                           position = "relative", top = "9px", right = "28px"),
+                          "Text shown in the tooltip.",
+                          show = FALSE,
+                          id = "mst_cluster_info"
+                        )
+                      )
+                    ),
+                    br(),
+                    fluidRow(
+                      column(
+                        width = 9,
+                        div(
+                          class = "mst-cluster-switch",
+                          materialSwitch(
+                            "mst_show_clusters",
+                            h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        dropMenu(
+                          actionBttn(
+                            "mst_cluster_col_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          width = 5,
+                          selectInput(
+                            "mst_cluster_col_scale",
+                            label = h5("Color Scale", style = "color:white; margin-bottom: 0px;"),
+                            choices = c("Viridis", "Rainbow"),
+                            width = "150px"
+                          ),
+                          selectInput(
+                            "mst_cluster_type",
+                            label = h5("Cluster Type", style = "color:white; margin-bottom: 0px;"),
+                            choices = c("Type 1", "Type 2"),
+                            width = "150px"
+                          )
+                        )
+                      )
+                    ),
+                    br(),
+                    fluidRow(
+                      column(
+                        width = 4,
+                        HTML(
+                          paste(
+                            tags$span(style='color: white; text-align: left; font-size: 14px; margin-left: 15px', 'Threshold')
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        uiOutput("mst_cluster")
+                      ),
+                      column(
+                        width = 4,
+                        actionButton(
+                          "mst_cluster_reset",
+                          label = "",
+                          icon = icon("rotate")
+                        ),
+                        bsTooltip("mst_cluster_reset", 
+                                  HTML("Reset to default Complex Type Distance"), 
+                                  placement = "top", trigger = "hover")
+                      )
+                    )
+                  ),
+                  br(),
+                )
+              ), br(), br(), br(), br(), br(), br()
+            )
+          )
+        ),
+        
+        ### Control Panels NJ ----
+        
+        conditionalPanel(
+          "input.tree_algo=='Neighbour-Joining'",
+          fluidRow(
+            column(
+              width = 1,
+              radioGroupButtons(
+                inputId = "nj_controls",
+                label = "",
+                choices = c("Layout", "Label", "Elements", "Variables"),
+                direction = "vertical"
+              )
+            ),
+            conditionalPanel(
+              "input.nj_controls=='Layout'",
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Theme"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "center",
+                        selectInput(
+                          inputId = "nj_layout",
+                          label = "",
+                          choices = list(
+                            Linear = list(
+                              "Rectangular" = "rectangular",
+                              "Roundrect" = "roundrect",
+                              "Slanted" = "slanted",
+                              "Ellipse" = "ellipse"
+                            ),
+                            Circular = list("Circular" = "circular",
+                                            "Inward" = "inward")
+                          ),
+                          selected = "rectangular",
+                          width = "90%"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch-layout",
+                          materialSwitch(
+                            "nj_rootedge_show",
+                            h5(p("Rootedge"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "nj_rootedge_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("nj_rootedge_length"),
+                              br(),
+                              selectInput(
+                                "nj_rootedge_line",
+                                label = h5("Rootedge Line", style = "color:white"),
+                                choices = c(Solid = "solid", Dashed = "dashed", Dotted = "dotted"),
+                                selected = c(Dotted = "solid"),
+                                width = "100px"
+                              ),
+                              br(),
+                              conditionalPanel(
+                                "input.nj_layout=='circular'",
+                                sliderInput(
+                                  "nj_xlim",
+                                  label = h5("Adjust Circular", style = "color:white"),
+                                  min = -50,
+                                  max = 0,
+                                  value = -10,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.nj_layout=='inward'",
+                                sliderInput(
+                                  "nj_inward_xlim",
+                                  label = h5("Adjust Circular", style = "color:white"),
+                                  min = 30,
+                                  max = 120,
+                                  value = 50,
+                                  ticks = FALSE,
+                                  width = "150px",
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch-re",
+                          materialSwitch(
+                            "nj_ladder",
+                            h5(p("Ladderize"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                            value = TRUE,
+                            right = TRUE
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Color"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Lines/Text"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
+                      ),
+                      column(
+                        width = 7,
+                        colorPickr(
+                          inputId = "nj_color",
+                          width = "90%",
+                          selected = "#000000",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    br(),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Background"), style = "color:white; position: relative; right: -15px; margin-top: 7px; margin-bottom: 38px")
+                      ),
+                      column(
+                        width = 7,
+                        colorPickr(
+                          inputId = "nj_bg",
+                          width = "90%",
+                          selected = "#ffffff",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ), 
+                    br()
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Title"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      textInput(
+                        "nj_title",
+                        label = "",
+                        width = "100%",
+                        placeholder = "Plot Title"
+                      ),
+                      textInput(
+                        "nj_subtitle",
+                        label = "",
+                        width = "100%",
+                        placeholder = "Plot Subtitle"
+                      ),
+                      br(),
+                      fluidRow(
+                        column(
+                          width = 7,
+                          colorPickr(
+                            inputId = "nj_title_color",
+                            selected = "#000000",
+                            label = "",
+                            update = "changestop",
+                            interaction = list(clear = FALSE,
+                                               save = FALSE),
+                            position = "right-start",
+                            width = "100%"
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "nj_title_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                numericInput(
+                                  "nj_title_size",
+                                  label = h5("Title Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 30,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                ),
+                                br(),
+                                numericInput(
+                                  "nj_subtitle_size",
+                                  label = h5("Subtitle Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 20,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      br()
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Sizing"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      br(),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Ratio", style = "color: white; font-size: 14px;")
+                        ),
+                        column(
+                          width = 6,
+                          align = "left",
+                          div(
+                            class = "ratio-sel",
+                            selectInput(
+                              "nj_ratio",
+                              "",
+                              choices = c("16:10" = (16/10), "16:9" = (16/9), "4:3" = (4/3))
+                            )
+                          )
+                        ),
+                        column(
+                          width = 3,
+                          dropMenu(
+                            actionBttn(
+                              "nj_size_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                sliderInput(
+                                  "nj_v",
+                                  label = h5("Vertical Position", style = "color:white; margin-bottom: 0px"),
+                                  min = -0.5,
+                                  max = 0.5,
+                                  step = 0.01,
+                                  value = 0,
+                                  width = "150px",
+                                  ticks = FALSE
+                                ),
+                                br(),
+                                sliderInput(
+                                  "nj_h",
+                                  label = h5("Horizontal Position", style = "color:white; margin-bottom: 0px"),
+                                  min = -0.5,
+                                  max = 0.5,
+                                  step = 0.01,
+                                  value = 0,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Size", style = "color: white; font-size: 14px; margin-top: 30px")
+                        ),
+                        column(
+                          width = 9,
+                          sliderInput(
+                            "nj_scale",
+                            "",
+                            min = 500,
+                            max = 1200,
+                            value = 800,
+                            step = 5,
+                            width = "95%",
+                            ticks = FALSE
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Zoom", style = "color: white; font-size: 14px; margin-top: 30px")
+                        ),
+                        column(
+                          width = 9,
+                          div(
+                            class = "zoom-slider",
+                            sliderInput(
+                              "nj_zoom",
+                              label = NULL,
+                              min = 0.5,
+                              max = 1.5,
+                              step = 0.05,
+                              value = 0.95,
+                              ticks = FALSE
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Tree Scale"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      fluidRow(
+                        column(
+                          width = 8,
+                          align = "left",
+                          div(
+                            class = "mat-switch-layout",
+                            materialSwitch(
+                              "nj_treescale_show",
+                              h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                              value = TRUE,
+                              right = TRUE
+                            )
+                          ),
+                          br()
+                        ),
+                        column(
+                          width = 4,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "nj_treescale_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                uiOutput("nj_treescale_width"),
+                                br(),
+                                uiOutput("nj_treescale_x"),
+                                br(),
+                                uiOutput("nj_treescale_y")
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Legend"), style = "color:white; position: relative; right: -15px; margin-top: 10px; margin-bottom: -2px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      fluidRow(
+                        column(
+                          width = 7,
+                          align = "left",
+                          prettyRadioButtons(
+                            "nj_legend_orientation",
+                            "",
+                            choices = c(Horizontal = "horizontal",
+                                        Vertical = "vertical"),
+                            selected = c(Vertical = "vertical"),
+                            inline = FALSE
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "nj_legend_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                numericInput(
+                                  "nj_legend_size",
+                                  label = h5("Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 10,
+                                  min = 5,
+                                  max = 25,
+                                  step = 1,
+                                  width = "80px"
+                                ),
+                                br(),
+                                sliderInput(
+                                  "nj_legend_x",
+                                  label = h5("Horizontal Position", style = "color:white; margin-bottom: 0px"),
+                                  value = 0.9,
+                                  min = -0.9,
+                                  max = 1.9,
+                                  step = 0.2,
+                                  width = "150px",
+                                  ticks = FALSE
+                                ),
+                                br(),
+                                sliderInput(
+                                  "nj_legend_y",
+                                  label = h5("Vertical Position", style = "color:white; margin-bottom: 0px"),
+                                  value = 0.2,
+                                  min = -1.5,
+                                  max = 1.5,
+                                  step = 0.1,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.nj_controls=='Label'",
+              column(
+                width = 4,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Tips"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 4,
+                            align = "left",
+                            div(
+                              class = "mat-switch-lab",
+                              materialSwitch(
+                                "nj_tiplab_show",
+                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                                value = TRUE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 4,
+                            align = "center",
+                            uiOutput("nj_tiplab")
+                          ),
+                          column(
+                            width = 3,
+                            div(
+                              class = "mat-switch-align",
+                              materialSwitch(
+                                "nj_align",
+                                h5(p("Align"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 1,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "nj_labeltext_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-start",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  sliderInput(
+                                    "nj_tiplab_alpha",
+                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                    min = 0.1,
+                                    max = 1,
+                                    value = 1,
+                                    width = "150px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  conditionalPanel(
+                                    "!(input.nj_layout=='inward'|input.nj_layout=='circular')",
+                                    sliderInput(
+                                      inputId = "nj_tiplab_nudge_x",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = 0,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  conditionalPanel(
+                                    "input.nj_layout=='circular'",
+                                    sliderInput(
+                                      inputId = "nj_tiplab_position",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = -0.05,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  conditionalPanel(
+                                    "input.nj_layout=='inward'",
+                                    sliderInput(
+                                      inputId = "nj_tiplab_position_inw",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = 1.1,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "nj_tiplab_angle",
+                                    label = h5("Angle", style = "color:white; margin-bottom: 0px"),
+                                    min = -90,
+                                    max = 90,
+                                    value = 0,
+                                    ticks = FALSE,
+                                    width = "150px",
+                                  )      
+                                ),
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  uiOutput("nj_tiplab_size"),
+                                  br(),
+                                  selectInput(
+                                    "nj_tiplab_fontface",
+                                    label = h5("Fontface", style = "color:white; margin-bottom: 5px; margin-top: 16px"),
+                                    width = "250px",
+                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 4,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px")
+                      ),
+                      column(
+                        width = 4,
+                        align = "center",
+                        colorPickr(
+                          inputId = "nj_tiplab_color",
+                          width = "100%",
+                          selected = "#000000",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 4,
+                        align = "left",
+                        br(),
+                        div(
+                          class = "mat-switch-geom",
+                          materialSwitch(
+                            "nj_geom",
+                            h5(p("Panels"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        colorPickr(
+                          inputId = "nj_tiplab_fill",
+                          width = "100%",
+                          selected = "#84D9A0",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "left",
+                        dropMenu(
+                          actionBttn(
+                            "nj_labelformat_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("nj_tiplab_padding"),
+                              br(),
+                              sliderInput(
+                                inputId = "nj_tiplab_labelradius",
+                                label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
+                                min = 0,
+                                max = 0.5,
+                                value = 0.2,
+                                width = "150px",
+                                ticks = FALSE
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 3,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Branches"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 5,
+                            align = "left",
+                            div(
+                              class = "mat-switch-lab",
+                              materialSwitch(
+                                "nj_show_branch_label",
+                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 5,
+                            align = "center",
+                            uiOutput("nj_branch_label")
+                          ),
+                          column(
+                            width = 2,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "nj_branch_label_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-start",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  sliderInput(
+                                    "nj_branchlab_alpha",
+                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                    min = 0.1,
+                                    max = 1,
+                                    value = 0.65,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "nj_branch_x",
+                                    label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+                                    min = -3,
+                                    max = 3,
+                                    value = 0,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "nj_branch_y",
+                                    label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+                                    min = -3,
+                                    max = 3,
+                                    value = 0,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  )
+                                ),
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  uiOutput("nj_branch_size"),
+                                  selectInput(
+                                    "nj_branchlab_fontface",
+                                    label = h5("Fontface", style = "color:white; margin-bottom: 0px;"),
+                                    width = "250px",
+                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    "nj_branch_labelradius",
+                                    label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
+                                    min = 0,
+                                    max = 0.5,
+                                    value = 0.5,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px; margin-bottom: 109px")
+                      ),
+                      column(
+                        width = 5,
+                        colorPickr(
+                          inputId = "nj_branch_label_color",
+                          width = "100%",
+                          selected = "#FFB7B7",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 3,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Custom Labels"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 6,
+                            textInput(
+                              "nj_new_label_name",
+                              "",
+                              placeholder = "New Label"
+                            )
+                          ),
+                          column(
+                            width = 3,
+                            actionButton(
+                              "nj_add_new_label",
+                              "",
+                              icon = icon("plus")
+                            )
+                          ),
+                          column(
+                            width = 2,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "nj_custom_label_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-end",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 12,
+                                  align = "center",
+                                  uiOutput("nj_custom_labelsize"),
+                                  br(),
+                                  uiOutput("nj_sliderInput_y"),
+                                  br(),
+                                  uiOutput("nj_sliderInput_x")
+                                )
+                              )
+                            )
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 6,
+                            uiOutput("nj_custom_label_select")
+                          ),
+                          column(
+                            width = 4,
+                            uiOutput("nj_del_label"),
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 12,
+                            align = "center",
+                            uiOutput("nj_cust_label_save")
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.nj_controls=='Elements'",
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Tip Points"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "nj_tippoint_show",
+                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "nj_tippoint_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              sliderInput(
+                                "nj_tippoint_alpha",
+                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                value = 0.5,
+                                min = 0.1,
+                                max = 1,
+                                width = "150px",
+                                ticks = FALSE
+                              ), 
+                              br(),
+                              uiOutput("nj_tippoint_size")
+                            )
+                          )
+                        )  
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        colorPickr(
+                          inputId = "nj_tippoint_color",
+                          width = "100%",
+                          selected = "#3A4657",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        conditionalPanel(
+                          "input.nj_tipshape_mapping_show==false",
+                          selectInput(
+                            "nj_tippoint_shape",
+                            "",
+                            width = "100%",
+                            choices = c(
+                              Circle = "circle", 
+                              Square = "square", 
+                              Diamond = "diamond", 
+                              Triangle = "triangle",
+                              Cross = "cross", 
+                              Asterisk = "asterisk"
+                            )
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.nj_tipshape_mapping_show==true",
+                          h5(p("Variable assigned"), style = "color:white; position: relative; right: -15px; margin-top: 30px; font-style: italic")
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Node Points"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "nj_nodepoint_show",
+                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "nj_nodepoint_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              sliderInput(
+                                "nj_nodepoint_alpha",
+                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                value = 1,
+                                min = 0.1,
+                                max = 1,
+                                width = "150px",
+                                ticks = FALSE
+                              ), 
+                              br(),
+                              uiOutput("nj_nodepoint_size")
+                            )
+                          )
+                        )  
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        colorPickr(
+                          inputId = "nj_nodepoint_color",
+                          width = "100%",
+                          selected = "#3A4657",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        selectInput(
+                          "nj_nodepoint_shape",
+                          "",
+                          choices = c(
+                            Circle = "circle", 
+                            Square = "square", 
+                            Diamond = "diamond", 
+                            Triangle = "triangle",
+                            Cross = "cross", 
+                            Asterisk = "asterisk"
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 6,
+                        h4(p("Tiles"), style = "color:white; position: relative; right: -15px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        div(
+                          class = "sel-tile-number",
+                          selectInput(
+                            "nj_tile_number",
+                            "",
+                            choices = 1:5,
+                            width = "70px"
+                          )
+                        )
+                      ),
+                      column(
+                        width = 7,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "nj_tile_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              conditionalPanel(
+                                "input.nj_tile_num == 1",
+                                sliderInput(
+                                  "nj_fruit_alpha",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.nj_tile_num == 2",
+                                sliderInput(
+                                  "nj_fruit_alpha_2",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.nj_tile_num == 3",
+                                sliderInput(
+                                  "nj_fruit_alpha_3",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.nj_tile_num == 4",
+                                sliderInput(
+                                  "nj_fruit_alpha_4",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.nj_tile_num == 5",
+                                sliderInput(
+                                  "nj_fruit_alpha_5",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.nj_tile_num == 1",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_width"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 68px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_offset_circ"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.nj_tile_num == 2",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_width2"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_offset_circ_2"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.nj_tile_num == 3",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_width3"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_offset_circ_3"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.nj_tile_num == 4",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_width4"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_offset_circ_4"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.nj_tile_num == 5",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_width5"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_offset_circ_5"),
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 6,
+                        h4(p("Heatmap"), style = "color:white; position: relative; right: -15px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        h5("Title", style = "color:white; margin-left: 15px; margin-top: 32px;")
+                      ),
+                      column(
+                        width = 6,
+                        align = "center",
+                        textInput(
+                          "nj_heatmap_title",
+                          label = "",
+                          value = "Heatmap",
+                          placeholder = "Heatmap" 
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "nj_heatmap_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("nj_colnames_angle"),
+                              br(),
+                              uiOutput("nj_colnames_y")
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5("Width", style = "color: white; margin-left: 15px; margin-top: 40px;")
+                      ),
+                      column(
+                        width = 7,
+                        uiOutput("nj_heatmap_width")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5("Position", style = "color:white; margin-left: 15px; margin-top: 36px;")
+                      ),
+                      column(
+                        width = 7,
+                        uiOutput("nj_heatmap_offset")
+                      )
+                    ),
+                    br(), br()
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Clade Highlight"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 12,
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "nj_nodelabel_show",
+                            h5(p("Toggle Node View"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        h5(p("Nodes"), style = "color:white; position: relative; right: -15px; margin-top: 20px")
+                      ),
+                      column(
+                        width = 9,
+                        uiOutput("nj_parentnode")
+                      )
+                    ),
+                    uiOutput("nj_clade_scale"),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Form"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
+                      ),
+                      column(
+                        width = 7,
+                        div(
+                          class = "sel-clade",
+                          selectInput(
+                            "nj_clade_type",
+                            "",
+                            choices = c("Rect" = "rect",
+                                        "Round" = "roundrect"),
+                            selected = c("Round" = "roundrect")
+                          ) 
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.nj_controls=='Variables'",
+              column(
+                width = 7,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 3,
+                        align = "center",
+                        h4(p("Element"), style = "color:white; margin-bottom: 20px")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        h4(p("Variable"), style = "color:white; margin-bottom: 20px; margin-right: 30px;")
+                      ),
+                      column(
+                        width = 6,
+                        align = "center",
+                        h4(p("Color Scale"), style = "color:white; margin-bottom: 20px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "nj_mapping_show",
+                            h5(p("Tip Label Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_color_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_tiplab_scale")
+                      ),
+                      uiOutput("nj_tiplab_mapping_info"),
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "nj_tipcolor_mapping_show",
+                            h5(p("Tip Point Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_tipcolor_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_tippoint_scale")
+                      ),
+                      uiOutput("nj_tipcolor_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "nj_tipshape_mapping_show",
+                            h5(p("Tip Point Shape"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_tipshape_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        HTML(
+                          paste(
+                            tags$span(style='color: white; font-size: 14px; font-style: italic; position: relative; bottom: -16px; right: -40px;', 'No scale for shapes')
+                          )
+                        )
+                      ),
+                      uiOutput("nj_tipshape_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        fluidRow(
+                          column(
+                            width = 8,
+                            conditionalPanel(
+                              "input.nj_tile_num == 1",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "nj_tiles_show_1",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px; margin-right: 10px"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.nj_tile_num == 2",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "nj_tiles_show_2",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.nj_tile_num == 3",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "nj_tiles_show_3",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.nj_tile_num == 4",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "nj_tiles_show_4",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.nj_tile_num == 5",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "nj_tiles_show_5",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            )
+                          ), 
+                          column(
+                            width = 4,
+                            align = "left",
+                            div(
+                              class = "tile-sel",
+                              selectInput(
+                                "nj_tile_num",
+                                "",
+                                choices = 1:5,
+                                width = "50px"
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        conditionalPanel(
+                          "input.nj_tile_num == 1",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_fruit_variable")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.nj_tile_num == 2",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_fruit_variable2")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.nj_tile_num == 3",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_fruit_variable3")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.nj_tile_num == 4",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_fruit_variable4")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.nj_tile_num == 5",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_fruit_variable5")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.nj_tile_num == 1",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_tiles_scale_1")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.nj_tile_num == 2",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_tiles_scale_2")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.nj_tile_num == 3",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_tiles_scale_3")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.nj_tile_num == 4",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_tiles_scale_4")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.nj_tile_num == 5",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_tiles_scale_5")
+                          )
+                        )
+                      ),
+                      uiOutput("nj_fruit_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "nj_heatmap_show",
+                            h5(p("Heatmap"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_heatmap_sel")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        div(
+                          class = "heatmap-scale",
+                          uiOutput("nj_heatmap_scale")
+                        )
+                      ),
+                      uiOutput("nj_heatmap_mapping_info")
+                    )
+                  )
+                )
+              )
+            )
+          ),
+          br(), br(), br(), br(), br(), br()
+        ),
+        
+        ### Control Panels UPGMA ----
+        
+        conditionalPanel(
+          "input.tree_algo=='UPGMA'",
+          fluidRow(
+            column(
+              width = 1,
+              radioGroupButtons(
+                inputId = "upgma_controls",
+                label = "",
+                choices = c("Layout", "Label", "Elements", "Variables"),
+                direction = "vertical"
+              )
+            ),
+            conditionalPanel(
+              "input.upgma_controls=='Layout'",
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Theme"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "center",
+                        selectInput(
+                          inputId = "upgma_layout",
+                          label = "",
+                          choices = list(
+                            Linear = list(
+                              "Rectangular" = "rectangular",
+                              "Roundrect" = "roundrect",
+                              "Slanted" = "slanted",
+                              "Ellipse" = "ellipse"
+                            ),
+                            Circular = list("Circular" = "circular",
+                                            "Inward" = "inward")
+                          ),
+                          selected = "rectangular",
+                          width = "90%"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch-layout",
+                          materialSwitch(
+                            "upgma_rootedge_show",
+                            h5(p("Rootedge"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_rootedge_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("upgma_rootedge_length"),
+                              br(),
+                              selectInput(
+                                "upgma_rootedge_line",
+                                label = h5("Rootedge Line", style = "color:white"),
+                                choices = c(Solid = "solid", Dashed = "dashed", Dotted = "dotted"),
+                                selected = c(Dotted = "solid"),
+                                width = "100px"
+                              ),
+                              br(),
+                              conditionalPanel(
+                                "input.upgma_layout=='circular'",
+                                sliderInput(
+                                  "upgma_xlim",
+                                  label = h5("Adjust Circular", style = "color:white"),
+                                  min = -50,
+                                  max = 0,
+                                  value = -10,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.upgma_layout=='inward'",
+                                sliderInput(
+                                  "upgma_inward_xlim",
+                                  label = h5("Adjust Circular", style = "color:white"),
+                                  min = 30,
+                                  max = 120,
+                                  value = 50,
+                                  ticks = FALSE,
+                                  width = "150px",
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch-re",
+                          materialSwitch(
+                            "upgma_ladder",
+                            h5(p("Ladderize"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                            value = TRUE,
+                            right = TRUE
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Color"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Lines/Text"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
+                      ),
+                      column(
+                        width = 7,
+                        colorPickr(
+                          inputId = "upgma_color",
+                          width = "90%",
+                          selected = "#000000",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    br(),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Background"), style = "color:white; position: relative; right: -15px; margin-top: 7px; margin-bottom: 38px")
+                      ),
+                      column(
+                        width = 7,
+                        colorPickr(
+                          inputId = "upgma_bg",
+                          width = "90%",
+                          selected = "#ffffff",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Title"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      textInput(
+                        "upgma_title",
+                        label = "",
+                        width = "100%",
+                        placeholder = "Plot Title"
+                      ),
+                      textInput(
+                        "upgma_subtitle",
+                        label = "",
+                        width = "100%",
+                        placeholder = "Plot Subtitle"
+                      ),
+                      br(),
+                      fluidRow(
+                        column(
+                          width = 7,
+                          colorPickr(
+                            inputId = "upgma_title_color",
+                            selected = "#000000",
+                            label = "",
+                            update = "changestop",
+                            interaction = list(clear = FALSE,
+                                               save = FALSE),
+                            position = "right-start",
+                            width = "100%"
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "upgma_title_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                numericInput(
+                                  "upgma_title_size",
+                                  label = h5("Title Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 30,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                ),
+                                br(),
+                                numericInput(
+                                  "upgma_subtitle_size",
+                                  label = h5("Subtitle Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 20,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Sizing"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      br(),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Ratio", style = "color: white; font-size: 14px;")
+                        ),
+                        column(
+                          width = 6,
+                          align = "left",
+                          div(
+                            class = "ratio-sel",
+                            selectInput(
+                              "upgma_ratio",
+                              "",
+                              choices = c("16:10" = (16/10), "16:9" = (16/9), "4:3" = (4/3))
+                            )
+                          )
+                        ),
+                        column(
+                          width = 3,
+                          dropMenu(
+                            actionBttn(
+                              "upgma_size_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                sliderInput(
+                                  "upgma_v",
+                                  label = "Vertical Position",
+                                  min = -0.5,
+                                  max = 0.5,
+                                  step = 0.01,
+                                  value = 0,
+                                  width = "150px",
+                                  ticks = FALSE
+                                ),
+                                br(),
+                                sliderInput(
+                                  "upgma_h",
+                                  label = "Horizontal Position",
+                                  min = -0.5,
+                                  max = 0.5,
+                                  step = 0.01,
+                                  value = 0,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Size", style = "color: white; font-size: 14px; margin-top: 30px")
+                        ),
+                        column(
+                          width = 9,
+                          sliderInput(
+                            "upgma_scale",
+                            "",
+                            min = 500,
+                            max = 1200,
+                            value = 800,
+                            step = 5,
+                            width = "95%",
+                            ticks = FALSE
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Zoom", style = "color: white; font-size: 14px; margin-top: 30px")
+                        ),
+                        column(
+                          width = 9,
+                          div(
+                            class = "zoom-slider",
+                            sliderInput(
+                              "upgma_zoom",
+                              label = NULL,
+                              min = 0.5,
+                              max = 1.5,
+                              step = 0.05,
+                              value = 0.95,
+                              ticks = FALSE
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Tree Scale"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      fluidRow(
+                        column(
+                          width = 8,
+                          align = "left",
+                          div(
+                            class = "mat-switch-layout",
+                            materialSwitch(
+                              "upgma_treescale_show",
+                              h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                              value = TRUE,
+                              right = TRUE
+                            )
+                          ),
+                          br()
+                        ),
+                        column(
+                          width = 4,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "upgma_treescale_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                uiOutput("upgma_treescale_width"),
+                                br(),
+                                uiOutput("upgma_treescale_x"),
+                                br(),
+                                uiOutput("upgma_treescale_y")
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Legend"), style = "color:white; position: relative; right: -15px; margin-top: 10px; margin-bottom: -2px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      fluidRow(
+                        column(
+                          width = 7,
+                          align = "left",
+                          prettyRadioButtons(
+                            "upgma_legend_orientation",
+                            "",
+                            choices = c(Horizontal = "horizontal",
+                                        Vertical = "vertical"),
+                            selected = c(Vertical = "vertical"),
+                            inline = FALSE
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "upgma_legend_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                numericInput(
+                                  "upgma_legend_size",
+                                  label = h5("Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 10,
+                                  min = 5,
+                                  max = 25,
+                                  step = 1,
+                                  width = "80px"
+                                ),
+                                br(),
+                                sliderInput(
+                                  "upgma_legend_x",
+                                  label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+                                  value = 0.9,
+                                  min = -0.9,
+                                  max = 1.9,
+                                  step = 0.2,
+                                  width = "150px",
+                                  ticks = FALSE
+                                ),
+                                br(),
+                                sliderInput(
+                                  "upgma_legend_y",
+                                  label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+                                  value = 0.2,
+                                  min = -1.5,
+                                  max = 1.5,
+                                  step = 0.1,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.upgma_controls=='Label'",
+              column(
+                width = 4,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Tips"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 4,
+                            align = "left",
+                            div(
+                              class = "mat-switch-lab",
+                              materialSwitch(
+                                "upgma_tiplab_show",
+                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                                value = TRUE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 4,
+                            align = "center",
+                            uiOutput("upgma_tiplab")
+                          ),
+                          column(
+                            width = 3,
+                            div(
+                              class = "mat-switch-align",
+                              materialSwitch(
+                                "upgma_align",
+                                h5(p("Align"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 1,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "upgma_labeltext_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-start",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  sliderInput(
+                                    "upgma_tiplab_alpha",
+                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                    min = 0.1,
+                                    max = 1,
+                                    value = 1,
+                                    width = "150px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  conditionalPanel(
+                                    "!(input.upgma_layout=='inward'|input.upgma_layout=='circular')",
+                                    sliderInput(
+                                      inputId = "upgma_tiplab_nudge_x",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = 0,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  conditionalPanel(
+                                    "input.upgma_layout=='circular'",
+                                    sliderInput(
+                                      inputId = "upgma_tiplab_position",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = -0.05,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  conditionalPanel(
+                                    "input.upgma_layout=='inward'",
+                                    sliderInput(
+                                      inputId = "upgma_tiplab_position_inw",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = 1.1,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "upgma_tiplab_angle",
+                                    label = h5("Angle", style = "color:white; margin-bottom: 0px"),
+                                    min = -90,
+                                    max = 90,
+                                    value = 0,
+                                    ticks = FALSE,
+                                    width = "150px",
+                                  )      
+                                ),
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  uiOutput("upgma_tiplab_size"),
+                                  br(),
+                                  selectInput(
+                                    "upgma_tiplab_fontface",
+                                    label = h5("Fontface", style = "color:white; margin-bottom: 5px; margin-top: 16px"),
+                                    width = "250px",
+                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 4,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px")
+                      ),
+                      column(
+                        width = 4,
+                        align = "center",
+                        colorPickr(
+                          inputId = "upgma_tiplab_color",
+                          width = "100%",
+                          selected = "#000000",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 4,
+                        align = "left",
+                        br(),
+                        div(
+                          class = "mat-switch-geom",
+                          materialSwitch(
+                            "upgma_geom",
+                            h5(p("Panels"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        colorPickr(
+                          inputId = "upgma_tiplab_fill",
+                          width = "100%",
+                          selected = "#84D9A0",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "left",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_labelformat_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("upgma_tiplab_padding"),
+                              br(),
+                              sliderInput(
+                                inputId = "upgma_tiplab_labelradius",
+                                label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
+                                min = 0,
+                                max = 0.5,
+                                value = 0.2,
+                                width = "150px",
+                                ticks = FALSE
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 3,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Branches"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 5,
+                            align = "left",
+                            div(
+                              class = "mat-switch-lab",
+                              materialSwitch(
+                                "upgma_show_branch_label",
+                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 5,
+                            align = "center",
+                            uiOutput("upgma_branch_label")
+                          ),
+                          column(
+                            width = 2,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "upgma_branch_label_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-start",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  sliderInput(
+                                    "upgma_branchlab_alpha",
+                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                    min = 0.1,
+                                    max = 1,
+                                    value = 0.65,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "upgma_branch_x",
+                                    label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+                                    min = -3,
+                                    max = 3,
+                                    value = 0,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "upgma_branch_y",
+                                    label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+                                    min = -3,
+                                    max = 3,
+                                    value = 0,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  )
+                                ),
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  uiOutput("upgma_branch_size"),
+                                  selectInput(
+                                    "upgma_branchlab_fontface",
+                                    label = h5("Fontface", style = "color:white; margin-bottom: 0px;"),
+                                    width = "250px",
+                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    "upgma_branch_labelradius",
+                                    label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
+                                    min = 0,
+                                    max = 0.5,
+                                    value = 0.5,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px; margin-bottom: 109px")
+                      ),
+                      column(
+                        width = 5,
+                        colorPickr(
+                          inputId = "upgma_branch_label_color",
+                          width = "100%",
+                          selected = "#FFB7B7",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        ),
+                        br(), br()
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 3,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Custom Labels"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 6,
+                            textInput(
+                              "upgma_new_label_name",
+                              "",
+                              placeholder = "New Label"
+                            )
+                          ),
+                          column(
+                            width = 3,
+                            actionButton(
+                              "upgma_add_new_label",
+                              "",
+                              icon = icon("plus")
+                            )
+                          ),
+                          column(
+                            width = 2,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "upgma_custom_label_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-end",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 12,
+                                  align = "center",
+                                  uiOutput("upgma_custom_labelsize"),
+                                  br(),
+                                  uiOutput("upgma_sliderInput_y"),
+                                  br(),
+                                  uiOutput("upgma_sliderInput_x")
+                                )
+                              )
+                            )
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 6,
+                            uiOutput("upgma_custom_label_select")
+                          ),
+                          column(
+                            width = 4,
+                            uiOutput("upgma_del_label"),
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 12,
+                            align = "center",
+                            uiOutput("upgma_cust_label_save")
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.upgma_controls=='Elements'",
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Tip Points"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "upgma_tippoint_show",
+                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_tippoint_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              sliderInput(
+                                "upgma_tippoint_alpha",
+                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                value = 0.5,
+                                min = 0.1,
+                                max = 1,
+                                width = "150px",
+                                ticks = FALSE
+                              ), 
+                              br(),
+                              uiOutput("upgma_tippoint_size")
+                            )
+                          )
+                        )  
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        colorPickr(
+                          inputId = "upgma_tippoint_color",
+                          width = "100%",
+                          selected = "#3A4657",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        conditionalPanel(
+                          "input.upgma_tipshape_mapping_show==false",
+                          selectInput(
+                            "upgma_tippoint_shape",
+                            "",
+                            width = "100%",
+                            choices = c(
+                              Circle = "circle", 
+                              Square = "square", 
+                              Diamond = "diamond", 
+                              Triangle = "triangle",
+                              Cross = "cross", 
+                              Asterisk = "asterisk"
+                            )
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.upgma_tipshape_mapping_show==true",
+                          h5(p("Variable assigned"), style = "color:white; position: relative; right: -15px; margin-top: 30px; font-style: italic")
+                        ),
+                        br()
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Node Points"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "upgma_nodepoint_show",
+                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_nodepoint_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              sliderInput(
+                                "upgma_nodepoint_alpha",
+                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                value = 1,
+                                min = 0.1,
+                                max = 1,
+                                width = "150px",
+                                ticks = FALSE
+                              ), 
+                              br(),
+                              uiOutput("upgma_nodepoint_size")
+                            )
+                          )
+                        )  
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        colorPickr(
+                          inputId = "upgma_nodepoint_color",
+                          width = "100%",
+                          selected = "#3A4657",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        selectInput(
+                          "upgma_nodepoint_shape",
+                          "",
+                          choices = c(
+                            Circle = "circle", 
+                            Square = "square", 
+                            Diamond = "diamond", 
+                            Triangle = "triangle",
+                            Cross = "cross", 
+                            Asterisk = "asterisk"
+                          )
+                        ),
+                        br()
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 6,
+                        h4(p("Tiles"), style = "color:white; position: relative; right: -15px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        div(
+                          class = "sel-tile-number",
+                          selectInput(
+                            "upgma_tile_number",
+                            "",
+                            choices = 1:5,
+                            width = "70px"
+                          )
+                        )
+                      ),
+                      column(
+                        width = 7,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_tile_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              conditionalPanel(
+                                "input.upgma_tile_num == 1",
+                                sliderInput(
+                                  "upgma_fruit_alpha",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.upgma_tile_num == 2",
+                                sliderInput(
+                                  "upgma_fruit_alpha_2",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.upgma_tile_num == 3",
+                                sliderInput(
+                                  "upgma_fruit_alpha_3",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.upgma_tile_num == 4",
+                                sliderInput(
+                                  "upgma_fruit_alpha_4",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.upgma_tile_num == 5",
+                                sliderInput(
+                                  "upgma_fruit_alpha_5",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.upgma_tile_num == 1",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_width"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 68px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_offset_circ"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.upgma_tile_num == 2",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_width2"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_offset_circ_2"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.upgma_tile_num == 3",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_width3"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_offset_circ_3"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.upgma_tile_num == 4",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_width4"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_offset_circ_4"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.upgma_tile_num == 5",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_width5"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_offset_circ_5"),
+                          br()
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 6,
+                        h4(p("Heatmap"), style = "color:white; position: relative; right: -15px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        h5("Title", style = "color:white; margin-left: 15px; margin-top: 32px;")
+                      ),
+                      column(
+                        width = 6,
+                        align = "center",
+                        textInput(
+                          "upgma_heatmap_title",
+                          label = "",
+                          value = "Heatmap",
+                          placeholder = "Heatmap" 
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_heatmap_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("upgma_colnames_angle"),
+                              br(),
+                              uiOutput("upgma_colnames_y")
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5("Width", style = "color: white; margin-left: 15px; margin-top: 40px;")
+                      ),
+                      column(
+                        width = 7,
+                        uiOutput("upgma_heatmap_width")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5("Position", style = "color:white; margin-left: 15px; margin-top: 36px;")
+                      ),
+                      column(
+                        width = 7,
+                        uiOutput("upgma_heatmap_offset")
+                      )
+                    ),
+                    br(), br()
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Clade Highlight"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 12,
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "upgma_nodelabel_show",
+                            h5(p("Toggle Node View"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        h5(p("Nodes"), style = "color:white; position: relative; right: -15px; margin-top: 20px")
+                      ),
+                      column(
+                        width = 9,
+                        uiOutput("upgma_parentnode")
+                      )
+                    ),
+                    uiOutput("upgma_clade_scale"),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Form"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
+                      ),
+                      column(
+                        width = 7,
+                        div(
+                          class = "sel-clade",
+                          selectInput(
+                            "upgma_clade_type",
+                            "",
+                            choices = c("Rect" = "rect",
+                                        "Round" = "roundrect"),
+                            selected = c("Round" = "roundrect")
+                          ) 
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.upgma_controls=='Variables'",
+              column(
+                width = 7,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 3,
+                        align = "center",
+                        h4(p("Element"), style = "color:white; margin-bottom: 20px")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        h4(p("Variable"), style = "color:white; margin-bottom: 20px; margin-right: 30px;")
+                      ),
+                      column(
+                        width = 6,
+                        align = "center",
+                        h4(p("Color Scale"), style = "color:white; margin-bottom: 20px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "upgma_mapping_show",
+                            h5(p("Tip Label Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_color_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_tiplab_scale")
+                      ),
+                      uiOutput("upgma_tiplab_mapping_info"),
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "upgma_tipcolor_mapping_show",
+                            h5(p("Tip Point Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_tipcolor_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_tippoint_scale")
+                      ),
+                      uiOutput("upgma_tipcolor_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "upgma_tipshape_mapping_show",
+                            h5(p("Tip Point Shape"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_tipshape_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        HTML(
+                          paste(
+                            tags$span(style='color: white; font-size: 14px; font-style: italic; position: relative; bottom: -16px; right: -40px;', 'No scale for shapes')
+                          )
+                        )
+                      ),
+                      uiOutput("upgma_tipshape_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        fluidRow(
+                          column(
+                            width = 8,
+                            conditionalPanel(
+                              "input.upgma_tile_num == 1",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "upgma_tiles_show_1",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px; margin-right: 10px"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.upgma_tile_num == 2",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "upgma_tiles_show_2",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.upgma_tile_num == 3",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "upgma_tiles_show_3",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.upgma_tile_num == 4",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "upgma_tiles_show_4",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.upgma_tile_num == 5",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "upgma_tiles_show_5",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            )
+                          ), 
+                          column(
+                            width = 4,
+                            align = "left",
+                            div(
+                              class = "tile-sel",
+                              selectInput(
+                                "upgma_tile_num",
+                                "",
+                                choices = 1:5,
+                                width = "50px"
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        conditionalPanel(
+                          "input.upgma_tile_num == 1",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_fruit_variable")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.upgma_tile_num == 2",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_fruit_variable2")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.upgma_tile_num == 3",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_fruit_variable3")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.upgma_tile_num == 4",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_fruit_variable4")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.upgma_tile_num == 5",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_fruit_variable5")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.upgma_tile_num == 1",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_tiles_scale_1")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.upgma_tile_num == 2",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_tiles_scale_2")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.upgma_tile_num == 3",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_tiles_scale_3")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.upgma_tile_num == 4",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_tiles_scale_4")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.upgma_tile_num == 5",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_tiles_scale_5")
+                          )
+                        )
+                      ),
+                      uiOutput("upgma_fruit_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "upgma_heatmap_show",
+                            h5(p("Heatmap"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_heatmap_sel")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        div(
+                          class = "heatmap-scale",
+                          uiOutput("upgma_heatmap_scale")
+                        )
+                      ),
+                      uiOutput("upgma_heatmap_mapping_info")
+                    )
+                  )
+                )
+              )
+            )
+          ),
+          br(), br(), br(), br(), br(), br()
+        )
+      ),
+      
+      ## Tab Utilities -------------------------------------------------------
+      
+      tabItem(
+        tabName = "utilities",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Utilities"), style = "color:white")
+          )
+        ),
+        br(),
+        hr(),
+        column(
+          width = 5,
+          align = "left",
+          shinyDirButton(
+            "hash_dir",
+            "Choose folder with .fasta files",
+            title = "Locate folder with loci",
+            buttonType = "default",
+            style = "border-color: white; margin: 10px; min-width: 200px; text-align: center"
+          ),
+          actionButton("hash_start", "Start Hashing", icon = icon("circle-play")),
+          shinyjs::hidden(
+            div(id = "hash_loading",
+                HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
+          )
+        )
+          # br(),
+          # actionButton(
+          #   "backup_database",
+          #   "Create backup",
+          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
+          # ),
+          # br(),
+          # actionButton(
+          #   "import_db_backup",
+          #   "Restore backup",
+          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
+          # )
+      ),
+      
+      
+      ## Tab Screening -------------------------------------------------------
+      
+      tabItem(
+        tabName = "gs_screening",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Screening"), style = "color:white; margin-bottom: -20px;")
+          ),
+          column(
+            width = 7,
+            align = "left",
+            uiOutput("gene_screening_info")
+          )
+        ),
+        br(),
+        hr(),
+        fluidRow(
+          uiOutput("screening_interface")
+        )
+      ),
+      
+      ## Tab Resistance Profile -------------------------------------------------------
+      
+      tabItem(
+        tabName = "gs_profile",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Browse Entries"), style = "color:white; margin-bottom: -20px")
+          ),
+          column(
+            width = 7,
+            align = "left",
+            uiOutput("gene_resistance_info")
+          )
+        ),
+        br(),
+        hr(),
+        br(), br(),
+        uiOutput("gs_table_selection"),
+        fluidRow(
+          column(1),
+          uiOutput("gs_profile_display")
+        )
+      )
+    ) # End tabItems
+  ) # End dashboardPage
+) # end UI
+
+# _______________________ ####
+
+# Server ----
+
+server <- function(input, output, session) {
+  
+  phylotraceVersion <- paste("1.5.0")
+  
+  #TODO Enable this, or leave disabled
+  # Kill server on session end
+  session$onSessionEnded( function() {
+    stopApp()
+  })
+  
+  # Disable various user inputs (visualization control)
+  shinyjs::disable('mst_edge_label') 
+  
+  ## Functions ----
+  
+  # Function to read and format FASTA sequences
+  format_fasta <- function(filepath) {
+    fasta <- readLines(filepath)
+    formatted_fasta <- list()
+    current_sequence <- ""
+    
+    for (line in fasta) {
+      if (startsWith(line, ">")) {
+        if (current_sequence != "") {
+          formatted_fasta <- append(formatted_fasta, list(current_sequence))
+          current_sequence <- ""
+        }
+        formatted_fasta <- append(formatted_fasta, list(line))
+      } else {
+        current_sequence <- paste0(current_sequence, line)
+      }
+    }
+    if (current_sequence != "") {
+      formatted_fasta <- append(formatted_fasta, list(current_sequence))
+    }
+    
+    formatted_fasta
+  }
+  
+  # Function to color-code the bases in a sequence
+  color_sequence <- function(sequence) {
+    sequence <- gsub("A", "<span class='base-a'>A</span>", sequence)
+    sequence <- gsub("T", "<span class='base-t'>T</span>", sequence)
+    sequence <- gsub("G", "<span class='base-g'>G</span>", sequence)
+    sequence <- gsub("C", "<span class='base-c'>C</span>", sequence)
+    sequence
+  }
+  
+  # Function to log messages to logfile
+  log_message <- function(log_file, message, append = TRUE) {
+    cat(format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "-", message, "\n", file = log_file, append = append)
+  }
+  
+  # Modified gheatmap function
+  gheatmap.mod <- function(p, data, offset=0, width=1, low="green", high="red", color="white",
+                           colnames=TRUE, colnames_position="bottom", colnames_angle=0, colnames_level=NULL,
+                           colnames_offset_x = 0, colnames_offset_y = 0, font.size=4, family="", hjust=0.5, legend_title = "value",
+                           colnames_color = "black") {
+    
+    colnames_position %<>% match.arg(c("bottom", "top"))
+    variable <- value <- lab <- y <- NULL
+    
+    ## if (is.null(width)) {
+    ##     width <- (p$data$x %>% range %>% diff)/30
+    ## }
+    
+    ## convert width to width of each cell
+    width <- width * (p$data$x %>% range(na.rm=TRUE) %>% diff) / ncol(data)
+    
+    isTip <- x <- y <- variable <- value <- from <- to <- NULL
+    
+    ## handle the display of heatmap on collapsed nodes
+    ## https://github.com/GuangchuangYu/ggtree/issues/242
+    ## extract data on leaves (& on collapsed internal nodes) 
+    ## (the latter is extracted only when the input data has data on collapsed
+    ## internal nodes)
+    df <- p$data
+    nodeCo <- intersect(df %>% filter(is.na(x)) %>% 
+                          select(.data$parent, .data$node) %>% unlist(), 
+                        df %>% filter(!is.na(x)) %>% 
+                          select(.data$parent, .data$node) %>% unlist())
+    labCo <- df %>% filter(.data$node %in% nodeCo) %>% 
+      select(.data$label) %>% unlist()
+    selCo <- intersect(labCo, rownames(data))
+    isSel <- df$label %in% selCo
+    
+    df <- df[df$isTip | isSel, ]
+    start <- max(df$x, na.rm=TRUE) + offset
+    
+    dd <- as.data.frame(data)
+    ## dd$lab <- rownames(dd)
+    i <- order(df$y)
+    
+    ## handle collapsed tree
+    ## https://github.com/GuangchuangYu/ggtree/issues/137
+    i <- i[!is.na(df$y[i])]
+    
+    lab <- df$label[i]
+    ## dd <- dd[lab, , drop=FALSE]
+    ## https://github.com/GuangchuangYu/ggtree/issues/182
+    dd <- dd[match(lab, rownames(dd)), , drop = FALSE]
+    
+    
+    dd$y <- sort(df$y)
+    dd$lab <- lab
+    ## dd <- melt(dd, id=c("lab", "y"))
+    dd <- gather(dd, variable, value, -c(lab, y))
+    
+    i <- which(dd$value == "")
+    if (length(i) > 0) {
+      dd$value[i] <- NA
+    }
+    if (is.null(colnames_level)) {
+      dd$variable <- factor(dd$variable, levels=colnames(data))
+    } else {
+      dd$variable <- factor(dd$variable, levels=colnames_level)
+    }
+    V2 <- start + as.numeric(dd$variable) * width
+    mapping <- data.frame(from=dd$variable, to=V2)
+    mapping <- unique(mapping)
+    
+    dd$x <- V2
+    dd$width <- width
+    dd[[".panel"]] <- factor("Tree")
+    if (is.null(color)) {
+      p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, inherit.aes=FALSE)
+    } else {
+      p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, color=color, inherit.aes=FALSE)
+    }
+    if (is(dd$value,"numeric")) {
+      p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value=NA, name = legend_title) # "white")
+    } else {
+      p2 <- p2 + scale_fill_discrete(na.value=NA, name = legend_title) #"white")
+    }
+    
+    if (colnames) {
+      if (colnames_position == "bottom") {
+        y <- 0
+      } else {
+        y <- max(p$data$y) + 1
+      }
+      mapping$y <- y
+      mapping[[".panel"]] <- factor("Tree")
+      p2 <- p2 + geom_text(data=mapping, aes(x=to, y = y, label=from), color = colnames_color, size=font.size, family=family, inherit.aes = FALSE,
+                           angle=colnames_angle, nudge_x=colnames_offset_x, nudge_y = colnames_offset_y, hjust=hjust)
+    }
+    
+    p2 <- p2 + theme(legend.position="right")
+    ## p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))
+    
+    if (!colnames) {
+      ## https://github.com/GuangchuangYu/ggtree/issues/204
+      p2 <- p2 + scale_y_continuous(expand = c(0,0))
+    }
+    
+    attr(p2, "mapping") <- mapping
+    return(p2)
+  }
+  
+  # Get rhandsontable
+  get.entry.table.meta <- reactive({
+    if(!is.null(hot_to_r(input$db_entries))){
+      table <- hot_to_r(input$db_entries)
+      select(select(table, -13), 1:(12 + nrow(DB$cust_var)))
+    }
+  })
+  
+  # Function to find columns with varying values
+  var_alleles <- function(dataframe) {
+    
+    varying_columns <- c()
+    
+    for (col in 1:ncol(dataframe)) {
+      unique_values <- unique(dataframe[, col])
+      
+      if (length(unique_values) > 1) {
+        varying_columns <- c(varying_columns, col)
+      }
+    }
+    
+    return(varying_columns)
+  }
+  
+  # Functions to compute hamming distances dependent on missing value handling
+  hamming.dist <- function(x, y) {
+    sum(x != y)
+  }
+  
+  hamming.distIgnore <- function(x, y) {
+    sum( (x != y) & !is.na(x) & !is.na(y) )
+  }
+  
+  hamming.distCategory <- function(x, y) {
+    sum((x != y | xor(is.na(x), is.na(y))) & !(is.na(x) & is.na(y)))
+  }
+  
+  compute.distMatrix <- function(profile, hamming.method) {
+    mat <- as.matrix(profile)
+    n <- nrow(mat)
+    dist_mat <- matrix(0, n, n)
+    for (i in 1:(n-1)) {
+      for (j in (i+1):n) {
+        dist_mat[i, j] <- hamming.method(x = mat[i, ], y = mat[j, ])
+        dist_mat[j, i] <- dist_mat[i, j]
+      }
+    }
+    return(dist_mat)
+  }
+  
+  # Function to determine entry table height
+  table_height <- reactive({
+    if (input$table_height == TRUE) {
+      NULL
+    } else {900}
+  })
+  
+  # Function to determine distance matrix height
+  distancematrix_height <- reactive({
+    if(DB$distancematrix_nrow > 33) {
+      800
+    } else {NULL}
+  })
+  
+  # Function to missing value table height
+  miss.val.height <- reactive({
+    if(input$miss_val_height == TRUE) {
+      NULL
+    } else {800}
+  })
+  
+  #Function to check custom variable classes
+  column_classes <- function(df) {
+    sapply(df, function(x) {
+      if (class(x) == "numeric") {
+        return("cont")
+      } else if (class(x) == "character") {
+        return("categ")
+      } else {
+        return(class(x))
+      }
+    })
+  }
+  
+  # Function to hash database
+  hash_database <- function(folder) {
+    loci_files <- list.files(folder)
+    loci_names <- sapply(strsplit(loci_files, "[.]"), function(x) x[1])
+    loci_paths <- file.path(folder, loci_files)
+    
+    hashes <- sapply(loci_paths, hash_locus)
+    names(hashes) <- loci_names
+    hashes
+  }
+  
+  # Function to hash a locus
+  hash_locus <- function(locus_path) {
+    locus_file <- readLines(locus_path)
+    seq_list <- locus_file[seq(2, length(locus_file), 3)]
+    seq_hash <- sha256(seq_list)
+    seq_idx <- paste0(">", seq_hash)
+    
+    locus_file[seq(1, length(locus_file), 3)] <- seq_idx
+    writeLines(locus_file, locus_path)
+    
+    seq_hash
+  }
+  
+  # Get locus hashes
+  get_locus_hashes <- function(locus_path) {
+    locus_file <- readLines(locus_path)
+    hash_list <- locus_file[seq(1, length(locus_file), 3)]
+    hash_list <- sapply(strsplit(hash_list, "[>]"), function(x) x[2])
+  }
+  
+  extract_seq <- function(locus_path, hashes) {
+    locus_file <- readLines(locus_path)
+    hash_list <- sapply(strsplit(locus_file[seq(1, length(locus_file), 3)], "[>]"), function(x) x[2])
+    seq_list <- locus_file[seq(2, length(locus_file), 3)]
+    seq_idx <- hash_list %in% hashes
+    
+    list(
+      idx = hash_list[seq_idx],
+      seq = seq_list[seq_idx]
+    )
+  }
+  
+  add_new_sequences <- function(locus_path, sequences) {
+    locus_file <- file(locus_path, open = "a+")
+    for (i in seq_along(sequences$idx)) {
+      writeLines(c("", paste0(">", sequences$idx[i]), sequences$seq[i]), locus_file)
+    }
+    close(locus_file)
+  }
+  
+  # Compute clusters to use in visNetwork
+  compute_clusters <- function(nodes, edges, threshold) {
+    groups <- rep(0, length(nodes$id))
+    edges_groups <- rep(0, length(edges$from))
+    
+    edges_table <- data.frame(
+      from = edges$from,
+      to = edges$to,
+      weight = edges$weight
+    )
+    
+    count <- 0
+    while (any(groups == 0)) {
+      group_na <- groups == 0
+      labels <- nodes$id[group_na]
+      
+      cluster <- nodes$id[group_na][1] # Initialize with 1 label
+      while (!is_empty(labels)) {
+        sub_tb <- edges_table[(edges_table$from %in% cluster | edges_table$to %in% cluster) & edges_table$weight <= threshold,]
+        
+        if (nrow(sub_tb) == 0 | length(unique(c(sub_tb$from, sub_tb$to))) == length(cluster)) {
+          count <- count + 1
+          groups[nodes$id %in% cluster] <- paste("Group", count)
+          edges_groups[edges$from %in% cluster & edges$to %in% cluster] <- paste("Group", count)
+          break
+        } else {
+          cluster <- unique(c(sub_tb$from, sub_tb$to))
+        }
+      }
+    }
+    list(groups = groups,
+         edges = edges_groups)
+  }
+  
+  # Check gene screening status
+  check_status <- function(isolate) {
+    iso_name <- gsub(".zip", "", basename(isolate))
+    if(file.exists(file.path(DB$database, gsub(" ", "_", DB$scheme),
+                             "Isolates", iso_name, "status.txt"))) {
+      if(str_detect(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
+                                        "Isolates", iso_name, "status.txt"))[1], 
+                    "successfully")) {
+        return("success")
+      } else {
+        return("fail")
+      }
+    } else {return("unfinished")}
+  }
+  
+  # Reset gene screening status
+  remove.screening.status <- function(isolate) {
+    if(file.exists(file.path(DB$database, 
+                             gsub(" ", "_", DB$scheme),
+                             "Isolates",
+                             isolate,
+                             "status.txt"))) {
+      file.remove(
+        file.path(DB$database, 
+                  gsub(" ", "_", DB$scheme),
+                  "Isolates",
+                  isolate,
+                  "status.txt")
+      )
+    }
+  }
+  
+  # Truncate hashes
+  truncHash <- function(hash) {
+    if(!is.na(hash)) {
+      paste0(str_sub(hash, 1, 4), "...", str_sub(hash, nchar(hash) - 3, nchar(hash))) 
+    } else {NA}
+  }
+  
+  # Function to check for duplicate isolate IDs for multi typing start
+  dupl_mult_id <- reactive({
+    req(Typing$multi_sel_table)
+    if(!is.null(DB$data)) {
+      selection <- Typing$multi_sel_table[which(unlist(Typing$multi_sel_table$Files) %in% unlist(DB$data["Assembly ID"])),]
+      selection$Files
+    } else {""}
+  })
+  
+  # Function to check single typing log file
+  check_new_entry <- reactive({
+    
+    invalidateLater(5000, session)
+    
+    if(!is.null(DB$database)) {
+      if(file_exists(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))) {
+        
+        Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
+        
+        if(is.null(DB$data)) {
+          if(nrow(Database[["Typing"]]) >= 1) {
+            TRUE
+          } else {FALSE}
+        } else {
+          if(nrow(DB$data) < nrow(Database[["Typing"]])) {
+            TRUE
+          } else {
+            FALSE
+          }
+        }
+      } else {FALSE}
+    }
+  })
+  
+  # Render Entry Table Highlights 
+  
+  diff_allele <- reactive({
+    if (!is.null(DB$data) & !is.null(input$compare_select) & !is.null(DB$cust_var)) {
+      var_alleles(select(DB$data, input$compare_select)) + (13 + nrow(DB$cust_var))
+    }
+  })
+  
+  err_thresh <- reactive({
+    if (!is.null(DB$data) & !is.null(DB$number_loci)) {
+      which(as.numeric(DB$data[["Errors"]]) >= (DB$number_loci * 0.05)) 
+    }
+  })
+  
+  err_thresh_na <- reactive({
+    if (!is.null(DB$na_table) & !is.null(DB$number_loci)) {
+      which(as.numeric(DB$na_table[["Errors"]]) >= (DB$number_loci * 0.05)) 
+    }
+  })
+  
+  true_rows <- reactive({
+    if (!is.null(DB$data)) {
+      which(DB$data$Include == TRUE)
+    }
+  })
+  
+  duplicated_names <- reactive({
+    if (!is.null(DB$meta)) {
+      which(duplicated(DB$meta$`Assembly Name`) | duplicated(DB$meta$`Assembly Name`, fromLast = TRUE))
+    }
+  })
+  
+  duplicated_ids <- reactive({
+    if (!is.null(DB$meta)) {
+      which(duplicated(DB$meta$`Assembly ID`) | duplicated(DB$meta$`Assembly ID`, fromLast = TRUE))
+    }
+  })
+  
+  # _______________________ ####
+  
+  ## Startup ----
+  shinyjs::addClass(selector = "body", class = "sidebar-collapse")
+  shinyjs::removeClass(selector = "body", class = "sidebar-toggle")
+  
+  output$messageMenu <- renderText({
+    HTML(format(Sys.time(), "%Y-%m-%d %H:%M:%S %Z"))
+  })
+  
+  # Initiate logging
+  if(!dir_exists(paste0(getwd(), "/logs"))) {
+    dir_create(paste0(getwd(), "/logs"))
+  }
+  
+  logfile <- file.path(paste0(getwd(), "/logs/phylotrace.log"))
+  
+  log <- log_open(logfile, logdir = FALSE)
+  
+  log_print("Session started")
+  
+  # Clear screening file
+  if(file.exists(paste0(getwd(), "/execute/screening/output_file.tsv"))) {
+    file.remove(paste0(getwd(), "/execute/screening/output_file.tsv"))
+  }
+  
+  if(file.exists(paste0(getwd(), "/execute/screening/error.txt"))) {
+    file.remove(paste0(getwd(), "/execute/screening/error.txt"))
+  }
+  
+  # Declare reactive variables
+  Startup <- reactiveValues(sidebar = TRUE, 
+                            header = TRUE) # reactive variables related to startup process
+  
+  DB <- reactiveValues(data = NULL, 
+                       block_db = FALSE, 
+                       load_selected = TRUE,
+                       no_na_switch = FALSE,
+                       first_look = FALSE) # reactive variables related to local database
+  
+  Typing <- reactiveValues(table = data.frame(), 
+                           single_path = data.frame(),
+                           progress = 0, 
+                           progress_format_start = 0, 
+                           progress_format_end = 0,
+                           result_list = NULL,
+                           status = "") # reactive variables related to typing process
+  
+  Screening <- reactiveValues(status = "idle",
+                              picker_status = TRUE,
+                              first_result = NULL) # reactive variables related to gene screening
+  
+  Vis <- reactiveValues(cluster = NULL, 
+                        metadata = list(),
+                        custom_label_nj = data.frame(),
+                        nj_label_pos_y = list(),
+                        nj_label_pos_x = list(),
+                        nj_label_size = list(),
+                        custom_label_upgma = data.frame(),
+                        upgma_label_pos_y = list(),
+                        upgma_label_pos_x = list(),
+                        upgma_label_size = list()) # reactive variables related to visualization
+  
+  Report <- reactiveValues() # reactive variables related to report functions
+  
+  Scheme <- reactiveValues() # reactive variables related to scheme  functions
+  
+  # Load last used database if possible
+  if(paste0(getwd(), "/execute/last_db.rds") %in% dir_ls(paste0(getwd(), "/execute"))) {
+    DB$last_db <- TRUE
+  }
+  
+  # Locate local Database
+  observe({
+    shinyDirChoose(input,
+                   "db_location",
+                   roots = c(Home = path_home(), Root = "/"),
+                   defaultRoot = "Home",
+                   session = session)
+    
+    if(!is.null(DB$select_new)) {
+      if(DB$select_new == FALSE) {
+        if(DB$block_db == FALSE) {
+          DB$database <- as.character(
+            parseDirPath(
+              roots = c(Home = path_home(), Root = "/"),
+              input$db_location
+            )
+          )
+          
+          DB$exist <- (length(dir_ls(DB$database)) == 0)  # Logical any local database present
+          
+          DB$available <- gsub("_", " ", basename(dir_ls(DB$database))) # List of local schemes available
+        }
+        
+      } else if (DB$select_new ==  TRUE) {
+        DB$database <- paste0(DB$new_database, "/Database")
+        
+      }
+    } else {
+      if(!is.null(DB$last_db) & file.exists(paste0(getwd(), "/execute/last_db.rds"))) {
+        
+        DB$database <- readRDS(paste0(getwd(), "/execute/last_db.rds"))
+        
+        if(dir_exists(DB$database)) {
+          DB$exist <- (length(dir_ls(DB$database)) == 0)  # Logical any local database present
+          
+          DB$available <- gsub("_", " ", basename(dir_ls(DB$database))) # List of local schemes available
+        }
+      }
+    }
+  })
+  
+  ### Set up typing environment ----
+  
+  # Null typing progress trackers
+  writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
+  writeLines("0\n", paste0(getwd(), "/logs/progress.txt"))
+  
+  if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
+    unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
+  }
+  
+  # Reset typing feedback values
+  Typing$pending <- FALSE
+  Typing$multi_started <- FALSE
+  Typing$multi_help <- FALSE
+  saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
+  Typing$last_success <- "0" # Null last multi typing success name
+  Typing$last_failure <- "0" # Null last multi typing failure name
+  
+  ### Landing page UI ----
+  observe({
+    if (Startup$sidebar == FALSE) {
+      shinyjs::removeClass(selector = "body", class = "sidebar-collapse")
+      shinyjs::addClass(selector = "body", class = "sidebar-toggle")
+    }
+  })
+  
+  output$start_message <- renderUI({
+    column(
+      width = 12, 
+      align = "center",
+      br(), br(), br(), br(), br(), br(),
+      div( 
+        class = "image",
+        imageOutput("imageOutput")
+      ),
+      br(), br(), br(),
+      p(
+        HTML(
+          paste(
+            tags$span(style='color: white; font-size: 16px;', 'Proceed by loading a compatible local database or create a new one.')
+          )
+        )
+      ),
+      br(), 
+      fluidRow(
+        column(
+          width = 6,
+          align = "right",
+          shinyDirButton(
+            "db_location",
+            "Browse",
+            icon = icon("folder-open"),
+            title = "Locate the database folder",
+            buttonType = "default",
+            root = path_home()
+          )
+        ),
+        column(
+          width = 6,
+          align = "left",
+          shinyDirButton(
+            "create_new_db",
+            "Create New",
+            icon = icon("plus"),
+            title = "Choose location for new PhyloTrace database",
+            buttonType = "default",
+            root = path_home()
+          )
+        )
+      ),
+      br(), br(),
+      fluidRow(
+        column(
+          width = 12,
+          align = "center",
+          uiOutput("load_db"),
+          br(), br(), br(), br(), br(), br(), br()
+        )
+      )
+    )
+  })
+  
+  # User selection new db or load db
+  observeEvent(input$create_new_db, {
+    log_print("Input create_new_db")
+    DB$select_new <- TRUE
+  })
+  
+  observeEvent(input$db_location, {
+    log_print("Input db_location")
+    DB$select_new <- FALSE
+  })
+  
+  # Load db & scheme selection UI
+  output$load_db <- renderUI({
+    if(!is.null(DB$select_new)) {
+      if(length(DB$new_database) > 0 & DB$select_new) {
+        column(
+          width = 12,
+          p(
+            tags$span(
+              style='color: white; font-size: 15px;',
+              HTML(
+                paste(
+                  'New database will be created in',
+                  DB$new_database
+                )
+              )
+            )
+          ),
+          br(),
+          actionButton(
+            "load",
+            "Create",
+            class = "load-start"
+          )
+        )
+      } else if(length(DB$available) > 0 & !(DB$select_new)) {
+        if(any(!(gsub(" ", "_", DB$available) %in% schemes))) {
+          column(
+            width = 12,
+            p(
+              tags$span(
+                style='color: white; font-size: 15px; font-style: italic;',
+                HTML(
+                  paste('Selected:', DB$database)
+                )
+              )
+            ),
+            uiOutput("scheme_db"),
+            br(), 
+            p(
+              HTML(
+                paste(
+                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
+                            'Warning: Folder contains invalid elements.')
+                )
+              )
+            ),
+            br(),
+            actionButton(
+              "load",
+              "Load",
+              class = "load-start"
+            )
+          )
+        } else {
+          column(
+            width = 12,
+            p(
+              tags$span(
+                style='color: white; font-size: 15px; font-style: italic;',
+                HTML(
+                  paste('Selected:', DB$database)
+                )
+              )
+            ),
+            uiOutput("scheme_db"),
+            br(), br(),
+            actionButton(
+              "load",
+              "Load",
+              class = "load-start"
+            )
+          )
+        }
+      } 
+    } else if((!is.null(DB$last_db)) & (!is.null(DB$available))) {
+      if (DB$last_db == TRUE & (length(DB$available) > 0)) {
+        if(any(!(gsub(" ", "_", DB$available) %in% schemes))) {
+          column(
+            width = 12,
+            p(
+              tags$span(
+                style='color: white; font-size: 15px; font-style: italic;',
+                HTML(
+                  paste('Last used:', DB$database)
+                )
+              )
+            ),
+            uiOutput("scheme_db"),
+            br(), 
+            p(
+              HTML(
+                paste(
+                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
+                            'Warning: Folder contains invalid elements.')
+                )
+              )
+            ),
+            br(),
+            actionButton(
+              "load",
+              "Load",
+              class = "load-start"
+            )
+          )
+        } else {
+          column(
+            width = 12,
+            p(
+              tags$span(
+                style='color: white; font-size: 15px; font-style: italic;',
+                HTML(
+                  paste('Last used:', DB$database)
+                )
+              )
+            ),
+            uiOutput("scheme_db"),
+            br(), br(),
+            actionButton(
+              "load",
+              "Load",
+              class = "load-start"
+            )
+          )
+        }
+      } else if (DB$last_db == TRUE & (length(DB$available) == 0)) {
+        column(
+          width = 12,
+          p(
+            tags$span(
+              style='color: white; font-size: 15px; font-style: italic;',
+              HTML(
+                paste('Last used:', DB$database)
+              )
+            )
+          ),
+          br(),
+          actionButton(
+            "load",
+            "Load",
+            class = "load-start"
+          )
+        )
+      }
+    }
+  })
+  
+  output$imageOutput <- renderImage({
+    # Path to your PNG image with a transparent background
+    image_path <- paste0(getwd(), "/www/PhyloTrace.png")
+    
+    # Use HTML to display the image with the <img> tag
+    list(src = image_path,
+         height = 180)
+  }, deleteFile = FALSE)
+  
+  ### Load app event ----
+  
+  observeEvent(input$load, {
+    
+    # Reset reactive screening variables 
+    output$screening_start <- NULL
+    output$screening_result_sel <- NULL
+    output$screening_result <- NULL
+    output$screening_fail <- NULL
+    Screening$status_df <- NULL
+    Screening$choices <- NULL
+    Screening$picker_status <- TRUE
+    Screening$status <- "idle"
+    Screening$first_result <- NULL
+    if(!is.null(input$screening_select)) {
+      if(!is.null(DB$data)) {
+        updatePickerInput(session, "screening_select", selected = character(0))
+      }
+    }
+    
+    log_print("Input load")
+    
+    # set typing start control variable
+    Typing$reload <- TRUE
+    
+    # reset typing status on start(
+    if(Typing$status == "Finalized") {Typing$status <- "Inactive"}
+    if(!is.null(Typing$single_path)) {Typing$single_path <- data.frame()}
+    
+    #### Render status bar ----
+    observe({
+      req(DB$scheme)
+      
+      if(is.null(input$scheme_position)) {
+        output$loaded_scheme <- renderUI({
+          fluidRow(
+            tags$li(
+              class = "dropdown", 
+              tags$span(HTML(
+                paste('<i class="fa-solid fa-layer-group"></i>', 
+                      "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
+                      DB$scheme,
+                      "</i>")), 
+                style = "color:white;")
+            )
+          )
+        })
+      } 
+      
+      if(!is.null(input$scheme_position)) {
+        output$loaded_scheme <- renderUI({
+          fluidRow(
+            tags$li(
+              class = "dropdown", 
+              tags$span(HTML(
+                paste('<i class="fa-solid fa-layer-group"></i>', 
+                      "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
+                      DB$scheme,
+                      "</i>")), 
+                style = "color:white;"),
+              div(
+                class = "reload-bttn",
+                style = paste0("margin-left:", 30 + input$scheme_position, "px; position: relative; top: -24px;"),
+                actionButton(
+                  "reload_db",
+                  label = "",
+                  icon = icon("rotate")
+                )
+              )
+            )
+          )
+        })
+      }
+    })
+    
+    observe({
+      if(!is.null(DB$database)){
+        if(nchar(DB$database) > 60) {
+          database <- paste0(substring(DB$database, first = 1, last = 60), "...")
+        } else {
+          database <- DB$database
+        }
+        output$databasetext <- renderUI({
+          fluidRow(
+            tags$li(
+              class = "dropdown", 
+              tags$span(HTML(
+                paste('<i class="fa-solid fa-folder-open"></i>', 
+                      "Database:&nbsp;&nbsp;&nbsp;<i>",
+                      database,
+                      "</i>")), 
+                style = "color:white;")
+            ),
+            if(nchar(database) > 60) {bsTooltip("databasetext", 
+                                                HTML(DB$database), 
+                                                placement = "bottom", 
+                                                trigger = "hover")}
+          )
+        })
+      }
+    })
+    
+    observe({
+      if(!is.null(DB$database)) {
+        if(Typing$status == "Finalized"){
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp; <i>typing finalized</i>")),
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(Typing$status == "Attaching"){
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp; <i>evaluating typing results</i>")),
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(Typing$status == "Processing") {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> pending typing</i>")), 
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(Screening$status == "started") {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> pending gene screening</i>")), 
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(Screening$status == "finished") {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> gene screening finalized</i>")), 
+                  style = "color:white;")
+              )
+            )
+          )
+        } else {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
+                  style = "color:white;")
+              )
+            )
+          )
+        }    
+      }
+    })
+    
+    # Null single typing status
+    if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
+      Typing$progress <- 0
+      
+      Typing$progress_format <- 900000
+      
+      output$single_typing_progress <- NULL
+      
+      output$typing_fin <- NULL
+      
+      output$single_typing_results <- NULL
+      
+      output$typing_formatting <- NULL
+      
+      Typing$single_path <- data.frame()
+      
+      # reset results file 
+      if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
+        unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
+        # Resetting single typing progress logfile bar 
+        con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
+        
+        cat("0\n", file = con)   
+        
+        close(con)
+      }
+    }
+    
+    shinyjs::runjs(
+      'if(document.querySelector("#loaded_scheme > div > li > span") !== null) {
+          // Select the span element
+          let spanElement = document.querySelector("#loaded_scheme > div > li > span");
+                    
+          // Get the bounding rectangle of the span element
+          let rect = spanElement.getBoundingClientRect();
+          
+          // Extract the width
+          let width = rect.width;
+          
+          Shiny.setInputValue("scheme_position", width);            
+        }'
+    )
+    
+    # Load app elements based on database availability and missing value presence
+    if(!is.null(DB$select_new)) {
+      if(DB$select_new & (paste0(DB$new_database, "/Database") %in% dir_ls(DB$new_database))) {
+        
+        log_print("Directory already contains a database")
+        
+        show_toast(
+          title = "Directory already contains a database",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+        DB$load_selected <- FALSE
+        
+      } else if(DB$select_new | (DB$select_new == FALSE & is.null(input$scheme_db))) {
+        
+        log_print(paste0("New database created in ", DB$new_database))
+        
+        DB$check_new_entries <- TRUE
+        DB$data <- NULL
+        DB$meta_gs <- NULL
+        DB$meta <- NULL
+        DB$meta_true <- NULL
+        DB$allelic_profile <- NULL
+        DB$allelic_profile_trunc <- NULL
+        DB$allelic_profile_true <- NULL
+        
+        # null Distance matrix, entry table and plots
+        output$db_distancematrix <- NULL 
+        output$db_entries_table <- NULL
+        output$tree_mst <- NULL
+        output$tree_nj <- NULL
+        output$tree_upgma <- NULL
+        
+        # null report values
+        Report$report_list_mst <- list()
+        Report$report_list_nj <- list()
+        Report$report_list_upgma <- list()
+        
+        # null plots
+        Vis$nj <- NULL
+        Vis$upgma <- NULL
+        Vis$ggraph_1 <- NULL
+        
+        removeModal()
+        
+        #### Render Menu Items ----
+        
+        Startup$sidebar <- FALSE
+        Startup$header <- FALSE
+        
+        output$menu_sep2 <- renderUI(hr())
+        
+        # Hide start message
+        output$start_message <- NULL
+        
+        DB$load_selected <- FALSE
+        
+        # Declare database path
+        DB$database <- file.path(DB$new_database, "Database")
+        
+        # Set database availability screening variables to present database
+        DB$block_db <- TRUE
+        DB$select_new <- FALSE
+        
+        # Render menu with Manage Schemes as start tab and no Missing values tab
+        output$menu <- renderMenu(
+          sidebarMenu(
+            menuItem(
+              text = "Database Browser",
+              tabName = "database",
+              icon = icon("hard-drive"),
+              startExpanded = TRUE,
+              menuSubItem(
+                text = "Browse Entries",
+                tabName = "db_browse_entries"
+              ),
+              menuSubItem(
+                text = "Scheme Info",
+                tabName = "db_schemeinfo"
+              ),
+              menuSubItem(
+                text = "Loci Info",
+                tabName = "db_loci_info"
+              ),
+              menuSubItem(
+                text = "Distance Matrix",
+                tabName = "db_distmatrix"
+              )
+            ),
+            menuItem(
+              text = "Manage Schemes",
+              tabName = "init",
+              icon = icon("layer-group"),
+              selected = TRUE
+            ),
+            menuItem(
+              text = "Allelic Typing",
+              tabName = "typing",
+              icon = icon("gears")
+            ),
+            menuItem(
+              text = "Resistance Profile",
+              tabName = "gene_screening",
+              icon = icon("dna"),
+              startExpanded = TRUE,
+              menuSubItem(
+                text = "Browse Entries",
+                tabName = "gs_profile"
+              ),
+              menuSubItem(
+                text = "Screening",
+                tabName = "gs_screening"
+              )
+            ),
+            menuItem(
+              text = "Visualization",
+              tabName = "visualization",
+              icon = icon("circle-nodes")
+            ),
+            menuItem(
+              text = "Utilities",
+              tabName = "utilities",
+              icon = icon("screwdriver-wrench")
+            )
+          )
+        )
+        
+        # Dont render these elements
+        output$db_no_entries <- NULL
+        output$distancematrix_no_entries <- NULL
+        output$db_entries <- NULL
+        output$edit_index <- NULL
+        output$edit_scheme_d <- NULL
+        output$edit_entries <- NULL
+        output$compare_select <- NULL
+        output$delete_select <- NULL
+        output$del_bttn <- NULL
+        output$compare_allele_box <- NULL
+        output$download_entries <- NULL
+        output$missing_values <- NULL
+        output$delete_box <- NULL
+        output$missing_values_sidebar <- NULL
+        output$distmatrix_sidebar <- NULL
+        output$download_scheme_info <- NULL
+        output$download_loci <- NULL
+        output$entry_table_controls <- NULL
+        output$multi_stop <- NULL
+        output$metadata_multi_box <- NULL
+        output$start_multi_typing_ui <- NULL
+        output$pending_typing <- NULL
+        output$multi_typing_results <- NULL
+        output$single_typing_progress <- NULL
+        output$metadata_single_box <- NULL
+        output$start_typing_ui <- NULL
+        
+      }
+    } else {
+      log_print(paste0("Loading existing ", input$scheme_db, " database from ", DB$database))
+    }
+    
+    if(DB$load_selected == TRUE) {
+      
+      if(gsub(" ", "_", input$scheme_db) %in% schemes) { #Check if selected scheme valid
+        
+        # Save database path for next start
+        saveRDS(DB$database, paste0(getwd(), "/execute/last_db.rds"))
+        
+        DB$check_new_entries <- TRUE
+        DB$data <- NULL
+        DB$meta_gs <- NULL
+        DB$meta <- NULL
+        DB$meta_true <- NULL
+        DB$allelic_profile <- NULL
+        DB$allelic_profile_trunc <- NULL
+        DB$allelic_profile_true <- NULL
+        DB$scheme <- input$scheme_db
+        
+        # null Distance matrix, entry table and plots
+        output$db_distancematrix <- NULL 
+        output$db_entries_table <- NULL
+        output$tree_mst <- NULL
+        output$tree_nj <- NULL
+        output$tree_upgma <- NULL
+        
+        # null typing initiation UI
+        output$multi_stop <- NULL
+        output$metadata_multi_box <- NULL
+        output$start_multi_typing_ui <- NULL
+        output$pending_typing <- NULL
+        output$multi_typing_results <- NULL
+        output$single_typing_progress <- NULL
+        output$metadata_single_box <- NULL
+        output$start_typing_ui <- NULL
+        
+        # null report values
+        Report$report_list_mst <- list()
+        Report$report_list_nj <- list()
+        Report$report_list_upgma <- list()
+        
+        # null plots
+        Vis$nj <- NULL
+        Vis$upgma <- NULL
+        Vis$ggraph_1 <- NULL
+        
+        removeModal()
+        
+        #### Render Menu Items ----
+        
+        Startup$sidebar <- FALSE
+        Startup$header <- FALSE
+        
+        output$menu_sep2 <- renderUI(hr())
+        
+        # Hide start message
+        output$start_message <- NULL
+        
+        if(any(grepl(gsub(" ", "_", DB$scheme), dir_ls(DB$database)))) {
+          
+          if(!any(grepl("alleles", dir_ls(paste0(
+            DB$database, "/", 
+            gsub(" ", "_", DB$scheme)))))) {
+            
+            log_print("Missing loci files")
+            
+            # Show message that loci files are missing
+            showModal(
+              modalDialog(
+                paste0("Whoops! No loci files are present in the local ", 
+                       DB$scheme, 
+                       " folder. Download the scheme again (no influence on already typed assemblies)."),
+                title = "Local Database Error",
+                fade = TRUE,
+                easyClose = TRUE,
+                footer = tagList(
+                  modalButton("Okay")
+                )
+              )
+            )
+            
+            # Render menu with Manage Schemes as start tab
+            output$menu <- renderMenu(
+              sidebarMenu(
+                menuItem(
+                  text = "Database Browser",
+                  tabName = "database",
+                  icon = icon("hard-drive"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "db_browse_entries"
+                  ),
+                  menuSubItem(
+                    text = "Scheme Info",
+                    tabName = "db_schemeinfo"
+                  ),
+                  menuSubItem(
+                    text = "Loci Info",
+                    tabName = "db_loci_info"
+                  ),
+                  menuSubItem(
+                    text = "Distance Matrix",
+                    tabName = "db_distmatrix"
+                  ),
+                  menuSubItem(
+                    text = "Missing Values",
+                    tabName = "db_missing_values",
+                    icon = icon("triangle-exclamation")
+                  )
+                ),
+                menuItem(
+                  text = "Manage Schemes",
+                  tabName = "init",
+                  icon = icon("layer-group"),
+                  selected = TRUE
+                ),
+                menuItem(
+                  text = "Allelic Typing",
+                  tabName = "typing",
+                  icon = icon("gears")
+                ),
+                menuItem(
+                  text = "Resistance Profile",
+                  tabName = "gene_screening",
+                  icon = icon("dna"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "gs_profile"
+                  ),
+                  menuSubItem(
+                    text = "Screening",
+                    tabName = "gs_screening"
+                  )
+                ),
+                menuItem(
+                  text = "Visualization",
+                  tabName = "visualization",
+                  icon = icon("circle-nodes")
+                ),
+                menuItem(
+                  text = "Utilities",
+                  tabName = "utilities",
+                  icon = icon("screwdriver-wrench")
+                )
+              )
+            )
+          } else if (!any(grepl("scheme_info.html", dir_ls(paste0(
+            DB$database, "/", 
+            gsub(" ", "_", DB$scheme)))))) {
+            
+            output$download_scheme_info <- NULL
+            
+            log_print("Scheme info file missing")
+            
+            # Show message that scheme info is missing
+            showModal(
+              modalDialog(
+                paste0("Whoops! Scheme info of the local ", 
+                       DB$scheme, 
+                       " database is missing. Download the scheme again (no influence on already typed assemblies)."),
+                title = "Local Database Error",
+                fade = TRUE,
+                easyClose = TRUE,
+                footer = tagList(
+                  modalButton("Okay")
+                )
+              )
+            )
+            
+            # Render menu with Manage Schemes as start tab
+            output$menu <- renderMenu(
+              sidebarMenu(
+                menuItem(
+                  text = "Database Browser",
+                  tabName = "database",
+                  icon = icon("hard-drive"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "db_browse_entries"
+                  ),
+                  menuSubItem(
+                    text = "Scheme Info",
+                    tabName = "db_schemeinfo"
+                  ),
+                  menuSubItem(
+                    text = "Loci Info",
+                    tabName = "db_loci_info"
+                  ),
+                  menuSubItem(
+                    text = "Distance Matrix",
+                    tabName = "db_distmatrix"
+                  ),
+                  menuSubItem(
+                    text = "Missing Values",
+                    tabName = "db_missing_values",
+                    icon = icon("triangle-exclamation")
+                  )
+                ),
+                menuItem(
+                  text = "Manage Schemes",
+                  tabName = "init",
+                  icon = icon("layer-group"),
+                  selected = TRUE
+                ),
+                menuItem(
+                  text = "Allelic Typing",
+                  tabName = "typing",
+                  icon = icon("gears")
+                ),
+                menuItem(
+                  text = "Resistance Profile",
+                  tabName = "gene_screening",
+                  icon = icon("dna"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "gs_profile"
+                  ),
+                  menuSubItem(
+                    text = "Screening",
+                    tabName = "gs_screening"
+                  )
+                ),
+                menuItem(
+                  text = "Visualization",
+                  tabName = "visualization",
+                  icon = icon("circle-nodes")
+                ),
+                menuItem(
+                  text = "Utilities",
+                  tabName = "utilities",
+                  icon = icon("screwdriver-wrench")
+                )
+              )
+            )
+            
+          } else if (!any(grepl("targets.csv", dir_ls(paste0(
+            DB$database, "/", 
+            gsub(" ", "_", DB$scheme)))))) {
+            
+            # Dont render target download button
+            output$download_loci <- NULL
+            
+            log_print("Missing loci info (targets.csv)")
+            
+            # Show message that scheme info is missing
+            showModal(
+              modalDialog(
+                paste0("Whoops! Loci info of the local ", 
+                       DB$scheme, 
+                       " database is missing. Download the scheme again (no influence on already typed assemblies)."),
+                title = "Local Database Error",
+                fade = TRUE,
+                easyClose = TRUE,
+                footer = tagList(
+                  modalButton("Okay")
+                )
+              )
+            )
+            
+            # Render menu with Manage Schemes as start tab
+            output$menu <- renderMenu(
+              sidebarMenu(
+                menuItem(
+                  text = "Database Browser",
+                  tabName = "database",
+                  icon = icon("hard-drive"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "db_browse_entries"
+                  ),
+                  menuSubItem(
+                    text = "Scheme Info",
+                    tabName = "db_schemeinfo"
+                  ),
+                  menuSubItem(
+                    text = "Loci Info",
+                    tabName = "db_loci_info"
+                  ),
+                  menuSubItem(
+                    text = "Distance Matrix",
+                    tabName = "db_distmatrix"
+                  ),
+                  menuSubItem(
+                    text = "Missing Values",
+                    tabName = "db_missing_values",
+                    icon = icon("triangle-exclamation")
+                  )
+                ),
+                menuItem(
+                  text = "Manage Schemes",
+                  tabName = "init",
+                  icon = icon("layer-group"),
+                  selected = TRUE
+                ),
+                menuItem(
+                  text = "Allelic Typing",
+                  tabName = "typing",
+                  icon = icon("gears")
+                ),
+                menuItem(
+                  text = "Resistance Profile",
+                  tabName = "gene_screening",
+                  icon = icon("dna"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "gs_profile"
+                  ),
+                  menuSubItem(
+                    text = "Screening",
+                    tabName = "gs_screening"
+                  )
+                ),
+                menuItem(
+                  text = "Visualization",
+                  tabName = "visualization",
+                  icon = icon("circle-nodes")
+                ),
+                menuItem(
+                  text = "Utilities",
+                  tabName = "utilities",
+                  icon = icon("screwdriver-wrench")
+                )
+              )
+            )
+            
+          } else {
+            # Produce Scheme Info Table
+            schemeinfo <-
+              read_html(paste0(
+                DB$database, "/",
+                gsub(" ", "_", DB$scheme),
+                "/scheme_info.html"
+              )) %>%
+              html_table(header = FALSE) %>%
+              as.data.frame(stringsAsFactors = FALSE)
+            names(schemeinfo) <- NULL
+            DB$schemeinfo <- schemeinfo
+            number_loci <- as.vector(DB$schemeinfo[6, 2])
+            DB$number_loci <- as.numeric(gsub(",", "", number_loci))
+            
+            # Produce Loci Info table
+            DB$loci_info <- read.csv(
+              file.path(DB$database, gsub(" ", "_", DB$scheme), "targets.csv"),
+              header = TRUE,
+              sep = "\t",
+              row.names = NULL,
+              colClasses = c(
+                "NULL",
+                "character",
+                "character",
+                "integer",
+                "integer",
+                "character",
+                "integer",
+                "NULL"
+              )
+            )
+            
+            # Check if number of loci/fastq-files of alleles is coherent with number of targets in scheme
+            if(DB$number_loci > length(dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")))) {
+              
+              log_print(paste0("Loci files are missing in the local ", DB$scheme, " folder"))
+              
+              # Show message that loci files are missing
+              showModal(
+                modalDialog(
+                  paste0("Whoops! Some loci files are missing in the local ", 
+                         DB$scheme, 
+                         " folder. Download the scheme again (no influence on already typed assemblies)."),
+                  title = "Local Database Error",
+                  fade = TRUE,
+                  easyClose = TRUE,
+                  footer = tagList(
+                    modalButton("Okay")
+                  )
+                )
+              )
+              
+              # Render menu with Manage Schemes as start tab
+              output$menu <- renderMenu(
+                sidebarMenu(
+                  menuItem(
+                    text = "Database Browser",
+                    tabName = "database",
+                    icon = icon("hard-drive"),
+                    startExpanded = TRUE,
+                    menuSubItem(
+                      text = "Browse Entries",
+                      tabName = "db_browse_entries"
+                    ),
+                    menuSubItem(
+                      text = "Scheme Info",
+                      tabName = "db_schemeinfo"
+                    ),
+                    menuSubItem(
+                      text = "Loci Info",
+                      tabName = "db_loci_info"
+                    ),
+                    menuSubItem(
+                      text = "Distance Matrix",
+                      tabName = "db_distmatrix"
+                    ),
+                    menuSubItem(
+                      text = "Missing Values",
+                      tabName = "db_missing_values",
+                      icon = icon("triangle-exclamation")
+                    )
+                  ),
+                  menuItem(
+                    text = "Manage Schemes",
+                    tabName = "init",
+                    icon = icon("layer-group"),
+                    selected = TRUE
+                  ),
+                  menuItem(
+                    text = "Allelic Typing",
+                    tabName = "typing",
+                    icon = icon("gears")
+                  ),
+                  menuItem(
+                    text = "Resistance Profile",
+                    tabName = "gene_screening",
+                    icon = icon("dna"),
+                    startExpanded = TRUE,
+                    menuSubItem(
+                      text = "Browse Entries",
+                      tabName = "gs_profile"
+                    ),
+                    menuSubItem(
+                      text = "Screening",
+                      tabName = "gs_screening"
+                    )
+                  ),
+                  menuItem(
+                    text = "Visualization",
+                    tabName = "visualization",
+                    icon = icon("circle-nodes")
+                  ),
+                  menuItem(
+                    text = "Utilities",
+                    tabName = "utilities",
+                    icon = icon("screwdriver-wrench")
+                  )
+                )
+              )
+              
+            } else {
+              ###### Alle checks bestanden -> Laden der DTB
+              # If typed entries present
+              if (any(grepl("Typing.rds", dir_ls(paste0(
+                DB$database, "/", gsub(" ", "_", DB$scheme)
+              ))))) {
+                
+                # Load database from files  
+                Database <- readRDS(file.path(DB$database, 
+                                              gsub(" ", "_", DB$scheme), 
+                                              "Typing.rds"))
+                
+                DB$data <- Database[["Typing"]]
+                
+                if(!is.null(DB$data)){
+                  if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+                    cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+                    DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
+                  } else {
+                    DB$cust_var <- data.frame()
+                  }
+                }
+                
+                DB$change <- FALSE
+                DB$meta_gs <- select(DB$data, c(1, 3:13))
+                DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+                DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+                DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+                DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
+                DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+                
+                # Null pipe 
+                con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
+                
+                cat("0\n", file = con)
+                
+                # Close the file connection
+                close(con)
+                
+                # Reset other reactive typing variables
+                Typing$progress_format_end <- 0 
+                Typing$progress_format_start <- 0
+                Typing$pending_format <- 0
+                Typing$entry_added <- 0
+                Typing$progress <- 0
+                Typing$progress_format <- 900000
+                output$single_typing_progress <- NULL
+                output$typing_fin <- NULL
+                output$single_typing_results <- NULL
+                output$typing_formatting <- NULL
+                Typing$single_path <- data.frame()
+                
+                # Null multi typing feedback variable
+                Typing$reset <- TRUE
+                
+                # Check need for new missing vlaue display
+                if(DB$first_look == TRUE) {
+                  if(sum(apply(DB$data, 1, anyNA)) >= 1) {
+                    DB$no_na_switch <- TRUE
+                  } else {
+                    DB$no_na_switch <- FALSE
+                  }
+                }
+                
+                DB$first_look <- TRUE
+                
+                output$initiate_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(),
+                    br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyFilesButton(
+                          "genome_file",
+                          "Browse" ,
+                          icon = icon("file"),
+                          title = "Select the assembly in .fasta/.fna/.fa format:",
+                          multiple = FALSE,
+                          buttonType = "default",
+                          class = NULL,
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("genome_path"),
+                        br()
+                      )
+                    )
+                  )
+                })
+                
+                output$initiate_multi_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(), br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyDirButton(
+                          "genome_file_multi",
+                          "Browse",
+                          icon = icon("folder-open"),
+                          title = "Select the folder containing the genome assemblies (FASTA)",
+                          buttonType = "default",
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("multi_select_info"),
+                        br()
+                      )
+                    ),
+                    uiOutput("multi_select_tab_ctrls"),
+                    br(),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "left",
+                        rHandsontableOutput("multi_select_table")
+                      )
+                    )
+                  )
+                })
+                
+                if(!anyNA(DB$allelic_profile)) {
+                  
+                  # no NA's -> dont render missing values sidebar elements
+                  output$missing_values_sidebar <- NULL
+                  
+                  # Render menu if no NA's present
+                  output$menu <- renderMenu(
+                    sidebarMenu(
+                      menuItem(
+                        text = "Database Browser",
+                        tabName = "database",
+                        icon = icon("hard-drive"),
+                        startExpanded = TRUE,
+                        menuSubItem(
+                          text = "Browse Entries",
+                          tabName = "db_browse_entries"
+                        ),
+                        menuSubItem(
+                          text = "Scheme Info",
+                          tabName = "db_schemeinfo"
+                        ),
+                        menuSubItem(
+                          text = "Loci Info",
+                          tabName = "db_loci_info"
+                        ),
+                        menuSubItem(
+                          text = "Distance Matrix",
+                          tabName = "db_distmatrix"
+                        )
+                      ),
+                      menuItem(
+                        text = "Manage Schemes",
+                        tabName = "init",
+                        icon = icon("layer-group")
+                      ),
+                      menuItem(
+                        text = "Allelic Typing",
+                        tabName = "typing",
+                        icon = icon("gears")
+                      ),
+                      menuItem(
+                        text = "Resistance Profile",
+                        tabName = "gene_screening",
+                        icon = icon("dna"),
+                        startExpanded = TRUE,
+                        menuSubItem(
+                          text = "Browse Entries",
+                          tabName = "gs_profile"
+                        ),
+                        menuSubItem(
+                          text = "Screening",
+                          tabName = "gs_screening"
+                        )
+                      ),
+                      menuItem(
+                        text = "Visualization",
+                        tabName = "visualization",
+                        icon = icon("circle-nodes")
+                      ),
+                      menuItem(
+                        text = "Utilities",
+                        tabName = "utilities",
+                        icon = icon("screwdriver-wrench")
+                      )
+                    )
+                  )
+                } else {
+                  output$menu <- renderMenu(
+                    sidebarMenu(
+                      menuItem(
+                        text = "Database Browser",
+                        tabName = "database",
+                        icon = icon("hard-drive"),
+                        startExpanded = TRUE,
+                        menuSubItem(
+                          text = "Browse Entries",
+                          tabName = "db_browse_entries",
+                          selected = TRUE
+                        ),
+                        menuSubItem(
+                          text = "Scheme Info",
+                          tabName = "db_schemeinfo"
+                        ),
+                        menuSubItem(
+                          text = "Loci Info",
+                          tabName = "db_loci_info"
+                        ),
+                        menuSubItem(
+                          text = "Distance Matrix",
+                          tabName = "db_distmatrix"
+                        ),
+                        menuSubItem(
+                          text = "Missing Values",
+                          tabName = "db_missing_values",
+                          icon = icon("triangle-exclamation")
+                        )
+                      ),
+                      menuItem(
+                        text = "Manage Schemes",
+                        tabName = "init",
+                        icon = icon("layer-group")
+                      ),
+                      menuItem(
+                        text = "Allelic Typing",
+                        tabName = "typing",
+                        icon = icon("gears")
+                      ),
+                      menuItem(
+                        text = "Resistance Profile",
+                        tabName = "gene_screening",
+                        icon = icon("dna"),
+                        startExpanded = TRUE,
+                        menuSubItem(
+                          text = "Browse Entries",
+                          tabName = "gs_profile"
+                        ),
+                        menuSubItem(
+                          text = "Screening",
+                          tabName = "gs_screening"
+                        )
+                      ),
+                      menuItem(
+                        text = "Visualization",
+                        tabName = "visualization",
+                        icon = icon("circle-nodes")
+                      ),
+                      menuItem(
+                        text = "Utilities",
+                        tabName = "utilities",
+                        icon = icon("screwdriver-wrench")
+                      )
+                    )
+                  )
+                }
+                
+                # Render custom variable display
+                output$show_cust_var <- renderTable(
+                  width = "100%", 
+                  {
+                    if((!is.null(DB$cust_var)) & (!is.null(input$cust_var_select))) {
+                      if(nrow(DB$cust_var) > 5) {
+                        low <- -4
+                        high <- 0
+                        for (i in 1:input$cust_var_select) {
+                          low <- low + 5
+                          if((nrow(DB$cust_var) %% 5) != 0) {
+                            if(i == ceiling(nrow(DB$cust_var) / 5 )) {
+                              high <- high + nrow(DB$cust_var) %% 5
+                            } else {
+                              high <- high + 5
+                            }
+                          } else {
+                            high <- high + 5
+                          }
+                        }
+                        DB$cust_var[low:high,]
+                      } else {
+                        DB$cust_var
+                      }
+                    } else if (!is.null(DB$cust_var)) {
+                      DB$cust_var
+                    }
+                  })
+                
+                # render visualization sidebar elements
+                observe({
+                  Vis$tree_algo <- input$tree_algo
+                })
+                
+                output$visualization_sidebar <- renderUI({
+                  if(!is.null(DB$data)) {
+                    column(
+                      width = 12,
+                      br(),
+                      fluidRow(
+                        column(1),
+                        column(
+                          width = 11,
+                          align = "left",
+                          prettyRadioButtons(
+                            "tree_algo",
+                            choices = c("Minimum-Spanning", "Neighbour-Joining", "UPGMA"),
+                            label = "",
+                            selected = if(!is.null(Vis$tree_algo)){Vis$tree_algo} else {"Minimum-Spanning"}
+                          ),
+                        )
+                      ),
+                      br(),
+                      fluidRow(
+                        column(
+                          width = 12,
+                          align = "center",
+                          tags$div(
+                            id = "button-wrapper",
+                            actionButton(
+                              "create_tree",
+                              h5("Create Tree", style = "position: relative; left: 15px; color: white; font-size: 15px;"),
+                              width = "100%"
+                            ),
+                            tags$img(
+                              src = "phylo.png",
+                              alt = "icon",
+                              class = "icon"
+                            )
+                          )
+                        )
+                      ), 
+                      br(),
+                      hr(),
+                      conditionalPanel(
+                        "input.tree_algo=='Minimum-Spanning'",
+                        fluidRow(
+                          column(
+                            width = 12,
+                            align = "left",
+                            br(),
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 16px; margin-left: 15px', "Sizing")
+                              )
+                            )
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 12,
+                            radioGroupButtons(
+                              "mst_ratio",
+                              "",
+                              choiceNames = c("16:10", "16:9", "4:3"),
+                              choiceValues = c((16/10), (16/9), (4/3)),
+                              width = "100%"
+                            ),
+                            br(),
+                            sliderInput(
+                              "mst_scale",
+                              "",
+                              min = 500,
+                              max = 1200,
+                              step = 5,
+                              value = 800,
+                              width = "95%",
+                              ticks = FALSE
+                            )
+                          )
+                        ),
+                        br(),
+                        hr(),
+                        fluidRow(
+                          column(
+                            width = 12,
+                            column(
+                              width = 5,
+                              align = "left",
+                              conditionalPanel(
+                                "input.mst_plot_format=='jpeg'",
+                                actionBttn(
+                                  "save_plot_jpeg",
+                                  style = "simple",
+                                  label = "Save Plot",
+                                  size = "sm",
+                                  icon = NULL,
+                                  color = "primary"
+                                )  
+                              ),
+                              conditionalPanel(
+                                "input.mst_plot_format=='png'",
+                                actionBttn(
+                                  "save_plot_png",
+                                  style = "simple",
+                                  label = "Save Plot",
+                                  size = "sm",
+                                  icon = NULL,
+                                  color = "primary"
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.mst_plot_format=='bmp'",
+                                actionBttn(
+                                  "save_plot_bmp",
+                                  style = "simple",
+                                  label = "Save Plot",
+                                  size = "sm",
+                                  icon = NULL,
+                                  color = "primary"
+                                )  
+                              ),
+                              conditionalPanel(
+                                "input.mst_plot_format=='html'",
+                                downloadBttn(
+                                  "save_plot_html",
+                                  style = "simple",
+                                  label = "Save Plot",
+                                  size = "sm",
+                                  icon = NULL,
+                                  color = "primary"
+                                )
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              div(
+                                style = "max-width: 150px",
+                                class = "format",
+                                selectInput(
+                                  inputId = "mst_plot_format",
+                                  label = "",
+                                  choices = c("html", "jpeg", "png", "bmp")
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.tree_algo=='Neighbour-Joining'",
+                        fluidRow(
+                          column(
+                            width = 12,
+                            column(
+                              width = 5,
+                              align = "left",
+                              downloadBttn(
+                                "download_nj",
+                                style = "simple",
+                                label = "Save Plot",
+                                size = "sm",
+                                icon = NULL,
+                                color = "primary"
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              div(
+                                style = "max-width: 150px",
+                                class = "format",
+                                selectInput(
+                                  inputId = "filetype_nj",
+                                  label = "",
+                                  choices = c("png", "jpeg", "bmp", "svg")
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.tree_algo=='UPGMA'",
+                        fluidRow(
+                          column(
+                            width = 12,
+                            column(
+                              width = 5,
+                              align = "left",
+                              downloadBttn(
+                                "download_upgma",
+                                style = "simple",
+                                label = "Save Plot",
+                                size = "sm",
+                                icon = NULL,
+                                color = "primary"
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              div(
+                                style = "max-width: 150px",
+                                class = "format",
+                                selectInput(
+                                  inputId = "filetype_upgma",
+                                  label = "",
+                                  choices = c("png", "jpeg", "bmp", "svg")
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 6,
+                          align = "left",
+                          br(),
+                          actionButton(
+                            "create_rep",
+                            "Print Report"
+                          )
+                        )
+                      )
+                    )
+                  }
+                })
+                
+                # Render entry table sidebar elements
+                output$entrytable_sidebar <- renderUI({
+                  if(!is.null(DB$data)) {
+                    column(
+                      width = 12,
+                      align = "center",
+                      br(), 
+                      fluidRow(
+                        column(1),
+                        column(
+                          width = 10,
+                          align = "left",
+                          if(nrow(DB$data) > 40) {
+                            div(
+                              class = "mat-switch-db-tab",
+                              materialSwitch(
+                                "table_height",
+                                h5(p("Show Full Table"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            )
+                          }
+                        )
+                      ),
+                      br(), br(), 
+                      fluidRow(
+                        column(
+                          width = 12,
+                          HTML(
+                            paste(
+                              tags$span(style='color: white; font-size: 18px; margin-bottom: 0px', 'Custom Variables')
+                            )
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 8,
+                          textInput(
+                            "new_var_name",
+                            label = "",
+                            placeholder = "New Variable"
+                          )
+                        ),
+                        column(
+                          width = 2,
+                          actionButton(
+                            "add_new_variable",
+                            "",
+                            icon = icon("plus")
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 8,
+                          align = "left",
+                          div(
+                            class = "textinput_var",
+                            selectInput(
+                              "del_which_var",
+                              "",
+                              DB$cust_var$Variable
+                            )
+                          )
+                        ),
+                        column(
+                          width = 2,
+                          align = "left",
+                          actionButton(
+                            "delete_new_variable",
+                            "",
+                            icon = icon("minus")
+                          )
+                        )
+                      ),
+                      br(), 
+                      fluidRow(
+                        column(1),
+                        column(
+                          width = 4,
+                          uiOutput("cust_var_info")
+                        )
+                      ),
+                      fluidRow(
+                        column(1),
+                        column(
+                          width = 11,
+                          align = "center",
+                          tableOutput("show_cust_var")
+                        )
+                      ),
+                      fluidRow(
+                        column(4),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("cust_var_select")
+                        )
+                      )
+                    )
+                  } 
+                })
+                
+                # Render missing values sidebar elements
+                output$missing_values_sidebar <- renderUI({
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        br(),
+                        materialSwitch(
+                          "miss_val_height",
+                          h5(p("Show Full Table"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                          value = FALSE,
+                          right = TRUE
+                        )
+                      ),
+                      br()
+                    ),
+                    fluidRow(
+                      column(
+                        width = 6,
+                        HTML(
+                          paste(
+                            tags$span(style='color: white; font-size: 14px; position: relative; bottom: -23px; right: -15px', 
+                                      'Download CSV')
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        downloadBttn(
+                          "download_na_matrix",
+                          style = "simple",
+                          label = "",
+                          size = "sm",
+                          icon = icon("download")
+                        )
+                      )
+                    )
+                  )
+                })
+                
+                # Render scheme info download button
+                output$download_loci <- renderUI({
+                  column(
+                    12,
+                    downloadBttn(
+                      "download_loci_info",
+                      style = "simple",
+                      label = "",
+                      size = "sm",
+                      icon = icon("download"),
+                      color = "primary"
+                    ),
+                    bsTooltip("download_loci_info_bttn", HTML("Save loci information <br> (without sequence)"), placement = "top", trigger = "hover")
+                  )
+                })
+                
+                # Render scheme info download button
+                output$download_scheme_info <- renderUI({
+                  downloadBttn(
+                    "download_schemeinfo",
+                    style = "simple",
+                    label = "",
+                    size = "sm",
+                    icon = icon("download"),
+                    color = "primary"
+                  )
+                })
+                
+                # Render distance matrix sidebar
+                output$distmatrix_sidebar <- renderUI({
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "center",
+                        selectInput(
+                          "distmatrix_label",
+                          label = "",
+                          choices = c("Index", "Assembly Name", "Assembly ID"),
+                          selected = c("Assembly Name"),
+                          width = "100%"
+                        ),
+                        br()
+                      )
+                    ),
+                    div(
+                      class = "mat-switch-dmatrix",
+                      materialSwitch(
+                        "distmatrix_true",
+                        h5(p("Only Included Entries"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                        value = FALSE,
+                        right = TRUE
+                      )
+                    ),
+                    div(
+                      class = "mat-switch-dmatrix",
+                      materialSwitch(
+                        "distmatrix_triangle",
+                        h5(p("Show Upper Triangle"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                        value = FALSE,
+                        right = TRUE
+                      )
+                    ),
+                    div(
+                      class = "mat-switch-dmatrix-last",
+                      materialSwitch(
+                        "distmatrix_diag",
+                        h5(p("Show Diagonal"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                        value = TRUE,
+                        right = TRUE
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 6,
+                        HTML(
+                          paste(
+                            tags$span(style='color: white; font-size: 14px; position: relative; bottom: 37px; right: -15px', 
+                                      'Download CSV')
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        downloadBttn(
+                          "download_distmatrix",
+                          style = "simple",
+                          label = "",
+                          size = "sm",
+                          icon = icon("download")
+                        )
+                      )
+                    )
+                  )
+                })
+                
+                # Render select input to choose displayed loci
+                output$compare_select <- renderUI({
+                  
+                  if(nrow(DB$data) == 1) {
+                    HTML(
+                      paste(
+                        tags$span(style='color: white; font-size: 15px;', "Type at least two assemblies to compare")
+                      )
+                    )
+                  } else {
+                    if(!is.null(input$compare_difference)) {
+                      if (input$compare_difference == FALSE) {
+                        pickerInput(
+                          inputId = "compare_select",
+                          label = "",
+                          width = "85%",
+                          choices = names(DB$allelic_profile),
+                          selected = names(DB$allelic_profile)[1:20],
+                          options = list(
+                            `live-search` = TRUE,
+                            `actions-box` = TRUE,
+                            size = 10,
+                            style = "background-color: white; border-radius: 5px;"
+                          ),
+                          multiple = TRUE
+                        )
+                      } else {
+                        pickerInput(
+                          inputId = "compare_select",
+                          label = "",
+                          width = "85%",
+                          choices = names(DB$allelic_profile),
+                          selected = names(DB$allelic_profile)[var_alleles(DB$allelic_profile)],
+                          options = list(
+                            `live-search` = TRUE,
+                            `actions-box` = TRUE,
+                            size = 10,
+                            style = "background-color: white; border-radius: 5px;"
+                          ),
+                          multiple = TRUE
+                        )
+                      }
+                    }
+                  }
+                })
+                
+                #### Render Entry Data Table ----
+                output$db_entries_table <- renderUI({
+                  if(!is.null(DB$data)) {
+                    if(between(nrow(DB$data), 1, 30)) {
+                      rHandsontableOutput("db_entries")
+                    } else {
+                      addSpinner(
+                        rHandsontableOutput("db_entries"),
+                        spin = "dots",
+                        color = "#ffffff"
+                      )
+                    }
+                  }
+                })
+                
+                if (!is.null(DB$data)) {
+                  
+                  observe({
+                    
+                    if (!is.null(DB$data)) {
+                      if (nrow(DB$data) == 1) {
+                        if(!is.null(DB$data) & !is.null(DB$cust_var)) {
+                          output$db_entries <- renderRHandsontable({
+                            rhandsontable(
+                              select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                              error_highlight = err_thresh() - 1,                              
+                              rowHeaders = NULL,
+                              contextMenu = FALSE,
+                              highlightCol = TRUE, 
+                              highlightRow = TRUE
+                            ) %>%
+                              hot_col(1, 
+                                      valign = "htMiddle",
+                                      halign = "htCenter") %>%
+                              hot_col(3, readOnly = TRUE) %>%
+                              hot_col(c(1, 5, 10, 11, 12, 13),
+                                      readOnly = TRUE) %>%
+                              hot_col(3:(13 + nrow(DB$cust_var)), 
+                                      valign = "htMiddle",
+                                      halign = "htLeft") %>%
+                              hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                              hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                              hot_col(8, type = "dropdown", source = country_names) %>%
+                              hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                                      validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                              hot_cols(fixedColumnsLeft = 1) %>%
+                              hot_col(2, type = "checkbox", width = "auto",
+                                      valign = "htTop",
+                                      halign = "htCenter") %>%
+                              hot_rows(fixedRowsTop = 0) %>%
+                              hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+                          })
+                        }
+                      } else if (between(nrow(DB$data), 2, 40)) {
+                        if (length(input$compare_select) > 0) {
+                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
+                            output$db_entries <- renderRHandsontable({
+                              
+                              entry_data <- DB$data %>%
+                                select(1:(13 + nrow(DB$cust_var))) %>%
+                                add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                              
+                              rhandsontable(
+                                entry_data,
+                                col_highlight = diff_allele() - 1,
+                                dup_names_high = duplicated_names() - 1,
+                                dup_ids_high = duplicated_ids() - 1,
+                                row_highlight = true_rows() - 1,
+                                error_highlight = err_thresh() - 1,
+                                rowHeaders = NULL,
+                                highlightCol = TRUE, 
+                                highlightRow = TRUE,
+                                contextMenu = FALSE
+                              )  %>%
+                                hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
+                                        valign = "htMiddle",
+                                        halign = "htCenter",
+                                        readOnly = TRUE) %>%
+                                hot_col(1, 
+                                        valign = "htMiddle",
+                                        halign = "htCenter") %>%
+                                hot_col(3, readOnly = TRUE) %>%
+                                hot_col(c(1, 5, 10, 11, 12, 13),
+                                        readOnly = TRUE) %>%
+                                hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
+                                        valign = "htMiddle",
+                                        halign = "htLeft") %>%
+                                hot_col(8, type = "dropdown", source = country_names) %>%
+                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                                        validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                                hot_col(2, type = "checkbox", width = "auto",
+                                        valign = "htTop",
+                                        halign = "htCenter",
+                                        strict = TRUE,
+                                        allowInvalid = FALSE,
+                                        copyable = TRUE) %>%
+                                hot_cols(fixedColumnsLeft = 1) %>%
+                                hot_rows(fixedRowsTop = 0) %>%
+                                hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+  
+                       }
+              }") %>%
+                                hot_col(diff_allele(),
+                                        renderer = "
+                  function(instance, td, row, col, prop, value, cellProperties) {
+                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
+  
+                    if (instance.params) {
+                          hcols = instance.params.col_highlight;
+                          hcols = hcols instanceof Array ? hcols : [hcols];
+                        }
+  
+                    if (instance.params && hcols.includes(col)) {
+                      td.style.background = 'rgb(116, 188, 139)';
+                    }
+                }"
+                                ) %>%
+                                hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+                            })
+                          }
+                        } else {
+                          if(!is.null(DB$data) & !is.null(DB$cust_var)) {
+                            output$db_entries <- renderRHandsontable({
+                              rhandsontable(
+                                select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                                rowHeaders = NULL,
+                                row_highlight = true_rows() - 1,
+                                dup_names_high = duplicated_names()- 1,
+                                dup_ids_high = duplicated_ids() - 1,
+                                error_highlight = err_thresh() - 1,
+                                contextMenu = FALSE,
+                                highlightCol = TRUE, 
+                                highlightRow = TRUE
+                              ) %>%
+                                hot_cols(fixedColumnsLeft = 1) %>%
+                                hot_col(1, 
+                                        valign = "htMiddle",
+                                        halign = "htCenter") %>%
+                                hot_col(3, readOnly = TRUE) %>%
+                                hot_col(c(1, 5, 10, 11, 12, 13),
+                                        readOnly = TRUE) %>%
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
+                                        valign = "htMiddle",
+                                        halign = "htLeft") %>%
+                                hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(8, type = "dropdown", source = country_names) %>%
+                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                                        validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                                hot_col(2, type = "checkbox", width = "auto",
+                                        valign = "htTop",
+                                        halign = "htCenter") %>%
+                                hot_rows(fixedRowsTop = 0) %>%
+                                hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+  
+                       }
+              }") %>%
+                                hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+                            })    
+                          }
+                        }
+                      } else {
+                        if (length(input$compare_select) > 0) {
+                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
+                            output$db_entries <- renderRHandsontable({
+                              
+                              entry_data <- DB$data %>%
+                                select(1:(13 + nrow(DB$cust_var))) %>%
+                                add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                              
+                              rhandsontable(
+                                entry_data,
+                                col_highlight = diff_allele() - 1,
+                                rowHeaders = NULL,
+                                height = table_height(),
+                                row_highlight = true_rows() - 1,
+                                dup_names_high = duplicated_names() - 1,
+                                dup_ids_high = duplicated_ids() - 1,
+                                error_highlight = err_thresh() - 1,
+                                contextMenu = FALSE,
+                                highlightCol = TRUE, 
+                                highlightRow = TRUE
+                              ) %>%
+                                hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
+                                        readOnly = TRUE, 
+                                        valign = "htMiddle",
+                                        halign = "htCenter") %>%
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
+                                        valign = "htMiddle",
+                                        halign = "htLeft") %>%
+                                hot_col(3, readOnly = TRUE) %>%
+                                hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(c(1, 5, 10, 11, 12, 13),
+                                        readOnly = TRUE) %>%
+                                hot_col(8, type = "dropdown", source = country_names) %>%
+                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                                        validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                                hot_col(1, 
+                                        valign = "htMiddle",
+                                        halign = "htCenter") %>%
+                                hot_col(2, type = "checkbox", width = "auto",
+                                        valign = "htTop",
+                                        halign = "htCenter",
+                                        allowInvalid = FALSE,
+                                        copyable = TRUE) %>%
+                                hot_cols(fixedColumnsLeft = 1) %>%
+                                hot_rows(fixedRowsTop = 0) %>%
+                                hot_col(1, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.row_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                                                             }
+                                                           }
+                                                       }") %>%
+                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") %>%
+                                hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(diff_allele(),
+                                        renderer = "
+                  function(instance, td, row, col, prop, value, cellProperties) {
+                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
+  
+                    if (instance.params) {
+                          hcols = instance.params.col_highlight;
+                          hcols = hcols instanceof Array ? hcols : [hcols];
+                        }
+  
+                    if (instance.params && hcols.includes(col)) {
+                      td.style.background = 'rgb(116, 188, 139)';
+                    }
+                }") 
+                            })    
+                          }
+                        } else {
+                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
+                            output$db_entries <- renderRHandsontable({
+                              rhandsontable(
+                                select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                                rowHeaders = NULL,
+                                height = table_height(),
+                                dup_names_high = duplicated_names() - 1,
+                                dup_ids_high = duplicated_ids() - 1,
+                                row_highlight = true_rows() - 1,
+                                error_highlight = err_thresh() - 1,
+                                contextMenu = FALSE,
+                                highlightCol = TRUE, 
+                                highlightRow = TRUE
+                              ) %>%
+                                hot_cols(fixedColumnsLeft = 1) %>%
+                                hot_col(1, 
+                                        valign = "htMiddle",
+                                        halign = "htCenter") %>%
+                                hot_col(3, readOnly = TRUE) %>%
+                                hot_col(c(1, 5, 10, 11, 12, 13),
+                                        readOnly = TRUE) %>%
+                                hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(8, type = "dropdown", source = country_names) %>%
+                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                                        validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
+                                        valign = "htMiddle",
+                                        halign = "htLeft") %>%
+                                hot_rows(fixedRowsTop = 0) %>%
+                                hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(2, type = "checkbox", width = "auto",
+                                        valign = "htTop", halign = "htCenter") %>%
+                                hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+                            })
+                          }
+                        }
+                      }
+                    }
+                    
+                    # Dynamic save button when rhandsontable changes or new entries
+                    output$edit_entry_table <- renderUI({
+                      if(check_new_entry() & DB$check_new_entries) {
+                        Typing$reload <- FALSE
+                        fluidRow(
+                          column(
+                            width = 8,
+                            align = "left",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: absolute; bottom: -30px; right: -5px', 
+                                          'New entries - reload database')
+                              )
+                            )
+                          ),
+                          column(
+                            width = 4,
+                            actionButton(
+                              "load",
+                              "",
+                              icon = icon("rotate"),
+                              class = "pulsating-button"
+                            )
+                          )
+                        )
+                      } else if(Typing$status == "Attaching") {
+                        fluidRow(
+                          column(
+                            width = 11,
+                            align = "left",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: absolute; bottom: -30px; right: -5px', 'No database changes possible - pending entry addition')
+                              )
+                            )
+                          ),
+                          column(
+                            width = 1,
+                            HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px; color:white; margin-top: 10px"></i>'))
+                          )
+                        )
+                      } else if((DB$change == TRUE) | !identical(get.entry.table.meta(), select(DB$meta, -13))) {
+                        
+                        if(!is.null(input$db_entries)) {
+                          fluidRow(
+                            column(
+                              width = 5,
+                              HTML(
+                                paste(
+                                  tags$span(style='color: white; font-size: 16px; position: absolute; bottom: -30px; right: -5px', 'Confirm changes')
+                                )
+                              )
+                            ),
+                            column(
+                              width = 3,
+                              actionButton(
+                                "edit_button",
+                                "",
+                                icon = icon("bookmark"),
+                                class = "pulsating-button"
+                              )
+                            ),
+                            column(
+                              width = 4,
+                              actionButton(
+                                "undo_changes",
+                                "Undo",
+                                icon = icon("repeat")
+                              )
+                            )
+                          )
+                        }
+                      } else {NULL}
+                    })
+                    
+                  })
+                  
+                  # Hide no entry message
+                  output$db_no_entries <- NULL
+                  output$distancematrix_no_entries <- NULL
+                  
+                } else {
+                  
+                  # If database loading not successful dont show entry table
+                  output$db_entries_table <- NULL
+                  output$entry_table_controls <- NULL
+                }
+                
+                # Render Entry table controls
+                output$entry_table_controls <- renderUI({
+                  fluidRow(
+                    column(1),
+                    column(
+                      width = 3,
+                      align = "center",
+                      fluidRow(
+                        column(
+                          width = 4,
+                          align = "center",
+                          actionButton(
+                            "sel_all_entries",
+                            "Select All",
+                            icon = icon("check")
+                          )
+                        ),
+                        column(
+                          width = 4,
+                          align = "left",
+                          actionButton(
+                            "desel_all_entries",
+                            "Deselect All",
+                            icon = icon("xmark")
+                          )
+                        )
+                      )
+                    ),
+                    column(
+                      width = 3,
+                      uiOutput("edit_entry_table")
+                    )
+                  )
+                })
+                
+                #### Render Distance Matrix ----
+                observe({
+                  if(!is.null(DB$data)) {
+                    
+                    if(any(duplicated(DB$meta$`Assembly Name`)) | any(duplicated(DB$meta$`Assembly ID`))) {
+                      output$db_distancematrix <- NULL
+                      
+                      if( (sum(duplicated(DB$meta$`Assembly Name`)) > 0) & (sum(duplicated(DB$meta$`Assembly ID`)) == 0) ) {
+                        duplicated_txt <- paste0(
+                          paste(
+                            paste0("Name  # ", which(duplicated(DB$meta$`Assembly Name`)), " - "),
+                            DB$meta$`Assembly Name`[which(duplicated(DB$meta$`Assembly Name`))]
+                          ),
+                          "<br>"
+                        )
+                      } else if ( (sum(duplicated(DB$meta$`Assembly ID`)) > 0) & (sum(duplicated(DB$meta$`Assembly Name`)) == 0) ){
+                        duplicated_txt <- paste0(
+                          paste(
+                            paste0("ID  # ", which(duplicated(DB$meta$`Assembly ID`)), " - "),
+                            DB$meta$`Assembly ID`[which(duplicated(DB$meta$`Assembly ID`))]
+                          ),
+                          "<br>"
+                        )
+                      } else {
+                        duplicated_txt <- c(
+                          paste0(
+                            paste(
+                              paste0("Name  # ", which(duplicated(DB$meta$`Assembly Name`)), " - "),
+                              DB$meta$`Assembly Name`[which(duplicated(DB$meta$`Assembly Name`))]
+                            ),
+                            "<br>"
+                          ),
+                          paste0(
+                            paste(
+                              paste0("ID  # ", which(duplicated(DB$meta$`Assembly ID`)), " - "),
+                              DB$meta$`Assembly ID`[which(duplicated(DB$meta$`Assembly ID`))]
+                            ),
+                            "<br>"
+                          )
+                        )
+                      }
+                      
+                      output$distancematrix_duplicated <- renderUI({
+                        column(
+                          width = 12,
+                          tags$span(style = "font-size: 15; color: white",
+                                    "Change duplicated entry names to display distance matrix."),
+                          br(), br(), br(),
+                          actionButton("change_entries", "Go to Entry Table", class = "btn btn-default"),
+                          br(), br(), br(),
+                          tags$span(
+                            style = "font-size: 15; color: white",
+                            HTML(
+                              append(
+                                "Duplicated:",
+                                append(
+                                  "<br>",
+                                  duplicated_txt
+                                )
+                              )
+                            )
+                          )
+                        )
+                      })
+                    } else {
+                      output$distancematrix_duplicated <- NULL
+                      if(!is.null(DB$data) & !is.null(DB$allelic_profile) & !is.null(DB$allelic_profile_true) & !is.null(DB$cust_var) & !is.null(input$distmatrix_label) & !is.null(input$distmatrix_diag) & !is.null(input$distmatrix_triangle)) {
+                        output$db_distancematrix <- renderRHandsontable({
+                          rhandsontable(hamming_df(), 
+                                        digits = 1, 
+                                        readOnly = TRUE,
+                                        contextMenu = FALSE,
+                                        highlightCol = TRUE, 
+                                        highlightRow = TRUE,
+                                        height = distancematrix_height(), rowHeaders = NULL) %>%
+                            hot_heatmap(renderer = paste0("
+                            function (instance, td, row, col, prop, value, cellProperties) {
+                              Handsontable.renderers.TextRenderer.apply(this, arguments);
+                              heatmapScale  = chroma.scale(['#17F556', '#ED6D47']);
+                            
+                              if (instance.heatmap[col]) {
+                                mn = ", DB$matrix_min, ";
+                                mx = ", DB$matrix_max, ";
+                            
+                                pt = (parseInt(value, 10) - mn) / (mx - mn);    
+                            
+                                td.style.backgroundColor = heatmapScale(pt).hex();
+                              }
+                            }")) %>%
+                            hot_rows(fixedRowsTop = 0) %>%
+                            hot_cols(fixedColumnsLeft = 1) %>%
+                            hot_col(1:(dim(DB$ham_matrix)[1]+1),
+                                    halign = "htCenter",
+                                    valign = "htMiddle") %>%
+                            hot_col(1, renderer = "
+                            function(instance, td, row, col, prop, value, cellProperties) {
+                              Handsontable.renderers.NumericRenderer.apply(this, arguments);
+                              td.style.background = '#F0F0F0'
+                            }"
+                            )
+                        })  
+                      }
+                    }
+                    
+                    # Render Distance Matrix UI
+                    
+                    output$distmatrix_show <- renderUI({
+                      if(!is.null(DB$data)) {
+                        if(nrow(DB$data) > 1) {
+                          column(
+                            width = 10,
+                            uiOutput("distancematrix_duplicated"),
+                            div(
+                              class = "distmatrix",
+                              rHandsontableOutput("db_distancematrix")
+                            )
+                          )
+                        } else {
+                          column(
+                            width = 10,
+                            align = "left",
+                            p(
+                              HTML(
+                                paste(
+                                  tags$span(style='color: white; font-size: 15px;', "Type at least two assemblies to display a distance matrix.")
+                                )
+                              )
+                            ),
+                            br(),
+                            br()
+                          )
+                        }
+                      }
+                    })
+                    
+                  }
+                })
+                
+                
+                # Render delete entry box UI
+                output$delete_box <- renderUI({
+                  box(
+                    solidHeader = TRUE,
+                    status = "primary",
+                    width = "100%",
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "center",
+                        h3(p("Delete Entries"), style = "color:white")
+                      )
+                    ),
+                    hr(),
+                    fluidRow(
+                      column(
+                        width = 2,
+                        offset = 1,
+                        align = "right",
+                        br(),
+                        h5("Index", style = "color:white; margin-bottom: 0px;")
+                      ),
+                      column(
+                        width = 6,
+                        align = "center",
+                        uiOutput("delete_select")
+                      ),
+                      column(
+                        width = 2,
+                        align = "center",
+                        br(),
+                        uiOutput("del_bttn")
+                      )
+                    ),
+                    br()
+                  )
+                })
+                
+                # Render loci comparison box UI
+                output$compare_allele_box <- renderUI({
+                  box(
+                    solidHeader = TRUE,
+                    status = "primary",
+                    width = "100%",
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "center",
+                        h3(p("Compare Loci"), style = "color:white")
+                      )
+                    ),
+                    hr(),
+                    column(
+                      width = 12,
+                      align = "center",
+                      br(),
+                      uiOutput("compare_select"),
+                      br(),
+                      column(2),
+                      column(
+                        width = 10,
+                        align = "left",
+                        uiOutput("compare_difference_box")
+                      )
+                    ),
+                    br()
+                  )
+                })
+                
+                # Render entry table download box UI
+                output$download_entries <- renderUI({
+                  fluidRow(
+                    column(
+                      width = 12,
+                      box(
+                        solidHeader = TRUE,
+                        status = "primary",
+                        width = "100%",
+                        fluidRow(
+                          column(
+                            width = 12,
+                            align = "center",
+                            h3(p("Download Table"), style = "color:white")
+                          )
+                        ),
+                        hr(),
+                        fluidRow(
+                          column(2),
+                          column(
+                            width = 10,
+                            align = "left",
+                            br(),
+                            div(
+                              class = "mat-switch-db",
+                              materialSwitch(
+                                "download_table_include",
+                                h5(p("Only Included Entries"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            ),
+                            div(
+                              class = "mat-switch-db",
+                              materialSwitch(
+                                "download_table_loci",
+                                h5(p("Include Displayed Loci"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            ),
+                            br(),
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 12,
+                            align = "center",
+                            downloadBttn(
+                              "download_entry_table",
+                              style = "simple",
+                              label = "",
+                              size = "sm",
+                              icon = icon("download"),
+                              color = "primary"
+                            )
+                          )
+                        ),
+                        br()
+                      )
+                    ),
+                    column(
+                      width = 12,
+                      fluidRow(
+                        column(
+                          width = 2,
+                          div(
+                            class = "rectangle-blue" 
+                          ),
+                          div(
+                            class = "rectangle-orange" 
+                          ),
+                          div(
+                            class = "rectangle-red" 
+                          ),
+                          div(
+                            class = "rectangle-green" 
+                          )
+                        ),
+                        column(
+                          width = 10,
+                          align = "left",
+                          p(
+                            HTML(
+                              paste(
+                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -12px", " = included for analyses")
+                              )
+                            )
+                          ),
+                          p(
+                            HTML(
+                              paste(
+                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -13px", " =  duplicated name/ID")
+                              )
+                            )
+                          ),
+                          p(
+                            HTML(
+                              paste(
+                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -14px", " =  ≥ 5% of loci missing")
+                              )
+                            )
+                          ),
+                          p(
+                            HTML(
+                              paste(
+                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -15px", " =  locus contains multiple variants")
+                              )
+                            )
+                          ),
+                        )
+                      )
+                    )
+                  )
+                })
+                
+                # Render entry deletion select input
+                output$delete_select <- renderUI({
+                  pickerInput("select_delete",
+                              label = "",
+                              choices = DB$data[, "Index"],
+                              options = list(
+                                `live-search` = TRUE,
+                                `actions-box` = TRUE,
+                                size = 10,
+                                style = "background-color: white; border-radius: 5px;"
+                              ),
+                              multiple = TRUE)
+                })
+                
+                # Render delete entry button
+                output$del_bttn <- renderUI({
+                  actionBttn(
+                    "del_button",
+                    label = "",
+                    color = "danger",
+                    size = "sm",
+                    style = "material-circle",
+                    icon = icon("xmark")
+                  )
+                })
+                
+                #### Missing Values UI ----
+                
+                # Missing values calculations and table 
+                observe({
+                  
+                  if (!is.null(DB$allelic_profile)) {
+                    NA_table <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) != 0]
+                    
+                    NA_table <- NA_table[rowSums(is.na(NA_table)) != 0,]
+                    
+                    NA_table[is.na(NA_table)] <- "NA"
+                    
+                    NA_table <- NA_table %>% 
+                      cbind("Assembly Name" = DB$meta[rownames(NA_table),]$`Assembly Name`) %>%
+                      cbind("Errors" = DB$meta[rownames(NA_table),]$Errors) %>%
+                      relocate("Assembly Name", "Errors")
+                    
+                    DB$na_table <- NA_table
+                    
+                    if(!is.null(input$miss_val_height)) {
+                      if(nrow(DB$na_table) < 31) {
+                        output$table_missing_values <- renderRHandsontable({
+                          rhandsontable(
+                            DB$na_table,
+                            readOnly = TRUE,
+                            rowHeaders = NULL,
+                            contextMenu = FALSE,
+                            highlightCol = TRUE, 
+                            highlightRow = TRUE,
+                            error_highlight = err_thresh_na() - 1
+                          ) %>%
+                            hot_cols(fixedColumnsLeft = 1) %>%
+                            hot_rows(fixedRowsTop = 0) %>%
+                            hot_col(1:ncol(DB$na_table), valign = "htMiddle", halign = "htLeft") %>%
+                            hot_col(2, renderer = "
+                            function (instance, td, row, col, prop, value, cellProperties) {
+                              Handsontable.renderers.TextRenderer.apply(this, arguments);
+                              if (instance.params) {
+                                hrows = instance.params.error_highlight
+                                hrows = hrows instanceof Array ? hrows : [hrows]
+                                if (hrows.includes(row)) { 
+                                  td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
+                                }
+                              }
+                            }") %>%
+                            hot_col(3:ncol(DB$na_table), renderer = htmlwidgets::JS(
+                              "function(instance, td, row, col, prop, value, cellProperties) {
+                                if (value.length > 8) {
+                                  value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                                }
+                                td.innerHTML = value;
+                                td.style.textAlign = 'center';
+                                return td;
+                               }"
+                            ))
+                        })
+                      } else {
+                        output$table_missing_values <- renderRHandsontable({
+                          rhandsontable(
+                            DB$na_table,
+                            readOnly = TRUE,
+                            rowHeaders = NULL,
+                            height = miss.val.height(),
+                            contextMenu = FALSE,
+                            highlightCol = TRUE, 
+                            highlightRow = TRUE,
+                            error_highlight = err_thresh() - 1
+                          ) %>%
+                            hot_cols(fixedColumnsLeft = 1) %>%
+                            hot_rows(fixedRowsTop = 0) %>%
+                            hot_col(1:ncol(DB$na_table), valign = "htMiddle", halign = "htLeft") %>%
+                            hot_col(2, renderer = "
+                            function (instance, td, row, col, prop, value, cellProperties) {
+                              Handsontable.renderers.TextRenderer.apply(this, arguments);
+                              if (instance.params) {
+                                hrows = instance.params.error_highlight
+                                hrows = hrows instanceof Array ? hrows : [hrows]
+                                if (hrows.includes(row)) { 
+                                  td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
+                                }
+                              }
+                            }") %>%
+                            hot_col(3:ncol(DB$na_table), renderer = htmlwidgets::JS(
+                              "function(instance, td, row, col, prop, value, cellProperties) {
+                                if (value.length > 8) {
+                                  value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                                }
+                                td.innerHTML = value;
+                                td.style.textAlign = 'center';
+                                return td;
+                               }"
+                            ))
+                        })
+                      }
+                    }
+                  }
+                  
+                })
+                
+                # Render missing value informatiojn box UI
+                output$missing_values <- renderUI({
+                  div(
+                    class = "miss_val_box",
+                    box(
+                      solidHeader = TRUE,
+                      status = "primary",
+                      width = "100%",
+                      fluidRow(
+                        div(
+                          class = "white",
+                          column(
+                            width = 12,
+                            align = "left",
+                            br(), 
+                            HTML(
+                              paste0("There are ", 
+                                     strong(as.character(sum(is.na(DB$data)))), 
+                                     " unsuccessful allele allocations (NA). ",
+                                     strong(sum(sapply(DB$allelic_profile, anyNA))),
+                                     " out of ",
+                                     strong(ncol(DB$allelic_profile)),
+                                     " total loci in this scheme contain NA's (",
+                                     strong(round((sum(sapply(DB$allelic_profile, anyNA)) / ncol(DB$allelic_profile) * 100), 1)),
+                                     " %). ",
+                                     "Decide how these missing values should be treated:")
+                              
+                            ),
+                            br()
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(1),
+                        column(
+                          width = 11,
+                          align = "left",
+                          br(),
+                          prettyRadioButtons(
+                            "na_handling",
+                            "",
+                            choiceNames = c("Ignore missing values for pairwise comparison",
+                                            "Omit loci with missing values for all assemblies",
+                                            "Treat missing values as allele variant"),
+                            choiceValues = c("ignore_na", "omit", "category"),
+                            shape = "curve",
+                            selected = c("ignore_na")
+                          ),
+                          br()
+                        )
+                      )
+                    )
+                  )
+                })  
+                
+              } else { 
+                #if no typed assemblies present
+                
+                # null underlying database
+                
+                DB$data <- NULL
+                DB$meta <- NULL
+                DB$meta_gs <- NULL
+                DB$meta_true <- NULL
+                DB$allelic_profile <- NULL
+                DB$allelic_profile_trunc <- NULL
+                DB$allelic_profile_true <- NULL
+                
+                # Render menu without missing values tab
+                output$menu <- renderMenu(
+                  sidebarMenu(
+                    menuItem(
+                      text = "Database Browser",
+                      tabName = "database",
+                      icon = icon("hard-drive"),
+                      startExpanded = TRUE,
+                      selected = TRUE,
+                      menuSubItem(
+                        text = "Browse Entries",
+                        tabName = "db_browse_entries"
+                      ),
+                      menuSubItem(
+                        text = "Scheme Info",
+                        tabName = "db_schemeinfo"
+                      ),
+                      menuSubItem(
+                        text = "Loci Info",
+                        tabName = "db_loci_info"
+                      ),
+                      menuSubItem(
+                        text = "Distance Matrix",
+                        tabName = "db_distmatrix"
+                      )
+                    ),
+                    menuItem(
+                      text = "Manage Schemes",
+                      tabName = "init",
+                      icon = icon("layer-group")
+                    ),
+                    menuItem(
+                      text = "Allelic Typing",
+                      tabName = "typing",
+                      icon = icon("gears")
+                    ),
+                    menuItem(
+                      text = "Resistance Profile",
+                      tabName = "gene_screening",
+                      icon = icon("dna"),
+                      startExpanded = TRUE,
+                      menuSubItem(
+                        text = "Browse Entries",
+                        tabName = "gs_profile"
+                      ),
+                      menuSubItem(
+                        text = "Screening",
+                        tabName = "gs_screening"
+                      )
+                    ),
+                    menuItem(
+                      text = "Visualization",
+                      tabName = "visualization",
+                      icon = icon("circle-nodes")
+                    ),
+                    menuItem(
+                      text = "Utilities",
+                      tabName = "utilities",
+                      icon = icon("screwdriver-wrench")
+                    )
+                  )
+                )
+                
+                observe({
+                  if(is.null(DB$data)) {
+                    if(check_new_entry()) {
+                      output$db_no_entries <- renderUI(
+                        column(
+                          width = 12,
+                          fluidRow(
+                            column(1),
+                            column(
+                              width = 3,
+                              align = "left",
+                              HTML(
+                                paste(
+                                  tags$span(style='color: white; font-size: 15px; position: absolute; bottom: -30px; right: -5px', 'New entries - reload database')
+                                )
+                              )
+                            ),
+                            column(
+                              width = 4,
+                              actionButton(
+                                "load",
+                                "",
+                                icon = icon("rotate"),
+                                class = "pulsating-button"
+                              )
+                            )
+                          )
+                        )
+                      )
+                    } else {
+                      output$db_no_entries <- renderUI(
+                        column(
+                          width = 12,
+                          fluidRow(
+                            column(1),
+                            column(
+                              width = 11,
+                              align = "left",
+                              HTML(
+                                paste(
+                                  "<span style='color: white;'>",
+                                  "No Entries for this scheme available.\n",
+                                  "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
+                                  sep = '<br/>'
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    }
+                  }
+                })
+                
+                output$distancematrix_no_entries <- renderUI(
+                  fluidRow(
+                    column(1),
+                    column(
+                      width = 11,
+                      align = "left",
+                      HTML(paste(
+                        "<span style='color: white;'>",
+                        "No Entries for this scheme available.",
+                        "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
+                        sep = '<br/>'
+                      ))
+                    )
+                  )
+                )
+                
+                output$db_entries <- NULL
+                output$edit_index <- NULL
+                output$edit_scheme_d <- NULL
+                output$edit_entries <- NULL
+                output$compare_select <- NULL
+                output$delete_select <- NULL
+                output$del_bttn <- NULL
+                output$compare_allele_box <- NULL
+                output$download_entries <- NULL
+                output$missing_values <- NULL
+                output$delete_box <- NULL
+                output$entry_table_controls <- NULL
+                output$multi_stop <- NULL
+                output$metadata_multi_box <- NULL
+                output$start_multi_typing_ui <- NULL
+                output$pending_typing <- NULL
+                output$multi_typing_results <- NULL
+                output$single_typing_progress <- NULL
+                output$metadata_single_box <- NULL
+                output$start_typing_ui <- NULL
+                
+                output$initiate_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(),
+                    br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyFilesButton(
+                          "genome_file",
+                          "Browse" ,
+                          icon = icon("file"),
+                          title = "Select the assembly in .fasta/.fna/.fa format:",
+                          multiple = FALSE,
+                          buttonType = "default",
+                          class = NULL,
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("genome_path"),
+                        br()
+                      )
+                    )
+                  )
+                })
+                
+                output$initiate_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(),
+                    br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyFilesButton(
+                          "genome_file",
+                          "Browse" ,
+                          icon = icon("file"),
+                          title = "Select the assembly in .fasta/.fna/.fa format:",
+                          multiple = FALSE,
+                          buttonType = "default",
+                          class = NULL,
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("genome_path"),
+                        br()
+                      )
+                    )
+                  )
+                })
+                
+                output$initiate_multi_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(), br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyDirButton(
+                          "genome_file_multi",
+                          "Browse",
+                          icon = icon("folder-open"),
+                          title = "Select the folder containing the genome assemblies (FASTA)",
+                          buttonType = "default",
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("multi_select_info"),
+                        br()
+                      )
+                    ),
+                    uiOutput("multi_select_tab_ctrls"),
+                    br(),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "left",
+                        rHandsontableOutput("multi_select_table")
+                      )
+                    )
+                  )
+                })
+              }
+            }
+          }
+        }
+      } else {
+        
+        log_print("Invalid scheme folder")
+        show_toast(
+          title = "Invalid scheme folder",
+          type = "warning",
+          position = "bottom-end",
+          timer = 4000
+        )
+      }
+    }
+    
+  })
+  
+  # _______________________ ####
+  
+  ## Database ----
+  
+  ### Conditional UI Elements rendering ----
+  
+  # Contro custom variables table
+  output$cust_var_select <- renderUI({
+    if(nrow(DB$cust_var) > 5) {
+      selectInput(
+        "cust_var_select",
+        "",
+        choices = 1:ceiling(nrow(DB$cust_var) / 5 )
+      )
+    }
+  })
+  
+  output$cust_var_info <- renderUI({
+    if((!is.null(DB$cust_var)) & (!is.null(input$cust_var_select))) {
+      if(nrow(DB$cust_var) > 5) {
+        low <- -4
+        high <- 0
+        for (i in 1:input$cust_var_select) {
+          low <- low + 5
+          if((nrow(DB$cust_var) %% 5) != 0) {
+            if(i == ceiling(nrow(DB$cust_var) / 5 )) {
+              high <- high + nrow(DB$cust_var) %% 5
+            } else {
+              high <- high + 5
+            }
+          } else {
+            high <- high + 5
+          }
+        }
+        h5(paste0("Showing ", low, " to ", high," of ", nrow(DB$cust_var), " variables"), style = "color: white; font-size: 10px;")
+      }
+    }
+  })
+  
+  # Message on Database tabs if no scheme available yet
+  observe({
+    if(!is.null(DB$exist)) {
+      if(DB$exist){
+        
+        # Message for tab Browse Entries
+        output$no_scheme_entries <- renderUI({
+          fluidRow(
+            column(1),
+            column(
+              width = 4,
+              align = "left",
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'No scheme available.')
+                  )
+                )
+              ),
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'Download a scheme first and type assemblies in the section Allelic Typing.')
+                  )
+                )
+              )
+            )
+          )
+        })
+        
+        # Message for Tab Scheme Info
+        output$no_scheme_info <- renderUI({
+          fluidRow(
+            column(1),
+            column(
+              width = 10,
+              align = "left",
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'No scheme available.')
+                  )
+                )
+              ),
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'Download a scheme first and type assemblies in the section Allelic Typing.')
+                  )
+                )
+              )
+            )
+          )
+        })
+        
+        # Message for Tab Distance Matrix
+        output$no_scheme_distancematrix <- renderUI({
+          fluidRow(
+            column(1),
+            column(
+              width = 10,
+              align = "left",
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'No scheme available.')
+                  )
+                )
+              ),
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'Download a scheme first and type assemblies in the section Allelic Typing.')
+                  )
+                )
+              )
+            )
+          )
+        })
+        
+      } else {
+        output$no_scheme_entries <- NULL
+        output$no_scheme_info <- NULL
+        output$no_scheme_distancematrix <- NULL
+      }
+    }
+    
+  })
+  
+  observe({
+    # Conditional Missing Values Tab
+    if(!is.null(DB$allelic_profile)) {
+      if(anyNA(DB$allelic_profile)) {
+        if(DB$no_na_switch == FALSE) {
+          output$menu <- renderMenu(
+            sidebarMenu(
+              menuItem(
+                text = "Database Browser",
+                tabName = "database",
+                icon = icon("hard-drive"),
+                startExpanded = TRUE,
+                menuSubItem(
+                  text = "Browse Entries",
+                  tabName = "db_browse_entries"
+                ),
+                menuSubItem(
+                  text = "Scheme Info",
+                  tabName = "db_schemeinfo"
+                ),
+                menuSubItem(
+                  text = "Loci Info",
+                  tabName = "db_loci_info"
+                ),
+                menuSubItem(
+                  text = "Distance Matrix",
+                  tabName = "db_distmatrix"
+                ),
+                menuSubItem(
+                  text = "Missing Values",
+                  tabName = "db_missing_values",
+                  selected = TRUE,
+                  icon = icon("triangle-exclamation")
+                )
+              ),
+              menuItem(
+                text = "Manage Schemes",
+                tabName = "init",
+                icon = icon("layer-group")
+              ),
+              menuItem(
+                text = "Allelic Typing",
+                tabName = "typing",
+                icon = icon("gears")
+              ),
+              menuItem(
+                text = "Resistance Profile",
+                tabName = "gene_screening",
+                icon = icon("dna"),
+                startExpanded = TRUE,
+                menuSubItem(
+                  text = "Browse Entries",
+                  tabName = "gs_profile"
+                ),
+                menuSubItem(
+                  text = "Screening",
+                  tabName = "gs_screening"
+                )
+              ),
+              menuItem(
+                text = "Visualization",
+                tabName = "visualization",
+                icon = icon("circle-nodes")
+              ),
+              menuItem(
+                text = "Utilities",
+                tabName = "utilities",
+                icon = icon("screwdriver-wrench")
+              )
+            )
+          )
+        }
+        
+      } else {
+        output$menu <- renderMenu(
+          sidebarMenu(
+            menuItem(
+              text = "Database Browser",
+              tabName = "database",
+              icon = icon("hard-drive"),
+              startExpanded = TRUE,
+              menuSubItem(
+                text = "Browse Entries",
+                tabName = "db_browse_entries"
+              ),
+              menuSubItem(
+                text = "Scheme Info",
+                tabName = "db_schemeinfo"
+              ),
+              menuSubItem(
+                text = "Loci Info",
+                tabName = "db_loci_info"
+              ),
+              menuSubItem(
+                text = "Distance Matrix",
+                tabName = "db_distmatrix"
+              )
+            ),
+            menuItem(
+              text = "Manage Schemes",
+              tabName = "init",
+              icon = icon("layer-group")
+            ),
+            menuItem(
+              text = "Allelic Typing",
+              tabName = "typing",
+              icon = icon("gears")
+            ),
+            menuItem(
+              text = "Resistance Profile",
+              tabName = "gene_screening",
+              icon = icon("dna"),
+              startExpanded = TRUE,
+              menuSubItem(
+                text = "Browse Entries",
+                tabName = "gs_profile"
+              ),
+              menuSubItem(
+                text = "Screening",
+                tabName = "gs_screening"
+              )
+            ),
+            menuItem(
+              text = "Visualization",
+              tabName = "visualization",
+              icon = icon("circle-nodes")
+            ),
+            menuItem(
+              text = "Utilities",
+              tabName = "utilities",
+              icon = icon("screwdriver-wrench")
+            )
+          )
+        )
+      }
+    }
+    
+  })
+  
+  observe({
+    
+    if (!is.null(DB$available)) {
+      output$scheme_db <- renderUI({
+        if (length(DB$available) > 5) {
+          selectInput(
+            "scheme_db",
+            label = "",
+            choices = if(!is.null(Typing$last_scheme)) {
+              Typing$last_scheme
+            } else {DB$available},
+            selected = if(!is.null(Typing$last_scheme)) {
+              Typing$last_scheme
+            } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}
+          )
+        } else {
+          prettyRadioButtons(
+            "scheme_db",
+            label = "",
+            choices = if(!is.null(Typing$last_scheme)) {
+              Typing$last_scheme
+            } else {DB$available},
+            selected = if(!is.null(Typing$last_scheme)) {
+              Typing$last_scheme
+            } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}
+          )
+        }
+      })
+      
+      if (!is.null(DB$schemeinfo)) {
+        
+        output$scheme_info <- renderTable({
+          DB$schemeinfo
+        })
+        
+        output$scheme_header <- renderUI(h3(p("cgMLST Scheme"), style = "color:white"))
+        
+      } else {
+        
+        output$scheme_info <- NULL
+        output$scheme_header <- NULL
+        
+      }
+      
+      if (!is.null(DB$loci_info)) {
+        loci_info <- DB$loci_info
+        names(loci_info)[6] <- "Allele Count"
+        
+        output$db_loci <- renderDataTable(
+          loci_info,
+          selection = "single",
+          options = list(pageLength = 10,
+                         columnDefs = list(list(searchable = TRUE,
+                                                targets = "_all")),
+                         initComplete = DT::JS(
+                           "function(settings, json) {",
+                           "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                           "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                           "}"
+                         ),
+                         drawCallback = DT::JS(
+                           "function(settings) {",
+                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                           "}"
+                         ))
+        )
+        
+        output$loci_header <- renderUI(h3(p("Loci"), style = "color:white"))
+        
+      } else {
+        output$db_loci <- NULL
+        output$loci_header <- NULL
+      }
+    } 
+  })
+  
+  # If only one entry available disable varying loci checkbox
+  
+  output$compare_difference_box <- renderUI({
+    if(!is.null(DB$data)) {
+      if(nrow(DB$data) > 1) {
+        div(
+          class = "mat-switch-db",
+          materialSwitch(
+            "compare_difference",
+            h5(p("Only Varying Loci"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+            value = FALSE,
+            right = TRUE
+          )
+        )
+      }
+    }
+  })
+  
+  ### Database Events ----
+  
+  # Invalid entries table input
+  observe({
+    req(DB$data, input$db_entries)
+    if (isTRUE(input$invalid_date)) {
+      show_toast(
+        title = "Invalid date",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+      DB$inhibit_change <- TRUE
+    } else if (isTRUE(input$empty_name)) {
+      show_toast(
+        title = "Empty name",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+      DB$inhibit_change <- TRUE
+    } else if (isTRUE(input$empty_id)) {
+      show_toast(
+        title = "Empty ID",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+      DB$inhibit_change <- TRUE
+    } else {
+      DB$inhibit_change <- FALSE
+    }
+  })
+  
+  # Change scheme
+  observeEvent(input$reload_db, {
+    log_print("Input reload_db")
+    
+    if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
+      show_toast(
+        title = "Pending Multi Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if(Screening$status == "started") {
+      show_toast(
+        title = "Pending Screening",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      showModal(
+        modalDialog(
+          selectInput(
+            "scheme_db",
+            label = "",
+            choices = DB$available,
+            selected = DB$scheme),
+          title = "Select a local database to load.",
+          easyClose = TRUE,
+          footer = tagList(
+            modalButton("Cancel"),
+            actionButton("load", "Load", class = "btn btn-default")
+          )
+        )
+      )
+    }
+  })
+  
+  # Create new database
+  observe({
+    shinyDirChoose(input,
+                   "create_new_db",
+                   roots = c(Home = path_home(), Root = "/"),
+                   defaultRoot = "Home",
+                   session = session)
+    
+    if(!is.null(input$create_new_db)) {
+      DB$new_database <- as.character(
+        parseDirPath(
+          roots = c(Home = path_home(), Root = "/"),
+          input$create_new_db
+        )
+      )
+    }
+  })
+  
+  # Undo db changes
+  observeEvent(input$undo_changes, {
+    log_print("Input undo_changes")
+    
+    DB$inhibit_change <- FALSE
+    
+    Data <- readRDS(paste0(
+      DB$database, "/",
+      gsub(" ", "_", DB$scheme),
+      "/Typing.rds"
+    ))
+    
+    DB$data <- Data[["Typing"]]
+    
+    if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+      cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+      DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
+    } else {
+      DB$cust_var <- data.frame()
+    }
+    
+    DB$change <- FALSE
+    DB$count <- 0
+    DB$no_na_switch <- TRUE
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
+    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+    DB$deleted_entries <- character(0)
+    
+    observe({
+      if (!is.null(DB$data)) {
+        if (nrow(DB$data) == 1) {
+          if(!is.null(DB$data) & !is.null(DB$cust_var)) {
+            output$db_entries <- renderRHandsontable({
+              rhandsontable(
+                select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                error_highlight = err_thresh() - 1,                              
+                rowHeaders = NULL,
+                contextMenu = FALSE,
+                highlightCol = TRUE, 
+                highlightRow = TRUE
+              ) %>%
+                hot_col(1, 
+                        valign = "htMiddle",
+                        halign = "htCenter") %>%
+                hot_col(3, readOnly = TRUE) %>%
+                hot_col(c(1, 5, 10, 11, 12, 13),
+                        readOnly = TRUE) %>%
+                hot_col(3:(13 + nrow(DB$cust_var)), 
+                        valign = "htMiddle",
+                        halign = "htLeft") %>%
+                hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                hot_col(8, type = "dropdown", source = country_names) %>%
+                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                        validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                hot_cols(fixedColumnsLeft = 1) %>%
+                hot_col(2, type = "checkbox", width = "auto",
+                        valign = "htTop",
+                        halign = "htCenter") %>%
+                hot_rows(fixedRowsTop = 0) %>%
+                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+            })
+          }
+        } else if (between(nrow(DB$data), 1, 40)) {
+          if (length(input$compare_select) > 0) {
+            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
+              output$db_entries <- renderRHandsontable({
+                
+                entry_data <- DB$data %>%
+                  select(1:(13 + nrow(DB$cust_var))) %>%
+                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                
+                rhandsontable(
+                  entry_data,
+                  col_highlight = diff_allele() - 1,
+                  dup_names_high = duplicated_names() - 1,
+                  dup_ids_high = duplicated_ids() - 1,
+                  row_highlight = true_rows() - 1,
+                  error_highlight = err_thresh() - 1,
+                  rowHeaders = NULL,
+                  highlightCol = TRUE, 
+                  highlightRow = TRUE,
+                  contextMenu = FALSE
+                )  %>%
+                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
+                          valign = "htMiddle",
+                          halign = "htCenter",
+                          readOnly = TRUE) %>%
+                  hot_col(1, 
+                          valign = "htMiddle",
+                          halign = "htCenter") %>%
+                  hot_col(3, readOnly = TRUE) %>%
+                  hot_col(c(1, 5, 10, 11, 12, 13),
+                          readOnly = TRUE) %>%
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
+                          valign = "htMiddle",
+                          halign = "htLeft") %>%
+                  hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(8, type = "dropdown", source = country_names) %>%
+                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                          validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                  hot_col(2, type = "checkbox", width = "auto",
+                          valign = "htTop",
+                          halign = "htCenter",
+                          strict = TRUE,
+                          allowInvalid = FALSE,
+                          copyable = TRUE) %>%
+                  hot_cols(fixedColumnsLeft = 1) %>%
+                  hot_rows(fixedRowsTop = 0) %>%
+                  hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+  
+                       }
+              }") %>%
+                  hot_col(diff_allele(),
+                          renderer = "
+                  function(instance, td, row, col, prop, value, cellProperties) {
+                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
+  
+                    if (instance.params) {
+                          hcols = instance.params.col_highlight;
+                          hcols = hcols instanceof Array ? hcols : [hcols];
+                        }
+  
+                    if (instance.params && hcols.includes(col)) {
+                      td.style.background = 'rgb(116, 188, 139)';
+                    }
+                }"
+                  ) %>%
+                  hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+              })
+            }
+          } else {
+            if(!is.null(DB$data) & !is.null(DB$cust_var)) {
+              output$db_entries <- renderRHandsontable({
+                rhandsontable(
+                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                  rowHeaders = NULL,
+                  row_highlight = true_rows() - 1,
+                  dup_names_high = duplicated_names()- 1,
+                  dup_ids_high = duplicated_ids() - 1,
+                  error_highlight = err_thresh() - 1,
+                  contextMenu = FALSE,
+                  highlightCol = TRUE, 
+                  highlightRow = TRUE
+                ) %>%
+                  hot_cols(fixedColumnsLeft = 1) %>%
+                  hot_col(1, 
+                          valign = "htMiddle",
+                          halign = "htCenter") %>%
+                  hot_col(3, readOnly = TRUE) %>%
+                  hot_col(c(1, 5, 10, 11, 12, 13),
+                          readOnly = TRUE) %>%
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
+                          valign = "htMiddle",
+                          halign = "htLeft") %>%
+                  hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(8, type = "dropdown", source = country_names) %>%
+                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                          validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                  hot_col(2, type = "checkbox", width = "auto",
+                          valign = "htTop",
+                          halign = "htCenter") %>%
+                  hot_rows(fixedRowsTop = 0) %>%
+                  hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+  
+                       }
+              }") %>%
+                  hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+              })    
+            }
+          }
+        } else {
+          if (length(input$compare_select) > 0) {
+            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
+              output$db_entries <- renderRHandsontable({
+                
+                entry_data <- DB$data %>%
+                  select(1:(13 + nrow(DB$cust_var))) %>%
+                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                
+                rhandsontable(
+                  entry_data,
+                  col_highlight = diff_allele() - 1,
+                  rowHeaders = NULL,
+                  height = table_height(),
+                  row_highlight = true_rows() - 1,
+                  dup_names_high = duplicated_names() - 1,
+                  dup_ids_high = duplicated_ids() - 1,
+                  error_highlight = err_thresh() - 1,
+                  contextMenu = FALSE,
+                  highlightCol = TRUE, 
+                  highlightRow = TRUE
+                ) %>%
+                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
+                          readOnly = TRUE, 
+                          valign = "htMiddle",
+                          halign = "htCenter") %>%
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
+                          valign = "htMiddle",
+                          halign = "htLeft") %>%
+                  hot_col(3, readOnly = TRUE) %>%
+                  hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(c(1, 5, 10, 11, 12, 13),
+                          readOnly = TRUE) %>%
+                  hot_col(8, type = "dropdown", source = country_names) %>%
+                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                          validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                  hot_col(1, 
+                          valign = "htMiddle",
+                          halign = "htCenter") %>%
+                  hot_col(2, type = "checkbox", width = "auto",
+                          valign = "htTop",
+                          halign = "htCenter",
+                          allowInvalid = FALSE,
+                          copyable = TRUE) %>%
+                  hot_cols(fixedColumnsLeft = 1) %>%
+                  hot_rows(fixedRowsTop = 0) %>%
+                  hot_col(1, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.row_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                                                             }
+                                                           }
+                                                       }") %>%
+                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") %>%
+                  hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(diff_allele(),
+                          renderer = "
+                  function(instance, td, row, col, prop, value, cellProperties) {
+                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
+  
+                    if (instance.params) {
+                          hcols = instance.params.col_highlight;
+                          hcols = hcols instanceof Array ? hcols : [hcols];
+                        }
+  
+                    if (instance.params && hcols.includes(col)) {
+                      td.style.background = 'rgb(116, 188, 139)';
+                    }
+                }") 
+              })    
+            }
+          } else {
+            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
+              output$db_entries <- renderRHandsontable({
+                rhandsontable(
+                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                  rowHeaders = NULL,
+                  height = table_height(),
+                  dup_names_high = duplicated_names() - 1,
+                  dup_ids_high = duplicated_ids() - 1,
+                  row_highlight = true_rows() - 1,
+                  error_highlight = err_thresh() - 1,
+                  contextMenu = FALSE,
+                  highlightCol = TRUE, 
+                  highlightRow = TRUE
+                ) %>%
+                  hot_cols(fixedColumnsLeft = 1) %>%
+                  hot_col(1, 
+                          valign = "htMiddle",
+                          halign = "htCenter") %>%
+                  hot_col(c(1, 5, 10, 11, 12, 13),
+                          readOnly = TRUE) %>%
+                  hot_col(3, readOnly = TRUE) %>%
+                  hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(8, type = "dropdown", source = country_names) %>%
+                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                          validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
+                          valign = "htMiddle",
+                          halign = "htLeft") %>%
+                  hot_rows(fixedRowsTop = 0) %>%
+                  hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(2, type = "checkbox", width = "auto",
+                          valign = "htTop", halign = "htCenter") %>%
+                  hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+              })
+            }
+          }
+        }
+      }
+    })
+  })
+  
+  observe({
+    if(!is.null(DB$data)){
+      if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+        cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+        DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
+        
+      } else {
+        DB$cust_var <- data.frame()
+      }
+    }
+  })
+  
+  DB$count <- 0
+  
+  observeEvent(input$add_new_variable, {
+    log_print("Input add_new_variable")
+    
+    if(nchar(input$new_var_name) > 12) {
+      log_print("Add variable; max. 10 character")
+      show_toast(
+        title = "Max. 10 characters",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      if (input$new_var_name == "") {
+        log_print("Add variable; min. 1 character")
+        show_toast(
+          title = "Min. 1 character",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+      } else {
+        if(trimws(input$new_var_name) %in% names(DB$meta)) {
+          log_print("Add variable; name already existing")
+          show_toast(
+            title = "Variable name already existing",
+            type = "warning",
+            position = "bottom-end",
+            timer = 6000
+          )
+        } else {
+          showModal(
+            modalDialog(
+              selectInput(
+                "new_var_type",
+                label = "",
+                choices = c("Categorical (character)",
+                            "Continous (numeric)")),
+              title = paste0("Select Data Type"),
+              easyClose = TRUE,
+              footer = tagList(
+                modalButton("Cancel"),
+                actionButton("conf_new_var", "Confirm", class = "btn btn-default")
+              )
+            )
+          )
+        }
+      }
+    }
+  })
+  
+  observeEvent(input$conf_new_var, {
+    log_print("Input conf_new_var")
+    
+    # User feedback variables
+    removeModal()
+    DB$count <- DB$count + 1
+    DB$change <- TRUE
+    
+    # Format variable name
+    name <- trimws(input$new_var_name)
+    
+    if(input$new_var_type == "Categorical (character)") {
+      DB$data <- DB$data %>%
+        mutate("{name}" := character(nrow(DB$data)), .after = 13)
+      
+      DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "categ"))
+    } else {
+      DB$data <- DB$data %>%
+        mutate("{name}" := numeric(nrow(DB$data)), .after = 13)
+      
+      DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "cont"))
+    }
+    
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+    
+    log_print(paste0("New custom variable added: ", input$new_var_name))
+    
+    show_toast(
+      title = paste0("Variable ", trimws(input$new_var_name), " added"),
+      type = "success",
+      position = "bottom-end",
+      timer = 6000
+    )
+    
+  })
+  
+  observeEvent(input$delete_new_variable, {
+    log_print("Input delete_new_variable")
+    
+    if (input$del_which_var == "") {
+      log_print("Delete custom variables; no custom variable")
+      show_toast(
+        title = "No custom variables",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      showModal(
+        modalDialog(
+          paste0(
+            "Confirmation will lead to irreversible deletion of the custom ",
+            input$del_which_var,
+            " variable. Continue?"
+          ),
+          title = "Delete custom variables",
+          fade = TRUE,
+          easyClose = TRUE,
+          footer = tagList(
+            modalButton("Cancel"),
+            actionButton("conf_var_del", "Delete", class = "btn btn-danger")
+          )
+        )
+      )
+    }
+  })
+  
+  observeEvent(input$conf_var_del, {
+    log_print("Input conf_var_del")
+    
+    DB$change <- TRUE
+    
+    removeModal()
+    
+    if(DB$count >= 1) {
+      DB$count <- DB$count - 1
+    } 
+    
+    show_toast(
+      title = paste0("Variable ", input$del_which_var, " removed"),
+      type = "warning",
+      position = "bottom-end",
+      timer = 6000
+    )
+    
+    log_print(paste0("Variable ", input$del_which_var, " removed"))
+    
+    DB$cust_var <- DB$cust_var[-which(DB$cust_var$Variable == input$del_which_var),]
+    DB$data <- select(DB$data, -(input$del_which_var))
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
+    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+  })
+  
+  # Select all button
+  
+  observeEvent(input$sel_all_entries, {
+    log_print("Input sel_all_entries")
+    
+    DB$data$Include <- TRUE
+  })
+  
+  observeEvent(input$desel_all_entries, {
+    log_print("Input desel_all_entries")
+    
+    DB$data$Include <- FALSE
+  })
+  
+  # Switch to entry table
+  
+  observeEvent(input$change_entries, {
+    log_print("Input change_entries")
+    
+    removeModal()
+    updateTabItems(session, "tabs", selected = "db_browse_entries")
+  })
+  
+  #### Save Missing Value as CSV ----
+  
+  output$download_na_matrix <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save missing values table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")))
+      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")
+    },
+    content = function(file) {
+      download_matrix <- hot_to_r(input$table_missing_values)
+      write.csv(download_matrix, file, sep = ",", row.names=FALSE, quote=FALSE) 
+    }
+  )
+  
+  #### Save scheme info table as CSV ----
+  
+  output$download_schemeinfo <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save scheme info table ", paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")))
+      
+      paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")
+    },
+    content = function(file) {
+      pub_index <- which(DB$schemeinfo[,1] == "Publications")
+      write.table(
+        DB$schemeinfo[1:(pub_index-1),],
+        file, 
+        sep = ";",
+        row.names = FALSE, 
+        quote = FALSE
+      ) 
+    }
+  )
+  
+  #### Save Loci info table as CSV ----
+  
+  output$download_loci_info <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save loci info table ", paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")))
+      
+      paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")
+    },
+    content = function(file) {
+      write.table(
+        DB$loci_info,
+        file, 
+        sep = ";",
+        row.names = FALSE, 
+        quote = FALSE
+      ) 
+    }
+  )
+  
+  #### Save entry table as CSV ----
+  
+  output$download_entry_table <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save entry table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")))
+      
+      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")
+    },
+    content = function(file) {
+      download_matrix <- hot_to_r(input$db_entries)
+      
+      if (input$download_table_include == TRUE) {
+        download_matrix <- download_matrix[which(download_matrix$Include == TRUE),]
+      }
+      
+      if (input$download_table_loci == FALSE) {
+        download_matrix <- select(download_matrix, 1:(13 + nrow(DB$cust_var)))
+      } 
+      
+      write.csv(download_matrix, file, row.names=FALSE, quote=FALSE) 
+    }
+  )
+  
+  # Save Edits Button
+  
+  observeEvent(input$edit_button, {
+    if(nrow(hot_to_r(input$db_entries)) > nrow(DB$data)) {
+      show_toast(
+        title = "Invalid rows entered. Saving not possible.",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      if(!isTRUE(DB$inhibit_change)) {
+        log_print("Input edit_button")
+        
+        showModal(
+          modalDialog(
+            if(length(DB$deleted_entries > 0)) {
+              paste0(
+                "Overwriting previous metadata of local ",
+                DB$scheme,
+                " database. Deleted entries will be irreversibly removed. Continue?"
+              )
+            } else {
+              paste0(
+                "Overwriting previous metadata of local ",
+                DB$scheme,
+                " database. Continue?"
+              )
+            },
+            title = "Save Database",
+            fade = TRUE,
+            easyClose = TRUE,
+            footer = tagList(
+              modalButton("Cancel"),
+              actionButton("conf_db_save", "Save", class = "btn btn-default")
+            )
+          )
+        )
+      } else {
+        log_print("Input edit_button, invalid values.")
+        show_toast(
+          title = "Invalid values entered. Saving not possible.",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+      }
+    }
+  })
+  
+  observeEvent(input$Cancel, {
+    log_print("Input Cancel")
+    removeModal()
+  })
+  
+  observeEvent(input$conf_db_save, {
+    log_print("Input conf_db_save")
+    
+    # Remove isolate assembly file if present
+    if(!is.null(DB$remove_iso)) {
+      if(length(DB$remove_iso) > 0) {
+        lapply(DB$remove_iso, unlink, recursive = TRUE, force = FALSE, expand = TRUE)
+      }
+    }
+    DB$remove_iso <- NULL
+    
+    Data <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
+    
+    if ((ncol(Data[["Typing"]]) - 13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+      cust_vars_pre <- select(Data[["Typing"]], 
+                              14:(ncol(Data[["Typing"]]) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+      cust_vars_pre <- names(cust_vars_pre)
+    } else {
+      cust_vars_pre <- character()
+    }
+    
+    Data[["Typing"]] <- select(Data[["Typing"]], -(1:(13 + length(cust_vars_pre))))
+    
+    meta_hot <- hot_to_r(input$db_entries)
+    
+    if(length(DB$deleted_entries > 0)) {
+      
+      meta_hot <- mutate(meta_hot, Index = as.character(1:nrow(DB$data)))
+      
+      Data[["Typing"]] <- mutate(Data[["Typing"]][-as.numeric(DB$deleted_entries),  ], 
+                                 meta_hot, .before = 1)
+      rownames(Data[["Typing"]]) <- Data[["Typing"]]$Index
+    } else {
+      Data[["Typing"]] <- mutate(Data[["Typing"]], meta_hot, .before = 1)
+    }
+    
+    # Ensure correct logical data type
+    Data[["Typing"]][["Include"]] <- as.logical(Data[["Typing"]][["Include"]])
+    saveRDS(Data, file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+    
+    # Load database from files  
+    Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+    
+    DB$data <- Database[["Typing"]]
+    
+    if(!is.null(DB$data)){
+      if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+        cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+        DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
+      } else {
+        DB$cust_var <- data.frame()
+      }
+    }
+    
+    DB$change <- FALSE
+    DB$count <- 0
+    DB$no_na_switch <- TRUE
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
+    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+    DB$deleted_entries <- character(0)
+    
+    removeModal()
+    
+    show_toast(
+      title = "Database successfully saved",
+      type = "success",
+      position = "bottom-end",
+      timer = 4000
+    )
+  })
+  
+  observeEvent(input$del_button, {
+    log_print("Input del_button")
+    
+    if (length(input$select_delete) < 1) {
+      log_print("Delete entries; no entry selected")
+      show_toast(
+        title = "No entry selected",
+        type = "warning",
+        position = "bottom-end",
+        timer = 4000
+      )
+    } else if((readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") |
+              (tail(readLogFile(), 1) != "0")) {
+      log_print("Delete entries; pending typing")
+      
+      show_toast(
+        title = "Pending Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 4000
+      )
+    } else {
+      if( (length(input$select_delete) - nrow(DB$data) ) == 0) {
+        showModal(
+          modalDialog(
+            paste0("Deleting will lead to removal of all entries and assemblies from local ", DB$scheme, " database. The data can not be recovered afterwards. Continue?"),
+            easyClose = TRUE,
+            title = "Deleting Entries",
+            footer = tagList(
+              modalButton("Cancel"),
+              actionButton("conf_delete_all", "Delete", class = "btn btn-danger")
+            )
+          )
+        )
+      } else {
+        showModal(
+          modalDialog(
+            paste0(
+              "Confirmation will lead to irreversible removal of selected entries and the respectively saved assembly. Continue?"
+            ),
+            title = "Deleting Entries",
+            fade = TRUE,
+            easyClose = TRUE,
+            footer = tagList(
+              modalButton("Cancel"),
+              actionButton(
+                "conf_delete", 
+                "Delete", 
+                class = "btn btn-danger")
+            )
+          )
+        )
+      }
+    }
+  })
+  
+  observeEvent(input$conf_delete_all, {
+    log_print("Input conf_delete_all")
+    
+    # remove file with typing data
+    file.remove(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+    unlink(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates"), recursive = TRUE, force = FALSE, expand =TRUE)
+    
+    showModal(
+      modalDialog(
+        selectInput(
+          "scheme_db",
+          label = "",
+          choices = if(!is.null(Typing$last_scheme)) {
+            Typing$last_scheme
+          } else {DB$available},
+          selected = if(!is.null(Typing$last_scheme)) {
+            Typing$last_scheme
+          } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}),
+        title = "All entries have been removed. Select a local database to load.",
+        footer = tagList(
+          actionButton("load", "Load", class = "btn btn-default")
+        )
+      )
+    )
+    
+  })
+  
+  DB$deleted_entries <- character(0)
+  
+  observeEvent(input$conf_delete, {
+    
+    log_print("Input conf_delete")
+    
+    # Get isolates selected for deletion
+    DB$deleted_entries <- append(DB$deleted_entries, DB$data$Index[as.numeric(input$select_delete)])
+    
+    # Set reactive status variables
+    DB$no_na_switch <- TRUE
+    DB$change <- TRUE
+    DB$check_new_entries <- FALSE
+    
+    # Set isolate directory deletion variables
+    isopath <- dir_ls(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates"))
+    DB$remove_iso <- isopath[which(basename(isopath) == DB$data$`Assembly ID`[as.numeric(input$select_delete)])]
+    
+    # Reload updated database reactive variables
+    DB$data <- DB$data[!(DB$data$Index %in% as.numeric(input$select_delete)),]
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
+    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+    
+    # User feedback
+    removeModal()
+    
+    if(length(input$select_delete) > 1) {
+      show_toast(
+        title = "Entries deleted",
+        type = "success",
+        position = "bottom-end",
+        timer = 4000
+      )
+    } else {
+      show_toast(
+        title = "Entry deleted",
+        type = "success",
+        position = "bottom-end",
+        timer = 4000
+      )
+    }
+  })
+  
+  
+  ### Distance Matrix ---- 
+  
+  hamming_df <- reactive({
+    if(input$distmatrix_true == TRUE) {
+      if(anyNA(DB$allelic_profile)) {
+        if(input$na_handling == "omit") {
+          allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
+          
+          allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
+          
+          hamming_mat <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
+          
+        } else if(input$na_handling == "ignore_na"){
+          hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
+          
+        } else {
+          hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
+          
+        } 
+      } else {
+        hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
+      }
+    } else {
+      if(anyNA(DB$allelic_profile)) {
+        if(input$na_handling == "omit") {
+          allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
+          hamming_mat <- compute.distMatrix(allelic_profile_noNA, hamming.dist)
+        } else if(input$na_handling == "ignore_na"){
+          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distIgnore)
+        } else {
+          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distCategory)
+        }  
+      } else {
+        hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.dist)
+      }
+    }
+    
+    # Extreme values for distance matrix heatmap display
+    DB$matrix_min <- min(hamming_mat, na.rm = TRUE)
+    DB$matrix_max <- max(hamming_mat, na.rm = TRUE)
+    
+    if(input$distmatrix_triangle == FALSE) {
+      hamming_mat[upper.tri(hamming_mat, diag = !input$distmatrix_diag)] <- NA
+    } 
+    
+    # Row- and colnames change
+    if(input$distmatrix_true == TRUE) {
+      rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label][which(DB$data$Include == TRUE),])
+    } else {
+      rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label])
+    }
+    colnames(hamming_mat) <- rownames(hamming_mat)
+    
+    mode(hamming_mat) <- "integer"
+    
+    DB$ham_matrix <- hamming_mat %>%
+      as.data.frame() %>%
+      mutate(Index = colnames(hamming_mat)) %>%
+      relocate(Index)
+    DB$distancematrix_nrow <- nrow(DB$ham_matrix)
+    
+    DB$ham_matrix
+  })
+  
+  output$download_distmatrix <- downloadHandler(
+    filename = function() {
+      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Distance_Matrix.csv")
+    },
+    content = function(file) {
+      download_matrix <- hot_to_r(input$db_distancematrix)
+      download_matrix[is.na(download_matrix)] <- ""
+      write.csv(download_matrix, file, row.names=FALSE, quote=FALSE) 
+    }
+  )
+  
+  # _______________________ ####
+  
+  ## Locus sequences ----
+  
+  observe({
+    if(!is.null(DB$database) & !is.null(DB$scheme)) {
+      DB$loci <- list.files(
+        path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
+        pattern = "\\.(fasta|fa|fna)$",
+        full.names = TRUE
+      )
+    }
+  })
+  
+  output$loci_sequences <- renderUI({
+    req(input$db_loci_rows_selected, DB$database, DB$scheme, input$seq_sel)
+    
+    DB$loci <- list.files(
+      path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
+      pattern = "\\.(fasta|fa|fna)$",
+      full.names = TRUE
+    )
+    
+    fasta <- format_fasta(DB$loci[input$db_loci_rows_selected])
+    
+    seq <- fasta[[which(fasta == paste0(">", gsub("Allele ", "", sub(" -.*", "", input$seq_sel)))) + 1]]
+    
+    DB$seq <- seq
+    
+    column(
+      width = 12,
+      HTML(
+        paste(
+          tags$span(style='color: white; font-size: 15px; position: relative; top: -15px; left: -50px', 
+                    sub(" -.*", "", input$seq_sel))
+        )
+      ),
+      tags$pre(HTML(color_sequence(seq)), class = "sequence")
+    )
+  })
+  
+  output$sequence_selector <- renderUI({
+    if(!is.null(input$db_loci_rows_selected)) {
+      
+      req(input$db_loci_rows_selected, DB$database, DB$scheme)
+      
+      DB$loci <- list.files(
+        path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
+        pattern = "\\.(fasta|fa|fna)$",
+        full.names = TRUE
+      )
+      
+      fasta <- format_fasta(DB$loci[input$db_loci_rows_selected])
+      
+      seq_names <- c()
+      for (i in seq_along(fasta)) {
+        if (startsWith(fasta[[i]], ">")) {
+          name <- sub(">", "", fasta[[i]])
+          seq_names <- c(seq_names, name)
+        }
+      }
+      
+      var_count <- table(DB$allelic_profile[gsub(".fasta", "", (basename(DB$loci[input$db_loci_rows_selected])))])
+      
+      vec <- prop.table(var_count)
+      
+      perc <- sapply(unname(vec), scales::percent, accuracy = 0.1)
+      
+      names(perc) <- names(vec)
+      
+      choices <- seq_names
+      
+      present <- which(choices %in% names(vec))
+      absent <- which(!(choices %in% names(vec)))
+      
+      choices[present] <- paste0("Allele ", choices[present], " - ", unname(var_count), " times in DB (", unname(perc), ")")
+      
+      choices[absent] <- paste0("Allele ", choices[absent], " - not present")
+      
+      choices <- c(choices[present], choices[absent])
+      
+      names(choices) <- sapply(choices, function(x) {
+        x <- strsplit(x, " ")[[1]]
+        x[2] <- paste0(substr(x[2], 1, 4), "...", substr(x[2], nchar(x[2])-3, nchar(x[2])))
+        paste(x, collapse = " ")
+      })
+      
+      column(
+        width = 3,
+        selectInput(
+          "seq_sel",
+          h5("Select Variant", style = "color:white;"),
+          choices = choices,
+          width = "80%"
+        ),
+        br(),
+        fluidRow(
+          column(
+            width = 8,
+            align = "left",
+            actionButton("copy_seq", "Copy Sequence",
+                         icon = icon("copy")),
+            bsTooltip("copy_seq", "Copy the variant sequence <br> to clipboard", placement = "top", trigger = "hover")
+          )
+        ),
+        br(),
+        fluidRow(
+          column(
+            width = 8,
+            align = "left",
+            downloadBttn(
+              "get_locus",
+              style = "simple",
+              label = "Save .fasta",
+              size = "sm",
+              icon = icon("download")
+            ),
+            bsTooltip("get_locus_bttn", "Save locus file with all variants", placement = "top", trigger = "hover")
+          )
+        ),
+        br(), br(), br(), br(), br(), br(), br()
+      )
+    }
+  })
+  
+  observeEvent(input$copy_seq, {
+    if(!is.null(DB$seq)) {
+      session$sendCustomMessage("txt", DB$seq)
+    }
+    show_toast(
+      title = "Copied sequence",
+      type = "success",
+      position = "bottom-end",
+      timer = 3000
+    )
+  })
+  
+  output$get_locus <- downloadHandler(
+    filename = function() {
+      fname <- basename(DB$loci[input$db_loci_rows_selected])
+      log_print(paste0("Get locus fasta ", fname))
+      fname
+    },
+    content = function(file) {
+      cont <- readLines(DB$loci[input$db_loci_rows_selected])
+      writeLines(cont, file)
+    }
+  )
+  
+  # _______________________ ####
+  
+  ## Download cgMLST ----
+  
+  observe({
+    if (input$select_cgmlst == "Acinetobacter baumanii") {
+      species <- "Abaumannii1907"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- Scheme$folder_name <- "Acinetobacter_baumanii"
+    } else if (input$select_cgmlst == "Bacillus anthracis") {
+      species <- "Banthracis1917"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Bacillus_anthracis"
+    } else if (input$select_cgmlst == "Bordetella pertussis") {
+      species <- "Bpertussis1917"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Bordetella_pertussis"
+    } else if (input$select_cgmlst == "Brucella melitensis") {
+      species <- "Bmelitensis1912"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Brucella_melitensis"
+    } else if (input$select_cgmlst == "Brucella spp.") {
+      species <- "Brucella1914"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Brucella_spp"
+    } else if (input$select_cgmlst == "Burkholderia mallei (FLI)") {
+      species <- "Bmallei_fli1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Burkholderia_mallei_FLI"
+    } else if (input$select_cgmlst == "Burkholderia mallei (RKI)") {
+      species <- "Bmallei_rki1909"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Burkholderia_mallei_RKI"
+    } else if (input$select_cgmlst == "Burkholderia pseudomallei") {
+      species <- "Bpseudomallei1906"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Burkholderia_pseudomallei"
+    } else if (input$select_cgmlst == "Campylobacter jejuni/coli") {
+      species <- "Cjejuni1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Campylobacter_jejuni_coli"
+    } else if (input$select_cgmlst == "Clostridioides difficile") {
+      species <- "Cdifficile1905"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Clostridioides_difficile"
+    } else if (input$select_cgmlst == "Clostridium perfringens") {
+      species <- "Cperfringens1907"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Clostridium_perfringens"
+    } else if (input$select_cgmlst == "Corynebacterium diphtheriae") {
+      species <- "Cdiphtheriae1907"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Corynebacterium_diphtheriae"
+    } else if (input$select_cgmlst == "Cronobacter sakazakii/malonaticus") {
+      species <- "Csakazakii1910"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Cronobacter_sakazakii_malonaticus"
+    } else if (input$select_cgmlst == "Enterococcus faecalis") {
+      species <- "Efaecalis1912"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Enterococcus_faecalis"
+    } else if (input$select_cgmlst == "Enterococcus faecium") {
+      species <- "Efaecium1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Enterococcus_faecium"
+    } else if (input$select_cgmlst == "Escherichia coli") {
+      species <- "Ecoli1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Escherichia_coli"
+    } else if (input$select_cgmlst == "Francisella tularensis") {
+      species <- "Ftularensis1913"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Francisella_tularensis"
+    } else if (input$select_cgmlst == "Klebsiella oxytoca sensu lato") {
+      species <- "Koxytoca717"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Klebsiella_oxytoca_sensu_lato"
+    } else if (input$select_cgmlst == "Klebsiella pneumoniae sensu lato") {
+      species <- "Kpneumoniae1909"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Klebsiella_pneumoniae_sensu_lato"
+    } else if (input$select_cgmlst == "Legionella pneumophila") {
+      species <- "Lpneumophila1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Legionella_pneumophila"
+    } else if (input$select_cgmlst == "Listeria monocytogenes") {
+      species <- "Lmonocytogenes1910"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Listeria_monocytogenes"
+    } else if (input$select_cgmlst == "Mycobacterium tuberculosis complex") {
+      species <- "Mtuberculosis1909"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Mycobacterium_tuberculosis_complex"
+    } else if (input$select_cgmlst == "Mycobacteroides abscessus") {
+      species <- "Mabscessus1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Mycobacteroides_abscessus"
+    } else if (input$select_cgmlst == "Mycoplasma gallisepticum") {
+      species <- "Mgallisepticum1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Mycoplasma_gallisepticum"
+    } else if (input$select_cgmlst == "Paenibacillus larvae") {
+      species <- "Plarvae1902"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Paenibacillus_larvae"
+    } else if (input$select_cgmlst == "Pseudomonas aeruginosa") {
+      species <- "Paeruginosa1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Pseudomonas_aeruginosa"
+    } else if (input$select_cgmlst == "Salmonella enterica") {
+      species <- "Senterica1913"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Salmonella_enterica"
+    } else if (input$select_cgmlst == "Serratia marcescens") {
+      species <- "Smarcescens1912"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Serratia_marcescens"
+    } else if (input$select_cgmlst == "Staphylococcus aureus") {
+      species <- "Saureus1908"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Staphylococcus_aureus"
+    } else if (input$select_cgmlst == "Staphylococcus capitis") {
+      species <- "Scapitis1905"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Staphylococcus_capitis"
+    } else if (input$select_cgmlst == "Streptococcus pyogenes") {
+      species <- "Spyogenes1904"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Streptococcus_pyogenes"
+    }
+  })
+  
+  observeEvent(input$download_cgMLST, {
+    log_print(paste0("Started download of scheme for ", Scheme$folder_name))
+    
+    shinyjs::hide("download_cgMLST")
+    shinyjs::show("loading")
+    
+    output$statustext <- renderUI(
+      fluidRow(
+        tags$li(
+          class = "dropdown", 
+          tags$span(HTML(
+            paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                  "Status:&nbsp;&nbsp;&nbsp; <i>Downloading scheme...</i>")),
+            style = "color:white;")
+        )
+      )
+    )
+    
+    show_toast(
+      title = "Download started",
+      type = "success",
+      position = "bottom-end",
+      timer = 5000
+    )
+    
+    if(length(DB$available) == 0) {
+      saveRDS(DB$new_database, paste0(getwd(), "/execute/new_db.rds"))
+      dir.create(file.path(readRDS(paste0(getwd(), "/execute/new_db.rds")), "Database"), recursive = TRUE)
+    }
+    
+    DB$load_selected <- TRUE
+    
+    # Check if .downloaded_schemes folder exists and if not create it
+    if (!dir.exists(file.path(DB$database, ".downloaded_schemes"))) {
+      dir.create(file.path(DB$database, ".downloaded_schemes"), recursive = TRUE)
+    }
+    
+    # Check if remains of old temporary folder exists and remove them
+    if (dir.exists(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")))) {
+      unlink(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")), recursive = TRUE)
+    }
+    
+    # Download Loci Fasta Files
+    options(timeout = 600)
+    
+    tryCatch({
+      download.file(Scheme$link_cgmlst, 
+                    file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")))
+      "Download successful!"
+    }, error = function(e) {
+      paste("Error: ", e$message)
+    })
+    
+    # Unzip the scheme in temporary folder
+    unzip(
+      zipfile = file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")),
+      exdir = file.path(DB$database, 
+                        Scheme$folder_name, 
+                        paste0(Scheme$folder_name, ".tmp")
+      )
+    )
+    
+    log_print("Hashing downloaded database")
+    # Hash temporary folder
+    hash_database(file.path(DB$database, 
+                            Scheme$folder_name, 
+                            paste0(Scheme$folder_name, ".tmp")))
+    
+    # Get list from local database
+    local_db_filelist <- list.files(file.path(DB$database, 
+                                              Scheme$folder_name, 
+                                              paste0(Scheme$folder_name, "_alleles")))
+    if (!is_empty(local_db_filelist)) {
+      # Get list from temporary database
+      tmp_db_filelist <- list.files(file.path(DB$database,
+                                              Scheme$folder_name,
+                                              paste0(Scheme$folder_name, ".tmp")))
+      
+      # Find the difference (extra files in local database)
+      local_db_extra <- setdiff(local_db_filelist, tmp_db_filelist)
+      
+      # Copy extra files to temporary folder
+      file.copy(file.path(DB$database,
+                          Scheme$folder_name, 
+                          paste0(Scheme$folder_name, "_alleles"), local_db_extra),
+                file.path(DB$database,
+                          Scheme$folder_name,
+                          paste0(Scheme$folder_name, ".tmp")))
+      
+      # Check differences in file pairs
+      local_db_hashes <- tools::md5sum(file.path(DB$database,
+                                                 Scheme$folder_name,
+                                                 paste0(Scheme$folder_name, "_alleles"),
+                                                 local_db_filelist))
+      tmp_db_hashes <- tools::md5sum(file.path(DB$database,
+                                               Scheme$folder_name,
+                                               paste0(Scheme$folder_name, ".tmp"),
+                                               local_db_filelist))
+      
+      diff_files <- local_db_hashes %in% tmp_db_hashes
+      diff_loci <- names(local_db_hashes)[diff_files == FALSE]
+      diff_loci <- sapply(strsplit(diff_loci, "/"), function(x) x[length(x)])
+      
+      # Check locus hashes
+      for (locus in diff_loci) {
+        local_db_hashes <- get_locus_hashes(file.path(DB$database,
+                                                      Scheme$folder_name,
+                                                      paste0(Scheme$folder_name, "_alleles"),
+                                                      locus))
+        tmp_db_hashes <- get_locus_hashes(file.path(DB$database,
+                                                    Scheme$folder_name,
+                                                    paste0(Scheme$folder_name, ".tmp"),
+                                                    locus))
+        diff_hashes <- setdiff(local_db_hashes, tmp_db_hashes)
+        
+        sequences <- extract_seq(file.path(DB$database,
+                                           Scheme$folder_name,
+                                           paste0(Scheme$folder_name, "_alleles"),
+                                           locus), diff_hashes)
+        if (!is_empty(sequences$idx) && !is_empty(sequences$seq) &&
+            length(sequences$idx) == length(sequences$seq)) {
+          add_new_sequences(file.path(DB$database,
+                                      Scheme$folder_name,
+                                      paste0(Scheme$folder_name, ".tmp"),
+                                      locus), sequences)
+        }
+      }
+    }
+    
+    unlink(file.path(DB$database, Scheme$folder_name, 
+                     paste0(Scheme$folder_name, "_alleles")), recursive = TRUE)
+    
+    file.rename(file.path(DB$database, Scheme$folder_name,
+                          paste0(Scheme$folder_name, ".tmp")),
+                file.path(DB$database, Scheme$folder_name,
+                          paste0(Scheme$folder_name, "_alleles")))
+    
+    # Download Scheme Info
+    download(
+      Scheme$link_scheme,
+      dest = file.path(DB$database, Scheme$folder_name, "scheme_info.html"),
+      mode = "wb"
+    )
+    
+    # Download Loci Info	
+    download(	
+      Scheme$link_targets,	
+      dest = file.path(DB$database, Scheme$folder_name, "targets.csv"),
+      mode = "wb"
+    )
+    
+    # Send downloaded scheme to database browser overview
+    DB$available <- gsub("_", " ", basename(dir_ls(DB$database)))
+    
+    Scheme$target_table <- read.csv(
+      file.path(DB$database, Scheme$folder_name, "targets.csv"),
+      header = TRUE,	
+      sep = "\t",	
+      row.names = NULL,	
+      colClasses = c(	
+        "NULL",	
+        "character",	
+        "character",	
+        "integer",	
+        "integer",	
+        "character",	
+        "integer",	
+        "NULL"	
+      )	
+    )
+    
+    DB$exist <- length(dir_ls(DB$database)) == 0
+    
+    shinyjs::show("download_cgMLST")
+    shinyjs::hide("loading")
+    
+    output$statustext <- renderUI(
+      fluidRow(
+        tags$li(
+          class = "dropdown", 
+          tags$span(HTML(
+            paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                  "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
+            style = "color:white;")
+        )
+      )
+    )
+    
+    show_toast(
+      title = "Download successful",
+      type = "success",
+      position = "bottom-end",
+      timer = 5000
+    )
+    
+    log_print("Download successful")
+    
+    showModal(
+      modalDialog(
+        selectInput(
+          "scheme_db",
+          label = "",
+          choices = if(!is.null(Typing$last_scheme)) {
+            Typing$last_scheme
+          } else {DB$available},
+          selected = if(!is.null(Typing$last_scheme)) {
+            Typing$last_scheme
+          } else {if(!is.null(DB$scheme)) {input$select_cgmlst} else {DB$available[1]}}),
+        title = "Select a local database to load.",
+        footer = tagList(
+          actionButton("load", "Load", class = "btn btn-default")
+        )
+      )
+    )
+  })
+  
+  # Download Target Info (CSV Table)
+  observe({
+    input$download_cgMLST
+    
+    scheme_overview <- read_html(Scheme$link_scheme) %>%
+      html_table(header = FALSE) %>%
+      as.data.frame(stringsAsFactors = FALSE)
+    
+    last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"],
+                                   format = "%B %d, %Y, %H:%M %p")
+    names(scheme_overview) <- NULL
+    
+    last_file_change <- format(
+      file.info(file.path(DB$database,
+                          ".downloaded_schemes",
+                          paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
+    
+    output$cgmlst_scheme <- renderTable({scheme_overview})
+    output$scheme_update_info <- renderText({
+      req(last_file_change)
+      if (last_file_change < last_scheme_change) {
+        "(Newer scheme available \u274c)"
+      } else {
+        "(Scheme is up-to-date \u2705)"
+      }
+    })
+  })
+  
+  # _______________________ ####
+  
+  ## Visualization ----
+  
+  # Render placeholder image
+  
+  output$placeholder <- renderImage({
+    # Path to your PNG image with a transparent background
+    image_path <- paste0(getwd(), "/www/PhyloTrace.png")
+    
+    # Use HTML to display the image with the <img> tag
+    list(src = image_path,
+         height = 180)
+  }, deleteFile = FALSE)
+  
+  # Render tree plot fields
+  
+  output$nj_field <- renderUI(
+    fluidRow(
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
+    )
+  )
+  
+  output$mst_field <- renderUI(
+    fluidRow(
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
+    )
+  )
+  
+  output$upgma_field <- renderUI(
+    fluidRow(
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
+    )
+  )
+  
+  ### Render Visualization Controls ----
+  
+  #### NJ and UPGMA controls ----
+  
+  # Control enable/disable of variable mapping inputs
+  observe({
+    shinyjs::toggleState(id = "nj_color_mapping", condition = isTRUE(input$nj_mapping_show))
+    shinyjs::toggleState(id = "nj_tiplab_scale", condition = isTRUE(input$nj_mapping_show))
+    shinyjs::toggleState(id = "upgma_color_mapping", condition = isTRUE(input$upgma_mapping_show))
+    shinyjs::toggleState(id = "upgma_tiplab_scale", condition = isTRUE(input$upgma_mapping_show))
+    
+    shinyjs::toggleState(id = "nj_tipcolor_mapping", condition = isTRUE(input$nj_tipcolor_mapping_show))
+    shinyjs::toggleState(id = "nj_tippoint_scale", condition = isTRUE(input$nj_tipcolor_mapping_show))
+    shinyjs::toggleState(id = "upgma_tipcolor_mapping", condition = isTRUE(input$upgma_tipcolor_mapping_show))
+    shinyjs::toggleState(id = "upgma_tippoint_scale", condition = isTRUE(input$upgma_tipcolor_mapping_show))
+    
+    shinyjs::toggleState(id = "nj_tipshape_mapping", condition = isTRUE(input$nj_tipshape_mapping_show))
+    shinyjs::toggleState(id = "upgma_tipshape_mapping", condition = isTRUE(input$upgma_tipshape_mapping_show))
+    
+    shinyjs::toggleState(id = "nj_fruit_variable", condition = isTRUE(input$nj_tiles_show_1))
+    shinyjs::toggleState(id = "upgma_fruit_variable", condition = isTRUE(input$upgma_tiles_show_1))
+    shinyjs::toggleState(id = "nj_fruit_variable_2", condition = isTRUE(input$nj_tiles_show_2))
+    shinyjs::toggleState(id = "upgma_fruit_variable_2", condition = isTRUE(input$upgma_tiles_show_2))
+    shinyjs::toggleState(id = "nj_fruit_variable_3", condition = isTRUE(input$nj_tiles_show_3))
+    shinyjs::toggleState(id = "upgma_fruit_variable_3", condition = isTRUE(input$upgma_tiles_show_3))
+    shinyjs::toggleState(id = "nj_fruit_variable_4", condition = isTRUE(input$nj_tiles_show_4))
+    shinyjs::toggleState(id = "upgma_fruit_variable_4", condition = isTRUE(input$upgma_tiles_show_4))
+    shinyjs::toggleState(id = "nj_fruit_variable_5", condition = isTRUE(input$nj_tiles_show_5))
+    shinyjs::toggleState(id = "upgma_fruit_variable_5", condition = isTRUE(input$upgma_tiles_show_5))
+    shinyjs::toggleState(id = "nj_tiles_scale_1", condition = isTRUE(input$nj_tiles_show_1))
+    shinyjs::toggleState(id = "upgma_tiles_scale_1", condition = isTRUE(input$upgma_tiles_show_1))
+    shinyjs::toggleState(id = "nj_tiles_scale_2", condition = isTRUE(input$nj_tiles_show_2))
+    shinyjs::toggleState(id = "upgma_tiles_scale_2", condition = isTRUE(input$upgma_tiles_show_2))
+    shinyjs::toggleState(id = "nj_tiles_scale_3", condition = isTRUE(input$nj_tiles_show_3))
+    shinyjs::toggleState(id = "upgma_tiles_scale_3", condition = isTRUE(input$upgma_tiles_show_3))
+    shinyjs::toggleState(id = "nj_tiles_scale_4", condition = isTRUE(input$nj_tiles_show_4))
+    shinyjs::toggleState(id = "upgma_tiles_scale_4", condition = isTRUE(input$upgma_tiles_show_4))
+    shinyjs::toggleState(id = "nj_tiles_scale_5", condition = isTRUE(input$nj_tiles_show_5))
+    shinyjs::toggleState(id = "upgma_tiles_scale_5", condition = isTRUE(input$upgma_tiles_show_5))
+    
+    shinyjs::toggleState(id = "nj_heatmap_sel", condition = isTRUE(input$nj_heatmap_show))
+    shinyjs::toggleState(id = "nj_heatmap_scale", condition = isTRUE(input$nj_heatmap_show))
+    shinyjs::toggleState(id = "upgma_heatmap_sel", condition = isTRUE(input$upgma_heatmap_show))
+    shinyjs::toggleState(id = "upgma_heatmap_scale", condition = isTRUE(input$upgma_heatmap_show))
+  })
+  
+  # Size scaling NJ
+  observe({
+    req(input$nj_ratio)
+    if(input$nj_ratio == "1.6") {
+      updateSliderInput(session, "nj_scale",
+                        step = 5, value = 800, min = 500, max = 1200)
+    } else if(input$nj_ratio == "1.77777777777778") {
+      updateSliderInput(session, "nj_scale",
+                        step = 9, value = 801, min = 504, max = 1197)
+    } else if(input$nj_ratio == "1.33333333333333"){
+      updateSliderInput(session, "nj_scale",
+                        step = 3, value = 801, min = 501, max = 1200)
+    }
+  })
+  
+  # Size scaling UPGMA
+  observe({
+    req(input$upgma_ratio)
+    if(input$upgma_ratio == "1.6") {
+      updateSliderInput(session, "upgma_scale",
+                        step = 5, value = 800, min = 500, max = 1200)
+    } else if(input$upgma_ratio == "1.77777777777778") {
+      updateSliderInput(session, "upgma_scale",
+                        step = 9, value = 801, min = 504, max = 1197)
+    } else if(input$upgma_ratio == "1.33333333333333"){
+      updateSliderInput(session, "upgma_scale",
+                        step = 3, value = 801, min = 501, max = 1200)
+    }
+  })
+  
+  # Size scaling MST
+  observe({
+    req(input$mst_ratio)
+    if(input$mst_ratio == "1.6") {
+      updateSliderInput(session, "mst_scale",
+                        step = 5, value = 800, min = 500, max = 1200)
+    } else if(input$mst_ratio == "1.77777777777778") {
+      updateSliderInput(session, "mst_scale",
+                        step = 9, value = 801, min = 504, max = 1197)
+    } else if(input$mst_ratio == "1.33333333333333"){
+      updateSliderInput(session, "mst_scale",
+                        step = 3, value = 801, min = 501, max = 1200)
+    }
+  })
+  
+  # Custom Labels
+  
+  # Add custom label
+  observeEvent(input$nj_add_new_label, {
+    
+    if(nchar(input$nj_new_label_name) > 0) {
+      if(!(input$nj_new_label_name %in% Vis$custom_label_nj)) {
+        Vis$custom_label_nj <- rbind(Vis$custom_label_nj, input$nj_new_label_name) 
+        if(!(nrow(Vis$custom_label_nj) == 1)) {
+          updateSelectInput(session, "nj_custom_label_sel", selected = input$nj_new_label_name)
+        }
+      } else {
+        show_toast(
+          title = "Label already exists",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+      }
+    } else {
+      show_toast(
+        title = "Min. 1 character",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    }
+  })
+  
+  observeEvent(input$upgma_add_new_label, {
+    
+    if(nchar(input$upgma_new_label_name) > 0) {
+      if(!(input$upgma_new_label_name %in% Vis$custom_label_upgma)) {
+        Vis$custom_label_upgma <- rbind(Vis$custom_label_upgma, input$upgma_new_label_name) 
+        if(!(nrow(Vis$custom_label_upgma) == 1)) {
+          updateSelectInput(session, "upgma_custom_label_sel", selected = input$upgma_new_label_name)
+        }
+      } else {
+        show_toast(
+          title = "Label already exists",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+      }
+    } else {
+      show_toast(
+        title = "Min. 1 character",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    }
+  })
+  
+  # Delete custom label
+  observeEvent(input$nj_del_label, {
+    
+    if(nrow(Vis$custom_label_nj) > 1) {
+      Vis$custom_label_nj <- Vis$custom_label_nj[-which(Vis$custom_label_nj[,1] == input$nj_custom_label_sel), , drop = FALSE]
+    } else if (nrow(Vis$custom_label_nj) == 1) {
+      Vis$nj_label_pos_x <- list()
+      Vis$nj_label_pos_y <- list()
+      Vis$nj_label_size <- list()
+      Vis$custom_label_nj <- data.frame()
+    }
+  })
+  
+  observeEvent(input$upgma_del_label, {
+    
+    if(nrow(Vis$custom_label_upgma) > 1) {
+      Vis$custom_label_upgma <- Vis$custom_label_upgma[-which(Vis$custom_label_upgma[,1] == input$upgma_custom_label_sel), , drop = FALSE]
+    } else if (nrow(Vis$custom_label_upgma) == 1) {
+      Vis$upgma_label_pos_x <- list()
+      Vis$upgma_label_pos_y <- list()
+      Vis$upgma_label_size <- list()
+      Vis$custom_label_upgma <- data.frame()
+    }
+  })
+  
+  # Select custom labels
+  output$nj_custom_label_select <- renderUI({
+    if(nrow(Vis$custom_label_nj) > 0) {
+      selectInput(
+        "nj_custom_label_sel",
+        "",
+        choices = Vis$custom_label_nj[,1]
+      )
+    }
+  })
+  
+  output$upgma_custom_label_select <- renderUI({
+    if(nrow(Vis$custom_label_upgma) > 0) {
+      selectInput(
+        "upgma_custom_label_sel",
+        "",
+        choices = Vis$custom_label_upgma[,1]
+      )
+    }
+  })
+  
+  # Select custom labels
+  output$nj_cust_label_save <- renderUI({
+    if(nrow(Vis$custom_label_nj) > 0) {
+      actionButton(
+        "nj_cust_label_save",
+        "Apply"
+      )
+    } else {
+      column(
+        width = 12,
+        br(), br(), br(), br(), br(), br(),
+        h5("test", style = "color: transparent; margin-bottom: 3px")
+      )
+    }
+  })
+  
+  output$upgma_cust_label_save <- renderUI({
+    if(nrow(Vis$custom_label_upgma) > 0) {
+      actionButton(
+        "upgma_cust_label_save",
+        "Apply"
+      )
+    } else {
+      column(
+        width = 12,
+        br(), br(), br(), br(), br(), br(),
+        h5("test", style = "color: transparent; margin-bottom: 3px")
+      )
+    }
+  })
+  
+  # Custom Label Size
+  output$nj_custom_labelsize <- renderUI({
+    if(length(Vis$custom_label_nj) > 0) {
+      if(!is.null(Vis$nj_label_size[[input$nj_custom_label_sel]])) {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_size"),
+                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
+                    min = 0, max = 10, step = 0.5, ticks = F,
+                    value = Vis$nj_label_size[[input$nj_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_size"),
+                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
+                    min = 0, max = 10, step = 0.5, ticks = F, value = 5,
+                    width = "150px")
+      }
+    } 
+  })
+  
+  output$upgma_custom_labelsize <- renderUI({
+    if(length(Vis$custom_label_upgma) > 0) {
+      if(!is.null(Vis$upgma_label_size[[input$upgma_custom_label_sel]])) {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_size"),
+                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
+                    min = 0, max = 10, step = 0.5, ticks = F,
+                    value = Vis$upgma_label_size[[input$upgma_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_size"),
+                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
+                    min = 0, max = 10, step = 0.5, ticks = F, value = 5,
+                    width = "150px")
+      }
+    } 
+  })
+  
+  # Render slider input based on selected label
+  output$nj_sliderInput_y <- renderUI({
+    if(length(Vis$custom_label_nj) > 0) {
+      if(!is.null(Vis$nj_label_pos_y[[input$nj_custom_label_sel]])) {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_y"),
+                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = 50, step = 1, ticks = F,
+                    value = Vis$nj_label_pos_y[[input$nj_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_y"),
+                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = sum(DB$data$Include), step = 1, ticks = F, 
+                    value = sum(DB$data$Include) / 2,
+                    width = "150px")
+      }
+    } 
+  })
+  
+  output$upgma_sliderInput_y <- renderUI({
+    if(length(Vis$custom_label_upgma) > 0) {
+      if(!is.null(Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]])) {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_y"),
+                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = 50, step = 1, ticks = F,
+                    value = Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_y"),
+                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = sum(DB$data$Include), step = 1, ticks = F, 
+                    value = sum(DB$data$Include) / 2,
+                    width = "150px")
+      }
+    } 
+  })
+  
+  output$nj_sliderInput_x <- renderUI({
+    if(length(Vis$custom_label_nj) > 0) {
+      if(!is.null(Vis$nj_label_pos_x[[input$nj_custom_label_sel]])) {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_x"),
+                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = 50, step = 1, ticks = F,
+                    value = Vis$nj_label_pos_x[[input$nj_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_x"),
+                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = round(Vis$nj_max_x, 0), step = 1, ticks = F, 
+                    value = round(Vis$nj_max_x / 2, 0),
+                    width = "150px")
+      }
+    }
+  })
+  
+  output$upgma_sliderInput_x <- renderUI({
+    if(length(Vis$custom_label_upgma) > 0) {
+      if(!is.null(Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]])) {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_x"),
+                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = 50, step = 1, ticks = F,
+                    value = Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_x"),
+                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = round(Vis$upgma_max_x, 0), step = 1, ticks = F, 
+                    value = round(Vis$upgma_max_x / 2, 0),
+                    width = "150px")
+      }
+    }
+  })
+  
+  # Apply custom label changes
+  observeEvent(input$nj_cust_label_save, {
+    
+    if(!is.null(Vis$nj_label_pos_y) &
+       !is.null(Vis$nj_label_pos_x) &
+       !is.null(Vis$nj_label_size) &
+       !is.null(input$nj_custom_label_sel)) {
+      Vis$nj_label_pos_y[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_y")]]
+      Vis$nj_label_pos_x[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_x")]]
+      Vis$nj_label_size[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_size")]]
+    }
+  })
+  
+  observeEvent(input$upgma_cust_label_save, {
+    
+    if(!is.null(Vis$upgma_label_pos_y) &
+       !is.null(Vis$upgma_label_pos_x) &
+       !is.null(Vis$upgma_label_size) &
+       !is.null(input$upgma_custom_label_sel)) {
+      Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_y")]]
+      Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_x")]]
+      Vis$upgma_label_size[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_size")]]
+    }
+  })
+  
+  # Show delete custom label button if custam label added
+  output$nj_del_label <- renderUI({
+    if(nrow(Vis$custom_label_nj) > 0) {
+      actionButton(
+        "nj_del_label",
+        "",
+        icon = icon("minus")
+      )
+    } else {NULL}
+  })
+  
+  output$upgma_del_label <- renderUI({
+    if(nrow(Vis$custom_label_upgma) > 0) {
+      actionButton(
+        "upgma_del_label",
+        "",
+        icon = icon("minus")
+      )
+    } else {NULL}
+  })
+  
+  # Mapping value number information
+  output$nj_tiplab_mapping_info <- renderUI({
+    if(!is.null(input$nj_color_mapping) & (!is.null(Vis$meta_nj))) {
+      if(is.numeric(unlist(Vis$meta_nj[input$nj_color_mapping]))) {
+        if(input$nj_tiplab_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+          column(
+            width = 3,
+            fluidRow(
+              column(
+                width = 4,
+                h5("Midpoint", style = "color: white; margin-top: 22px;")
+              ),
+              column(
+                width = 8,
+                div(
+                  class = "divmid-sel1",
+                  selectInput(
+                    "nj_color_mapping_div_mid",
+                    label = "",
+                    choices = c("Zero", "Mean", "Median"),
+                    selected = "Mean"
+                  )
+                )
+              )
+            )
+          )
+        } else {
+          column(
+            width = 3,
+            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
+          ) 
+        }
+      } else {
+        if(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))) > 7) {
+          column(
+            width = 3,
+            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$upgma_tiplab_mapping_info <- renderUI({
+    if(!is.null(input$upgma_color_mapping) & (!is.null(Vis$meta_upgma))) {
+      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) {
+        if(input$upgma_tiplab_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+          column(
+            width = 3,
+            fluidRow(
+              column(
+                width = 4,
+                h5("Midpoint", style = "color: white; margin-top: 22px;")
+              ),
+              column(
+                width = 8,
+                div(
+                  class = "divmid-sel1",
+                  selectInput(
+                    "upgma_color_mapping_div_mid",
+                    label = "",
+                    choices = c("Zero", "Mean", "Median"),
+                    selected = "Mean"
+                  )
+                )
+              )
+            )
+          )
+        } else {
+          column(
+            width = 3,
+            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
+          ) 
+        }
+      } else {
+        if(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) > 7) {
+          column(
+            width = 3,
+            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$nj_tipcolor_mapping_info <- renderUI({
+    if(!is.null(input$nj_tipcolor_mapping) & (!is.null(Vis$meta_nj))) {
+      if(is.numeric(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) {
+        if(input$nj_tippoint_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+          column(
+            width = 3,
+            fluidRow(
+              column(
+                width = 4,
+                h5("Midpoint", style = "color: white; margin-top: 22px;")
+              ),
+              column(
+                width = 8,
+                div(
+                  class = "divmid-sel1",
+                  selectInput(
+                    "nj_tipcolor_mapping_div_mid",
+                    label = "",
+                    choices = c("Zero", "Mean", "Median"),
+                    selected = "Mean"
+                  )
+                )
+              )
+            )
+          )
+        } else {
+          column(
+            width = 3,
+            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+          ) 
+        }
+      } else {
+        if(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) > 7) {
+          column(
+            width = 3,
+            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$upgma_tipcolor_mapping_info <- renderUI({
+    if(!is.null(input$upgma_tipcolor_mapping) & (!is.null(Vis$meta_upgma))) {
+      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) {
+        if(input$upgma_tippoint_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+          column(
+            width = 3,
+            fluidRow(
+              column(
+                width = 4,
+                h5("Midpoint", style = "color: white; margin-top: 22px;")
+              ),
+              column(
+                width = 8,
+                div(
+                  class = "divmid-sel1",
+                  selectInput(
+                    "upgma_tipcolor_mapping_div_mid",
+                    label = "",
+                    choices = c("Zero", "Mean", "Median"),
+                    selected = "Mean"
+                  )
+                )
+              )
+            )
+          )
+        } else {
+          column(
+            width = 3,
+            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+          ) 
+        }
+      } else {
+        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) > 7) {
+          column(
+            width = 3,
+            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$nj_tipshape_mapping_info <- renderUI({
+    if(!is.null(input$nj_tipshape_mapping) & (!is.null(Vis$meta_nj))) {
+      if(is.numeric(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))) {
+        column(
+          width = 3,
+          h5("Mapping continous variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
+        )
+      } else {
+        if(length(unique(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))) > 6) {
+          column(
+            width = 3,
+            h5("Mapping > 6 variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )    
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$upgma_tipshape_mapping_info <- renderUI({
+    if(!is.null(input$upgma_tipshape_mapping) & (!is.null(Vis$meta_upgma))) {
+      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))) {
+        column(
+          width = 3,
+          h5("Mapping continous variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
+        )
+      } else {
+        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))) > 6) {
+          column(
+            width = 3,
+            h5("Mapping > 6 variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )    
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$nj_fruit_mapping_info <- renderUI({
+    if(input$nj_tile_num == 1) {
+      if(!is.null(input$nj_fruit_variable) & (!is.null(Vis$meta_nj))) {
+        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable]))) {
+          if(input$nj_tiles_scale_1 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_tiles_mapping_div_mid_1",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$nj_tile_num == 2) {
+      if(!is.null(input$nj_fruit_variable_2) & (!is.null(Vis$meta_nj))) {
+        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) {
+          if(input$nj_tiles_scale_2 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_tiles_mapping_div_mid_2",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$nj_tile_num == 3) {
+      if(!is.null(input$nj_fruit_variable_3) & (!is.null(Vis$meta_nj))) {
+        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) {
+          if(input$nj_tiles_scale_3 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_tiles_mapping_div_mid_3",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$nj_tile_num == 4) {
+      if(!is.null(input$nj_fruit_variable_4) & (!is.null(Vis$meta_nj))) {
+        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) {
+          if(input$nj_tiles_scale_4 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_tiles_mapping_div_mid_4",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$nj_tile_num == 5) {
+      if(!is.null(input$nj_fruit_variable_5) & (!is.null(Vis$meta_nj))) {
+        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) {
+          if(input$nj_tiles_scale_5 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_tiles_mapping_div_mid_5",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  output$upgma_fruit_mapping_info <- renderUI({
+    if(input$upgma_tile_num == 1) {
+      if(!is.null(input$upgma_fruit_variable) & (!is.null(Vis$meta_upgma))) {
+        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) {
+          if(input$upgma_tiles_scale_1 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_tiles_mapping_div_mid_1",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$upgma_tile_num == 2) {
+      if(!is.null(input$upgma_fruit_variable_2) & (!is.null(Vis$meta_upgma))) {
+        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) {
+          if(input$upgma_tiles_scale_2 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_tiles_mapping_div_mid_2",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$upgma_tile_num == 3) {
+      if(!is.null(input$upgma_fruit_variable_3) & (!is.null(Vis$meta_upgma))) {
+        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) {
+          if(input$upgma_tiles_scale_3 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_tiles_mapping_div_mid_3",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$upgma_tile_num == 4) {
+      if(!is.null(input$upgma_fruit_variable_4) & (!is.null(Vis$meta_upgma))) {
+        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) {
+          if(input$upgma_tiles_scale_4 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_tiles_mapping_div_mid_4",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$upgma_tile_num == 5) {
+      if(!is.null(input$upgma_fruit_variable_5) & (!is.null(Vis$meta_upgma))) {
+        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) {
+          if(input$upgma_tiles_scale_5 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_tiles_mapping_div_mid_5",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  output$nj_heatmap_mapping_info <- renderUI({
+    if(!is.null(input$nj_heatmap_select) & (!is.null(Vis$meta_nj))) {
+      if (any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)) & 
+          any(!sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric))) {
+        column(
+          width = 3,
+          h5("Heatmap with categorical and continous values not possible", 
+             style = "color: #E18B00; font-size: 12px; font-style: italic; margin-top: 15px;  margin-left: 40px")
+        ) 
+      } else {
+        if(any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric))) {
+          if(input$nj_heatmap_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_heatmap_div_mid",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_heatmap_select]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Categorical values", style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$upgma_heatmap_mapping_info <- renderUI({
+    if(!is.null(input$upgma_heatmap_select) & (!is.null(Vis$meta_upgma))) {
+      if (any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)) & 
+          any(!sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric))) {
+        column(
+          width = 3,
+          h5("Heatmap with categorical and continous values not possible", 
+             style = "color: #E18B00; font-size: 12px; font-style: italic; margin-top: 15px;  margin-left: 40px")
+        ) 
+      } else {
+        if(any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric))) {
+          if(input$upgma_heatmap_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_heatmap_div_mid",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_heatmap_select]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Categorical values", style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      }
+    } else {NULL}
+  })
+  
+  # Tiles offset
+  output$nj_fruit_offset_circ <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "nj_fruit_offset_circ",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_fruit_offset_circ",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_fruit_offset_circ <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        offset <- 0.15
+        step <- 0.1
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.05
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "upgma_fruit_offset_circ",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_fruit_offset_circ",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.05,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$nj_fruit_offset_circ_2 <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "nj_fruit_offset_circ_2",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_fruit_offset_circ_2",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_fruit_offset_circ_2 <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "upgma_fruit_offset_circ_2",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_fruit_offset_circ_2",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$nj_fruit_offset_circ_3 <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "nj_fruit_offset_circ_3",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_fruit_offset_circ_3",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_fruit_offset_circ_3 <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "upgma_fruit_offset_circ_3",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_fruit_offset_circ_3",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$nj_fruit_offset_circ_4 <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "nj_fruit_offset_circ_4",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_fruit_offset_circ_4",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_fruit_offset_circ_4 <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "upgma_fruit_offset_circ_4",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_fruit_offset_circ_4",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$nj_fruit_offset_circ_5 <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "nj_fruit_offset_circ_5",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_fruit_offset_circ_5",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_fruit_offset_circ_5 <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "upgma_fruit_offset_circ_5",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_fruit_offset_circ_5",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  # For Layout change update tiles offset position
+  observeEvent(input$nj_layout, {
+    
+    if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+      offset <- 0.05
+      step <- 0.01
+      min <- -0.2
+      max <- 0.2
+    } else {
+      offset <- 0.15
+      step <- 0.03
+      min <- -0.6
+      max <- 0.6
+    }
+    
+    updateSliderInput(session, "nj_fruit_offset_circ", min = min, step = step, max = max)
+    updateSliderInput(session, "nj_fruit_offset_circ_2", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "nj_fruit_offset_circ_3", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "nj_fruit_offset_circ_4", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "nj_fruit_offset_circ_5", min = min, step = step, max = max, value = offset) 
+  })
+  
+  observeEvent(input$upgma_layout, {
+    
+    if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+      offset <- 0.05
+      step <- 0.01
+      min <- -0.2
+      max <- 0.2
+    } else {
+      offset <- 0.15
+      step <- 0.03
+      min <- -0.6
+      max <- 0.6
+    }
+    
+    updateSliderInput(session, "upgma_fruit_offset_circ", min = min, step = step, max = max)
+    updateSliderInput(session, "upgma_fruit_offset_circ_2", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "upgma_fruit_offset_circ_3", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "upgma_fruit_offset_circ_4", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "upgma_fruit_offset_circ_5", min = min, step = step, max = max, value = offset) 
+  })
+  
+  # Heatmap width
+  output$nj_heatmap_width <- renderUI({
+    if(!is.null(input$nj_heatmap_select)) {
+      length_input <- length(input$nj_heatmap_select)
+      if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
+        if(length_input < 3) {
+          width <- 0.1
+        } else {
+          if (length_input >= 3 && length_input <= 50) {
+            width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+          } else {
+            width <- 1.5
+          }   
+        }
+      } else {
+        if(length_input < 3) {
+          width <- 0.3
+        } else if (length_input >= 3 && length_input <= 27) {
+          width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 3
+        }
+      }
+      
+      sliderInput(
+        "nj_heatmap_width",
+        label = "",
+        min = 0.05,
+        max = 1.5,
+        value = width,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_heatmap_width",
+        label = "",
+        min = 0.05,
+        max = 1.5,
+        value = 0.1,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_heatmap_width <- renderUI({
+    if(!is.null(input$upgma_heatmap_select)) {
+      length_input <- length(input$upgma_heatmap_select)
+      if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
+        if(length_input < 3) {
+          width <- 0.1
+        } else {
+          if (length_input >= 3 && length_input <= 50) {
+            width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+          } else {
+            width <- 1.5
+          }   
+        }
+      } else {
+        if(length_input < 3) {
+          width <- 0.3
+        } else if (length_input >= 3 && length_input <= 27) {
+          width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 3
+        }
+      }
+      
+      sliderInput(
+        "upgma_heatmap_width",
+        label = "",
+        min = 0.05,
+        max = 1.5,
+        value = width,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_heatmap_width",
+        label = "",
+        min = 0.05,
+        max = 1.5,
+        value = 0.1,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  # Update value if new variables added
+  observeEvent(input$nj_heatmap_select, {
+    
+    length_input <- length(input$nj_heatmap_select)
+    if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
+      if(length_input < 3) {
+        width <- 0.1
+      } else {
+        if (length_input >= 3 && length_input <= 50) {
+          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 1.5
+        }   
+      }
+    } else {
+      if(length_input < 3) {
+        width <- 0.3
+      } else if (length_input >= 3 && length_input <= 27) {
+        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+      } else {
+        width <- 3
+      }
+    }
+    updateSliderInput(session, "nj_heatmap_width", value = width)
+  })
+  
+  observeEvent(input$upgma_heatmap_select, {
+    
+    length_input <- length(input$upgma_heatmap_select)
+    if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
+      if(length_input < 3) {
+        width <- 0.1
+      } else {
+        if (length_input >= 3 && length_input <= 50) {
+          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 1.5
+        }   
+      }
+    } else {
+      if(length_input < 3) {
+        width <- 0.3
+      } else if (length_input >= 3 && length_input <= 27) {
+        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+      } else {
+        width <- 3
+      }
+    }
+    updateSliderInput(session, "upgma_heatmap_width", value = width)
+  })
+  
+  # Update value if layout changed
+  observeEvent(input$nj_layout, {
+    length_input <- length(input$nj_heatmap_select)
+    if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
+      if(length_input < 3) {
+        width <- 0.1
+      } else {
+        if (length_input >= 3 && length_input <= 50) {
+          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 1.5
+        }   
+      }
+    } else {
+      if(length_input < 3) {
+        width <- 0.3
+      } else if (length_input >= 3 && length_input <= 27) {
+        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+      } else {
+        width <- 3
+      }
+    }
+    updateSliderInput(session, "nj_heatmap_width", value = width)
+  })
+  
+  observeEvent(input$upgma_layout, {
+    length_input <- length(input$upgma_heatmap_select)
+    if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
+      if(length_input < 3) {
+        width <- 0.1
+      } else {
+        if (length_input >= 3 && length_input <= 50) {
+          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 1.5
+        }   
+      }
+    } else {
+      if(length_input < 3) {
+        width <- 0.3
+      } else if (length_input >= 3 && length_input <= 27) {
+        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+      } else {
+        width <- 3
+      }
+    }
+    updateSliderInput(session, "upgma_heatmap_width", value = width)
+  })
+  
+  # Heatmap column titles position
+  observeEvent(input$nj_layout, {
+    if(!(input$nj_layout == "inward" | input$nj_layout == "circular")) {
+      updateSliderInput(session, "nj_colnames_y", value = -1)
+    } else {
+      updateSliderInput(session, "nj_colnames_y", value = 0)
+    }
+  })
+  
+  observeEvent(input$upgma_layout, {
+    if(!(input$upgma_layout == "inward" | input$upgma_layout == "circular")) {
+      updateSliderInput(session, "upgma_colnames_y", value = -1)
+    } else {
+      updateSliderInput(session, "upgma_colnames_y", value = 0)
+    }
+  })
+  
+  output$nj_colnames_y <- renderUI({
+    if(!is.null(sum(DB$data$Include))) {
+      if(input$nj_layout == "inward" | input$nj_layout == "circular") {
+        min <- 0
+        val <- 0
+      } else {
+        val <- -1
+        if((sum(DB$data$Include) * -0.1) > -2) {
+          min <- -2
+        } else {
+          min <- round(sum(DB$data$Include) * -0.1, 0)
+        }
+      }
+      sliderInput(
+        "nj_colnames_y",
+        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
+        min = min,
+        max = sum(DB$data$Include),
+        value = val,
+        step = 1,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_colnames_y",
+        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
+        min = -10,
+        max = 10,
+        value = 0,
+        step = 1,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_colnames_y <- renderUI({
+    if(!is.null(sum(DB$data$Include))) {
+      if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
+        min <- 0
+        val <- 0
+      } else {
+        val <- -1
+        if((sum(DB$data$Include) * -0.1) > -2) {
+          min <- -2
+        } else {
+          min <- round(sum(DB$data$Include) * -0.1, 0)
+        }
+      }
+      sliderInput(
+        "upgma_colnames_y",
+        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
+        min = min,
+        max = sum(DB$data$Include),
+        value = val,
+        step = 1,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_colnames_y",
+        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
+        min = -10,
+        max = 10,
+        value = 0,
+        step = 1,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  # Heatmap column titles angle
+  output$nj_colnames_angle <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        angle <- 90
+      } else {angle <- -90}
+      sliderInput(
+        "nj_colnames_angle",
+        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
+        min = -90,
+        max = 90,
+        value = angle,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_colnames_angle",
+        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
+        min = -90,
+        max = 90,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_colnames_angle <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        angle <- 90
+      } else {angle <- -90}
+      sliderInput(
+        "upgma_colnames_angle",
+        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
+        min = -90,
+        max = 90,
+        value = angle,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_colnames_angle",
+        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
+        min = -90,
+        max = 90,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  # Change heatmap column titles angle and label align when switching layout
+  observeEvent(input$nj_layout, {
+    if(input$nj_layout == "circular" | input$nj_layout == "inward"){
+      angle <- 90
+      val <- TRUE
+    } else {
+      angle <- -90
+      val <- FALSE
+    }
+    updateSwitchInput(session, "nj_align", value = val)
+    updateSliderInput(session, "nj_colnames_angle", value = angle)
+  })
+  
+  observeEvent(input$upgma_layout, {
+    if(input$upgma_layout == "circular" | input$upgma_layout == "inward"){
+      angle <- 90
+      val <- TRUE
+    } else {
+      angle <- -90
+      val <- FALSE
+    }
+    updateSwitchInput(session, "upgma_align", value = val)
+    updateSliderInput(session, "upgma_colnames_angle", value = angle)
+  })
+  
+  # Tile number selector update each other
+  observeEvent(input$nj_tile_num, {
+    updateSelectInput(session, "nj_tile_number", selected = input$nj_tile_num)
+  })
+  
+  observeEvent(input$nj_tile_number, {
+    updateSelectInput(session, "nj_tile_num", selected = input$nj_tile_number)
+  })
+  
+  observeEvent(input$upgma_tile_num, {
+    updateSelectInput(session, "upgma_tile_number", selected = input$upgma_tile_num)
+  })
+  
+  observeEvent(input$upgma_tile_number, {
+    updateSelectInput(session, "upgma_tile_num", selected = input$upgma_tile_number)
+  })
+  
+  # Clade coloring
+  output$nj_clade_scale <- renderUI({
+    if(length(input$nj_parentnode) <= 1) {
+      fluidRow(
+        column(
+          width = 5,
+          h5("Color", style = "color:white; position: relative; right: -15px; margin-top: 30px")
+        ),
+        column(
+          width = 7,
+          align = "center",
+          colorPickr(
+            inputId = "nj_clade_scale",
+            selected = "#D0F221",
+            label = "",
+            update = "changestop",
+            interaction = list(clear = FALSE,
+                               save = FALSE),
+            position = "right-start",
+            width = "100%"
+          )
+        )
+      )
+    } else {
+      fluidRow(
+        column(
+          width = 5,
+          h5("Scale", style = "color:white; position: relative; right: -15px; margin-top: 30px")
+        ),
+        column(
+          width = 7,
+          align = "center",
+          div(
+            class = "sel-clade-scale",
+            selectInput(
+              "nj_clade_scale",
+              "",
+              choices = list(
+                Qualitative = list(
+                  "Set1",
+                  "Set2",
+                  "Set3",
+                  "Pastel1",
+                  "Pastel2",
+                  "Paired",
+                  "Dark2",
+                  "Accent"
+                ),
+                Sequential = list(
+                  "YlOrRd",
+                  "YlOrBr",
+                  "YlGnBu",
+                  "YlGn",
+                  "Reds",
+                  "RdPu",
+                  "Purples",
+                  "PuRd",
+                  "PuBuGn",
+                  "PuBu",
+                  "OrRd",
+                  "Oranges",
+                  "Greys",
+                  "Greens",
+                  "GnBu",
+                  "BuPu",
+                  "BuGn",
+                  "Blues"
+                )
+              )
+            )
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_clade_scale <- renderUI({
+    if(length(input$upgma_parentnode) <= 1) {
+      fluidRow(
+        column(
+          width = 5,
+          h5("Color", style = "color:white; position: relative; right: -15px; margin-top: 30px")
+        ),
+        column(
+          width = 7,
+          align = "center",
+          colorPickr(
+            inputId = "upgma_clade_scale",
+            selected = "#D0F221",
+            label = "",
+            update = "changestop",
+            interaction = list(clear = FALSE,
+                               save = FALSE),
+            position = "right-start",
+            width = "100%"
+          )
+        )
+      )
+    } else {
+      fluidRow(
+        column(
+          width = 5,
+          h5("Scale", style = "color:white; position: relative; right: -15px; margin-top: 30px")
+        ),
+        column(
+          width = 7,
+          align = "center",
+          div(
+            class = "sel-clade-scale",
+            selectInput(
+              "upgma_clade_scale",
+              "",
+              choices = list(
+                Qualitative = list(
+                  "Set1",
+                  "Set2",
+                  "Set3",
+                  "Pastel1",
+                  "Pastel2",
+                  "Paired",
+                  "Dark2",
+                  "Accent"
+                ),
+                Sequential = list(
+                  "YlOrRd",
+                  "YlOrBr",
+                  "YlGnBu",
+                  "YlGn",
+                  "Reds",
+                  "RdPu",
+                  "Purples",
+                  "PuRd",
+                  "PuBuGn",
+                  "PuBu",
+                  "OrRd",
+                  "Oranges",
+                  "Greys",
+                  "Greens",
+                  "GnBu",
+                  "BuPu",
+                  "BuGn",
+                  "Blues"
+                )
+              )
+            )
+          )
+        )
+      )
+    }
+  })
+  
+  # Heatmap variable color scale
+  output$nj_heatmap_scale <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_heatmap_select])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_heatmap_scale",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_heatmap_select]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_heatmap_scale",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_heatmap_scale",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Paired"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_heatmap_scale <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_heatmap_select])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_heatmap_scale",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_heatmap_select]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_heatmap_scale",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_heatmap_scale",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Paired"
+          )
+        )
+      }
+    }
+  })
+  
+  # Tiles variable color scale
+  output$nj_tiles_scale_1 <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiles_scale_1",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_1",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_1",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiles_scale_1 <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiles_scale_1",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_1",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_1",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$nj_tiles_scale_2 <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_2])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiles_scale_2",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_2",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_2",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiles_scale_2 <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiles_scale_2",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_2",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_2",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$nj_tiles_scale_3 <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_3])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiles_scale_3",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_3",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_3",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiles_scale_3 <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiles_scale_3",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_3",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_3",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$nj_tiles_scale_4 <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_4])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiles_scale_4",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) > 7) {
+        shinyjs::disabled(selectInput(
+          "nj_tiles_scale_4",
+          "",
+          choices = list(
+            Gradient = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            )
+          ),
+          selected = "turbo"
+        ))
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_4",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiles_scale_4 <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiles_scale_4",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_4",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_4",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$nj_tiles_scale_5 <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_5])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiles_scale_5",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_5",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_5",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiles_scale_5 <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiles_scale_5",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_5",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_5",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  # Tip Labels Variable Color Scale
+  output$nj_tiplab_scale <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_color_mapping])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiplab_scale",
+          "",
+          selectize = FALSE,
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiplab_scale",
+            "",
+            selectize = FALSE,
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiplab_scale",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            )
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiplab_scale <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_color_mapping])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiplab_scale",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiplab_scale",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiplab_scale",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            )
+          )
+        )
+      }
+    }
+  })
+  
+  # Tippoint Scale
+  output$nj_tippoint_scale <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      if(class(unlist(Vis$meta_nj[input$nj_tipcolor_mapping])) == "numeric") {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tippoint_scale",
+            "",
+            choices = list(
+              Continous = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              ),
+              Diverging = list(
+                "Spectral",
+                "RdYlGn",
+                "RdYlBu",
+                "RdGy",
+                "RdBu",
+                "PuOr",
+                "PRGn",
+                "PiYG",
+                "BrBG"
+              )
+            )
+          )
+        )
+      } else {
+        if(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) > 7) {
+          shinyjs::disabled(
+            selectInput(
+              "nj_tippoint_scale",
+              "",
+              choices = list(
+                Gradient = list(
+                  "Magma" = "magma",
+                  "Inferno" = "inferno",
+                  "Plasma" = "plasma",
+                  "Viridis" = "viridis",
+                  "Cividis" = "cividis",
+                  "Rocket" = "rocket",
+                  "Mako" = "mako",
+                  "Turbo" = "turbo"
+                )
+              ),
+              selected = "turbo"
+            )
+          )
+        } else {
+          shinyjs::disabled(
+            selectInput(
+              "nj_tippoint_scale",
+              "",
+              choices = list(
+                Qualitative = list(
+                  "Set1",
+                  "Set2",
+                  "Set3",
+                  "Pastel1",
+                  "Pastel2",
+                  "Paired",
+                  "Dark2",
+                  "Accent"
+                ),
+                Sequential = list(
+                  "YlOrRd",
+                  "YlOrBr",
+                  "YlGnBu",
+                  "YlGn",
+                  "Reds",
+                  "RdPu",
+                  "Purples",
+                  "PuRd",
+                  "PuBuGn",
+                  "PuBu",
+                  "OrRd",
+                  "Oranges",
+                  "Greys",
+                  "Greens",
+                  "GnBu",
+                  "BuPu",
+                  "BuGn",
+                  "Blues"
+                )
+              ),
+              selected = "Set2"
+            )
+          )
+        }
+      }
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tippoint_scale",
+          "",
+          choices = list(
+            Qualitative = list(
+              "Set1",
+              "Set2",
+              "Set3",
+              "Pastel1",
+              "Pastel2",
+              "Paired",
+              "Dark2",
+              "Accent"
+            ),
+            Sequential = list(
+              "YlOrRd",
+              "YlOrBr",
+              "YlGnBu",
+              "YlGn",
+              "Reds",
+              "RdPu",
+              "Purples",
+              "PuRd",
+              "PuBuGn",
+              "PuBu",
+              "OrRd",
+              "Oranges",
+              "Greys",
+              "Greens",
+              "GnBu",
+              "BuPu",
+              "BuGn",
+              "Blues"
+            )
+          ),
+          selected = "Set2"
+        )
+      )
+    }
+  })
+  
+  output$upgma_tippoint_scale <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      if(class(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping])) == "numeric") {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tippoint_scale",
+            "",
+            choices = list(
+              Continous = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              ),
+              Diverging = list(
+                "Spectral",
+                "RdYlGn",
+                "RdYlBu",
+                "RdGy",
+                "RdBu",
+                "PuOr",
+                "PRGn",
+                "PiYG",
+                "BrBG"
+              )
+            ),
+            selected = c("Viridis" = "viridis")
+          )
+        )
+      } else {
+        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) > 7) {
+          shinyjs::disabled(
+            selectInput(
+              "upgma_tippoint_scale",
+              "",
+              choices = list(
+                Gradient = list(
+                  "Magma" = "magma",
+                  "Inferno" = "inferno",
+                  "Plasma" = "plasma",
+                  "Viridis" = "viridis",
+                  "Cividis" = "cividis",
+                  "Rocket" = "rocket",
+                  "Mako" = "mako",
+                  "Turbo" = "turbo"
+                )
+              ),
+              selected = "turbo"
+            )
+          )
+        } else {
+          shinyjs::disabled(
+            selectInput(
+              "upgma_tippoint_scale",
+              "",
+              choices = list(
+                Qualitative = list(
+                  "Set1",
+                  "Set2",
+                  "Set3",
+                  "Pastel1",
+                  "Pastel2",
+                  "Paired",
+                  "Dark2",
+                  "Accent"
+                ),
+                Sequential = list(
+                  "YlOrRd",
+                  "YlOrBr",
+                  "YlGnBu",
+                  "YlGn",
+                  "Reds",
+                  "RdPu",
+                  "Purples",
+                  "PuRd",
+                  "PuBuGn",
+                  "PuBu",
+                  "OrRd",
+                  "Oranges",
+                  "Greys",
+                  "Greens",
+                  "GnBu",
+                  "BuPu",
+                  "BuGn",
+                  "Blues"
+                )
+              ),
+              selected = "Set2"
+            )
+          )
+        }
+      }
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tippoint_scale",
+          "",
+          choices = list(
+            Qualitative = list(
+              "Set1",
+              "Set2",
+              "Set3",
+              "Pastel1",
+              "Pastel2",
+              "Paired",
+              "Dark2",
+              "Accent"
+            ),
+            Sequential = list(
+              "YlOrRd",
+              "YlOrBr",
+              "YlGnBu",
+              "YlGn",
+              "Reds",
+              "RdPu",
+              "Purples",
+              "PuRd",
+              "PuBuGn",
+              "PuBu",
+              "OrRd",
+              "Oranges",
+              "Greys",
+              "Greens",
+              "GnBu",
+              "BuPu",
+              "BuGn",
+              "Blues"
+            )
+          ),
+          selected = "Set2"
+        )
+      )
+    }
+  })
+  
+  # Clade Highlights
+  output$nj_parentnode <- renderUI({
+    if(!is.null(Vis$nj_parentnodes)) {
+      pickerInput(
+        "nj_parentnode",
+        label = "",
+        choices = sort(unique(as.numeric(Vis$nj_parentnodes))),
+        multiple = TRUE,
+        options = list(
+          `live-search` = TRUE,
+          size = 10,
+          style = "background-color: white; border-radius: 5px;"
+        ),
+        width = "99%"
+      )
+    } else {
+      pickerInput(
+        "nj_parentnode",
+        label = "",
+        choices = c(),
+        multiple = TRUE,
+        options = list(
+          `live-search` = TRUE,
+          size = 10,
+          style = "background-color: white; border-radius: 5px;"
+        ),
+        width = "99%"
+      )
+    }
+  })
+  
+  output$upgma_parentnode <- renderUI({
+    if(!is.null(Vis$upgma_parentnodes)) {
+      pickerInput(
+        "upgma_parentnode",
+        label = "",
+        choices = sort(unique(as.numeric(Vis$upgma_parentnodes))),
+        multiple = TRUE,
+        options = list(
+          `live-search` = TRUE,
+          size = 10,
+          style = "background-color: white; border-radius: 5px;"
+        ),
+        width = "99%"
+      )
+    } else {
+      pickerInput(
+        "upgma_parentnode",
+        label = "",
+        choices = c(),
+        multiple = TRUE,
+        options = list(
+          `live-search` = TRUE,
+          size = 10,
+          style = "background-color: white; border-radius: 5px;"
+        ),
+        width = "99%"
+      )
+    }
+  })
+  
+  # Branch label size
+  output$nj_branch_size <- renderUI(
+    numericInput(
+      "nj_branch_size",
+      label = h5("Size", style = "color:white; margin-bottom: 0px"),
+      min = 2,
+      max = 10,
+      step = 0.5,
+      value = Vis$branch_size_nj,
+      width = "80px"
+    )
+  )
+  
+  output$upgma_branch_size <- renderUI(
+    numericInput(
+      "upgma_branch_size",
+      label = h5("Size", style = "color:white; margin-bottom: 0px"),
+      min = 2,
+      max = 10,
+      step = 0.5,
+      value = Vis$branch_size_upgma,
+      width = "80px"
+    )
+  )
+  
+  # Tippanel size
+  output$nj_tiplab_padding <- renderUI(
+    if(!is.null(Vis$tiplab_padding_nj)) {
+      sliderInput(
+        inputId = "nj_tiplab_padding",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 0.05,
+        max = 1,
+        value = Vis$tiplab_padding_nj,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "nj_tiplab_padding",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 0.05,
+        max = 1,
+        value = 0.2,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  output$upgma_tiplab_padding <- renderUI(
+    if(!is.null(Vis$tiplab_padding_upgma)) {
+      sliderInput(
+        inputId = "upgma_tiplab_padding",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 0.05,
+        max = 1,
+        value = Vis$tiplab_padding_upgma,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "upgma_tiplab_padding",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 0.05,
+        max = 1,
+        value = 0.2,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  # Nodepoint size
+  output$nj_nodepoint_size <- renderUI(
+    if(!is.null(Vis$nodepointsize_nj)) {
+      sliderInput(
+        inputId = "nj_nodepoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        value = Vis$nodepointsize_nj,
+        step = 0.5,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "nj_nodepoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        value = 2.5,
+        step = 0.5,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  output$upgma_nodepoint_size <- renderUI(
+    if(!is.null(Vis$nodepointsize_upgma)) {
+      sliderInput(
+        inputId = "upgma_nodepoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        value = Vis$nodepointsize_upgma,
+        step = 0.5,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "upgma_nodepoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        value = 2.5,
+        step = 0.5,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  # Tippoint size 
+  output$nj_tippoint_size <- renderUI(
+    if(!is.null(Vis$tippointsize_nj)) {
+      sliderInput(
+        inputId = "nj_tippoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        step = 0.5,
+        value = Vis$tippointsize_nj,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "nj_tippoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        step = 0.5,
+        value = 4,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  output$upgma_tippoint_size <- renderUI(
+    if(!is.null(Vis$tippointsize_upgma)) {
+      sliderInput(
+        inputId = "upgma_tippoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        step = 0.5,
+        value = Vis$tippointsize_upgma,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "upgma_tippoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        step = 0.5,
+        value = 4,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  # Tiplabel size
+  output$nj_tiplab_size <- renderUI(
+    if(!is.null(Vis$labelsize_nj)) {
+      numericInput(
+        "nj_tiplab_size",
+        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        step = 0.5,
+        value = Vis$labelsize_nj,
+        width = "80px"
+      )
+    } else {
+      numericInput(
+        "nj_tiplab_size",
+        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        step = 0.5,
+        value = 4,
+        width = "80px"
+      )
+    }
+  )
+  
+  output$upgma_tiplab_size <- renderUI(
+    if(!is.null(Vis$labelsize_upgma)) {
+      numericInput(
+        "upgma_tiplab_size",
+        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        step = 0.5,
+        value = Vis$labelsize_upgma,
+        width = "80px"
+      )
+    } else {
+      numericInput(
+        "upgma_tiplab_size",
+        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        step = 0.5,
+        value = 4,
+        width = "80px"
+      )
+    }
+  )
+  
+  # Rootedge length 
+  output$nj_rootedge_length <- renderUI({
+    if(!is.null(Vis$nj_max_x)) {
+      if(round(ceiling(Vis$nj_max_x) * 0.02, 0) < 1) {
+        min <- 1
+      } else {
+        min <- round(ceiling(Vis$nj_max_x) * 0.02, 0)  
+      }
+      max <- round(ceiling(Vis$nj_max_x) * 0.2, 0)
+      sliderInput(
+        "nj_rootedge_length",
+        label = h5("Rootedge Length", style = "color:white; margin-bottom: 0px"),
+        min = min,
+        max = max,
+        value = round(ceiling(Vis$nj_max_x) * 0.05, 0),
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_rootedge_length",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        value = 2,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_rootedge_length <- renderUI({
+    if(!is.null(Vis$upgma_max_x)) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.02, 0) < 1) {
+        min <- 1
+      } else {
+        min <- round(ceiling(Vis$upgma_max_x) * 0.02, 0)  
+      }
+      max <- round(ceiling(Vis$upgma_max_x) * 0.2, 0)
+      sliderInput(
+        "upgma_rootedge_length",
+        label = h5("Rootedge Length", style = "color:white; margin-bottom: 0px"),
+        min = min,
+        max = max,
+        value = round(ceiling(Vis$upgma_max_x) * 0.05, 0),
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_rootedge_length",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        value = 2,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  # Treescale 
+  output$nj_treescale_width <- renderUI({
+    if(!is.null(Vis$nj_max_x)) {
+      numericInput(
+        "nj_treescale_width",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        value = round(ceiling(Vis$nj_max_x) * 0.1, 0),
+        min = 1,
+        max = round(floor(Vis$nj_max_x) * 0.5, 0),
+        step = 1,
+        width = "80px"
+      )
+    } else {
+      numericInput(
+        "nj_treescale_width",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        value = 2,
+        min = 1,
+        max = 10,
+        step = 1,
+        width = "80px"
+      )
+    }
+  })
+  
+  output$upgma_treescale_width <- renderUI({
+    if(!is.null(Vis$upgma_max_x)) {
+      numericInput(
+        "upgma_treescale_width",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        value = round(ceiling(Vis$upgma_max_x) * 0.1, 0),
+        min = 1,
+        max = round(floor(Vis$upgma_max_x) * 0.5, 0),
+        step = 1,
+        width = "80px"
+      )
+    } else {
+      numericInput(
+        "upgma_treescale_width",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        value = 2,
+        min = 1,
+        max = 10,
+        step = 1,
+        width = "80px"
+      )
+    }
+  })
+  
+  output$nj_treescale_x <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(ceiling(Vis$nj_min_x) < 1) {
+        floor <- 1
+      } else {
+        floor <- ceiling(Vis$nj_min_x)
+      }
+      sliderInput(
+        "nj_treescale_x",
+        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+        min = floor,
+        max = round(floor(Vis$nj_max_x)),
+        value = round(ceiling(Vis$nj_max_x) * 0.2, 0),
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_treescale_x",
+        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        value = 2,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_treescale_x <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(ceiling(Vis$upgma_min_x) < 1) {
+        floor <- 1
+      } else {
+        floor <- ceiling(Vis$upgma_min_x)
+      }
+      sliderInput(
+        "upgma_treescale_x",
+        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+        min = floor,
+        max = round(floor(Vis$upgma_max_x)),
+        value = round(ceiling(Vis$upgma_max_x) * 0.2, 0),
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_treescale_x",
+        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        value = 2,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$nj_treescale_y <- renderUI({
+    if(!is.null(sum(DB$data$Include))) {
+      sliderInput(
+        "nj_treescale_y",
+        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+        min = 0,
+        max = sum(DB$data$Include),
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_treescale_y",
+        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+        min = 0,
+        max = 10,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_treescale_y <- renderUI({
+    if(!is.null(sum(DB$data$Include))) {
+      sliderInput(
+        "upgma_treescale_y",
+        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+        min = 0,
+        max = sum(DB$data$Include),
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_treescale_y",
+        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+        min = 0,
+        max = 10,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  ### Heatmap 
+  # Heatmap picker
+  output$nj_heatmap_sel <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      meta <- select(Vis$meta_nj, -c(taxa, Index, `Assembly ID`, `Assembly Name`,
+                                     Scheme, `Typing Date`, Successes, Errors))
+      
+      # Identify numeric columns
+      numeric_columns <- sapply(meta, is.numeric)
+      
+      numeric_column_names <- names(meta[numeric_columns])
+      
+      non_numeric_column_names <- names(meta)[!numeric_columns]
+      
+      choices <- list()
+      
+      # Add Continuous list only if there are numeric columns
+      if (length(numeric_column_names) > 0) {
+        choices$Continuous <- as.list(setNames(numeric_column_names, numeric_column_names))
+      }
+      
+      # Add Diverging list
+      choices$Categorical <- as.list(setNames(non_numeric_column_names, non_numeric_column_names))
+      
+      div(
+        class = "heatmap-picker",
+        shinyjs::disabled(
+          pickerInput(
+            inputId = "nj_heatmap_select",
+            label = "",
+            width = "100%",
+            choices = if(ncol(Vis$meta_nj) == 11) {
+              c(
+                `Isolation Date` = "Isolation Date",
+                Host = "Host",
+                Country = "Country",
+                City = "City"
+              )
+            } else {choices},
+            options = list(
+              `dropdown-align-center` = TRUE,
+              size = 10,
+              style = "background-color: white; border-radius: 5px;"
+            ),
+            multiple = TRUE
+          )
+        )
+      )
+    } else {
+      div(
+        class = "heatmap-picker",
+        shinyjs::disabled(
+          pickerInput(
+            inputId = "nj_heatmap_select",
+            label = "",
+            width = "100%",
+            choices = c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            ),
+            multiple = TRUE
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_heatmap_sel <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      meta <- select(Vis$meta_upgma, -c(taxa, Index, `Assembly ID`, `Assembly Name`,
+                                        Scheme, `Typing Date`, Successes, Errors))
+      
+      # Identify numeric columns
+      numeric_columns <- sapply(meta, is.numeric)
+      
+      numeric_column_names <- names(meta[numeric_columns])
+      
+      non_numeric_column_names <- names(meta)[!numeric_columns]
+      
+      choices <- list()
+      
+      # Add Continuous list only if there are numeric columns
+      if (length(numeric_column_names) > 0) {
+        choices$Continuous <- as.list(setNames(numeric_column_names, numeric_column_names))
+      }
+      
+      # Add Diverging list
+      choices$Categorical <- as.list(setNames(non_numeric_column_names, non_numeric_column_names))
+      
+      div(
+        class = "heatmap-picker",
+        shinyjs::disabled(
+          pickerInput(
+            inputId = "upgma_heatmap_select",
+            label = "",
+            width = "100%",
+            choices = if(ncol(Vis$meta_upgma) == 11) {
+              c(
+                `Isolation Date` = "Isolation Date",
+                Host = "Host",
+                Country = "Country",
+                City = "City"
+              )
+            } else {choices},
+            options = list(
+              `dropdown-align-center` = TRUE,
+              size = 10,
+              style = "background-color: white; border-radius: 5px;"
+            ),
+            multiple = TRUE
+          )
+        )
+      )
+    } else {
+      div(
+        class = "heatmap-picker",
+        shinyjs::disabled(
+          pickerInput(
+            inputId = "upgma_heatmap_select",
+            label = "",
+            width = "100%",
+            choices = c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            ),
+            multiple = TRUE
+          )
+        )
+      )
+    }
+  })
+  
+  # Heatmap offset
+  output$nj_heatmap_offset <- renderUI({
+    if(!is.null(Vis$nj_max_x)) {
+      sliderInput(
+        "nj_heatmap_offset",
+        label = "",
+        min = 0,
+        max = round(ceiling(Vis$nj_max_x)*1.5, 0),
+        step = 1,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_heatmap_offset",
+        label = "",
+        min = 0,
+        max = 10,
+        step = 1,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_heatmap_offset <- renderUI({
+    if(!is.null(Vis$upgma_max_x)) {
+      sliderInput(
+        "upgma_heatmap_offset",
+        label = "",
+        min = 0,
+        max = round(ceiling(Vis$upgma_max_x)*1.5, 0),
+        step = 1,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_heatmap_offset",
+        label = "",
+        min = 0,
+        max = 10,
+        step = 1,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  ### Tiling 
+  # Geom Fruit select Variable
+  output$nj_fruit_variable <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$nj_fruit_variable2 <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_2",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_2",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$nj_fruit_variable3 <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_3",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_3",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$nj_fruit_variable4 <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_4",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_4",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$nj_fruit_variable5 <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_5",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_5",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_fruit_variable <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_fruit_variable2 <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_2",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_2",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_fruit_variable3 <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(selectInput(
+        "upgma_fruit_variable_3",
+        "",
+        choices = if(ncol(Vis$meta_upgma) == 11) {
+          c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        } else {
+          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+        },
+        selected = c(`Isolation Date` = "Isolation Date"),
+        width = "100%"
+      ))
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_3",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_fruit_variable4 <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_4",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_4",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_fruit_variable5 <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_5",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_5",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  # Geom Fruit Width
+  output$nj_fruit_width <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "nj_fruit_width_circ",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        sliderInput(
+          "nj_fruit_width_circ",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "nj_fruit_width_circ",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$nj_fruit_width2 <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "nj_fruit_width_circ_2",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        sliderInput(
+          "nj_fruit_width_circ_2",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "nj_fruit_width_circ_2",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$nj_fruit_width3 <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "nj_fruit_width_circ_3",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        sliderInput(
+          "nj_fruit_width_circ_3",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "nj_fruit_width_circ_3",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$nj_fruit_width4 <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "nj_fruit_width_circ_4",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        sliderInput(
+          "nj_fruit_width_circ_4",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "nj_fruit_width_circ_4",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$nj_fruit_width5 <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "nj_fruit_width_circ_5",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        sliderInput(
+          "nj_fruit_width_circ_5",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "nj_fruit_width_circ_5",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$upgma_fruit_width <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "upgma_fruit_width_circ",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        sliderInput(
+          "upgma_fruit_width_circ",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "upgma_fruit_width_circ",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$upgma_fruit_width2 <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "upgma_fruit_width_circ_2",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        sliderInput(
+          "upgma_fruit_width_circ_2",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "upgma_fruit_width_circ_2",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$upgma_fruit_width3 <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "upgma_fruit_width_circ_3",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        sliderInput(
+          "upgma_fruit_width_circ_3",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "upgma_fruit_width_circ_3",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$upgma_fruit_width4 <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "upgma_fruit_width_circ_4",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        sliderInput(
+          "upgma_fruit_width_circ_4",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "upgma_fruit_width_circ_4",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$upgma_fruit_width5 <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "upgma_fruit_width_circ_5",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        sliderInput(
+          "upgma_fruit_width_circ_5",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "upgma_fruit_width_circ_5",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  # For Layout change update tiles 
+  observeEvent(input$nj_layout, {
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+        } else {
+          width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+        }
+      }
+      
+      updateSliderInput(session, "nj_fruit_width_circ", value = width)
+      updateSliderInput(session, "nj_fruit_width_circ_2", value = width)
+      updateSliderInput(session, "nj_fruit_width_circ_3", value = width)
+      updateSliderInput(session, "nj_fruit_width_circ_4", value = width)
+      updateSliderInput(session, "nj_fruit_width_circ_5", value = width) 
+    }
+  })
+  
+  observeEvent(input$upgma_layout, {
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+        } else {
+          width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+        }
+      }
+      
+      updateSliderInput(session, "upgma_fruit_width_circ", value = width)
+      updateSliderInput(session, "upgma_fruit_width_circ_2", value = width)
+      updateSliderInput(session, "upgma_fruit_width_circ_3", value = width)
+      updateSliderInput(session, "upgma_fruit_width_circ_4", value = width)
+      updateSliderInput(session, "upgma_fruit_width_circ_5", value = width) 
+    }
+  })
+  
+  # Tip color mapping 
+  output$nj_tipcolor_mapping <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tipcolor_mapping",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Assembly Name` = "Assembly Name",
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Assembly Name` = "Assembly Name", `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(City = "City"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tipcolor_mapping",
+          "",
+          choices = c(
+            `Assembly Name` = "Assembly Name",
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c(City = "City")
+        )
+      )
+    }
+  })
+  
+  output$upgma_tipcolor_mapping <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tipcolor_mapping",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Assembly Name` = "Assembly Name",
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Assembly Name` = "Assembly Name", `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(City = "City"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tipcolor_mapping",
+          "",
+          choices = c(
+            `Assembly Name` = "Assembly Name",
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c(City = "City")
+        )
+      )
+    }
+  })
+  
+  # Tip shape Mapping 
+  output$nj_tipshape_mapping <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tipshape_mapping",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c("Host" = "Host"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tipshape_mapping",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c("Host" = "Host"),
+          width = "100%"
+        )
+      )
+    }
+  })
+  
+  output$upgma_tipshape_mapping <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tipshape_mapping",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c("Host" = "Host"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tipshape_mapping",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c("Host" = "Host"),
+          width = "100%"
+        )
+      )
+    }
+  })
+  
+  # Branch label 
+  output$nj_branch_label <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      selectInput(
+        "nj_branch_label",
+        "",
+        choices = if(ncol(Vis$meta_nj) == 11) {
+          c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        } else {
+          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                 names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+        },
+        selected = c("Host" = "Host"),
+        width = "100%"
+      )
+    } else {
+      selectInput(
+        "nj_branch_label",
+        "",
+        choices = c(
+          `Isolation Date` = "Isolation Date",
+          Host = "Host",
+          Country = "Country",
+          City = "City"
+        ),
+        selected = c("Host" = "Host"),
+        width = "100%"
+      )
+    }
+  })
+  
+  output$upgma_branch_label <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      selectInput(
+        "upgma_branch_label",
+        "",
+        choices = if(ncol(Vis$meta_upgma) == 11) {
+          c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        } else {
+          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+        },
+        selected = c("Host" = "Host"),
+        width = "100%"
+      )
+    } else {
+      selectInput(
+        "upgma_branch_label",
+        "",
+        choices = c(
+          `Isolation Date` = "Isolation Date",
+          Host = "Host",
+          Country = "Country",
+          City = "City"
+        ),
+        selected = c("Host" = "Host"),
+        width = "100%"
+      )
+    }
+  })
+  
+  # Color mapping 
+  output$nj_color_mapping <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_color_mapping",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(Country = "Country"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_color_mapping",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c(Country = "Country"),
+          width = "100%"
+        )
+      )
+    }
+  })
+  
+  output$upgma_color_mapping <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_color_mapping",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(Country = "Country"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_color_mapping",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c(Country = "Country"),
+          width = "100%"
+        )
+      )
+    }
+  })
+  
+  # Tip labels 
+  output$nj_tiplab <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      selectInput(
+        "nj_tiplab",
+        label = "",
+        choices = if(ncol(Vis$meta_nj) == 11) {
+          c(
+            Index = "Index",
+            `Assembly ID` = "Assembly ID",
+            `Assembly Name` = "Assembly Name",
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        } else {
+          append(c(Index = "Index", `Assembly ID` = "Assembly ID", `Assembly Name` = "Assembly Name",
+                   `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                 names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+        },
+        selected = c(`Assembly Name` = "Assembly Name"),
+        width = "100%"
+      )
+    } else {
+      selectInput(
+        "nj_tiplab",
+        label = "",
+        choices = c(
+          Index = "Index",
+          `Assembly ID` = "Assembly ID",
+          `Assembly Name` = "Assembly Name",
+          `Isolation Date` = "Isolation Date",
+          Host = "Host",
+          Country = "Country",
+          City = "City"
+        ),
+        selected = c(`Assembly Name` = "Assembly Name"),
+        width = "100%"
+      )
+    }
+  })
+  
+  output$upgma_tiplab <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      selectInput(
+        "upgma_tiplab",
+        label = "",
+        choices = if(ncol(Vis$meta_upgma) == 11) {
+          c(
+            Index = "Index",
+            `Assembly ID` = "Assembly ID",
+            `Assembly Name` = "Assembly Name",
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        } else {
+          append(c(Index = "Index", `Assembly ID` = "Assembly ID", `Assembly Name` = "Assembly Name",
+                   `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+        },
+        selected = c(`Assembly Name` = "Assembly Name"),
+        width = "100%"
+      )
+    } else {
+      selectInput(
+        "upgma_tiplab",
+        label = "",
+        choices = c(
+          Index = "Index",
+          `Assembly ID` = "Assembly ID",
+          `Assembly Name` = "Assembly Name",
+          `Isolation Date` = "Isolation Date",
+          Host = "Host",
+          Country = "Country",
+          City = "City"
+        ),
+        selected = c(`Assembly Name` = "Assembly Name"),
+        width = "100%"
+      )
+    }
+  })
+  
+  #### MST controls ----
+  
+  # Clustering UI
+  output$mst_cluster <- renderUI({
+    req(DB$schemeinfo)
+    numericInput(
+      inputId = "mst_cluster_threshold",
+      label = NULL,
+      value = as.numeric(DB$schemeinfo[7, 2]),
+      min = 1,
+      max = 99
+    )
+  })
+  
+  # MST color mapping
+  output$mst_color_mapping <- renderUI({
+    if(input$mst_color_var == FALSE) {
+      fluidRow(
+        column(
+          width = 7,
+          div(
+            class = "node_color",
+            colorPickr(
+              inputId = "mst_color_node",
+              width = "100%",
+              selected = "#B2FACA",
+              label = "",
+              update = "changestop",
+              interaction = list(clear = FALSE,
+                                 save = FALSE),
+              position = "right-start"
+            )
+          )
+        ),
+        column(
+          width = 5,
+          dropMenu(
+            actionBttn(
+              "mst_node_menu",
+              label = "",
+              color = "default",
+              size = "sm",
+              style = "material-flat",
+              icon = icon("sliders")
+            ),
+            placement = "top-start",
+            theme = "translucent",
+            width = 5,
+            numericInput(
+              "node_opacity",
+              label = h5("Opacity", style = "color:white; margin-bottom: 0px;"),
+              value = 1,
+              step = 0.1,
+              min = 0,
+              max = 1,
+              width = "80px"
+            )
+          )
+        )
+      ) 
+    } else {
+      fluidRow(
+        column(
+          width = 9,
+          div(
+            class = "mst_col_sel",
+            selectInput(
+              "mst_col_var",
+              label = "",
+              choices = if(any(DB$cust_var[DB$cust_var$Variable[which(DB$cust_var$Variable %in% c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)]))],]$Type != "categ")) {
+                selection <- c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)])
+                cust_vars <- DB$cust_var$Variable[which(DB$cust_var$Variable %in% selection)]
+                selection[-which(selection == cust_vars[DB$cust_var[cust_vars,]$Type != "categ"])]
+              } else {c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)])},
+              width = "100%"
+            )
+          )
+        ),
+        column(
+          width = 3,
+          dropMenu(
+            actionBttn(
+              "mst_col_menu",
+              label = "",
+              color = "default",
+              size = "sm",
+              style = "material-flat",
+              icon = icon("sliders")
+            ),
+            placement = "top-start",
+            theme = "translucent",
+            width = 5,
+            selectInput(
+              "mst_col_scale",
+              label = h5("Color Scale", style = "color:white; margin-bottom: 0px;"),
+              choices = c("Viridis", "Rainbow"),
+              width = "150px"
+            ),
+            br(), br(), br(), br()
+          )
+        )
+      ) 
+    }
+  })
+  
+  observeEvent(input$mst_color_var, {
+    
+    if(input$mst_color_var == TRUE) {
+      updateSelectizeInput(session, inputId = "mst_node_shape", choices = c("Pie Nodes" = "custom"))
+      updateSelectizeInput(session, inputId = "mst_node_label", choices = c("Assembly Name"))
+    } else {
+      updateSelectizeInput(session, inputId = "mst_node_shape", 
+                           choices = list(`Label inside` = c("Circle" = "circle", "Box" = "box", "Text" = "text"),
+                                          `Label outside` = c("Diamond" = "diamond", "Hexagon" = "hexagon","Dot" = "dot", "Square" = "square")),
+                           selected = c("Dot" = "dot"))
+      updateSelectizeInput(session, inputId = "mst_node_label",
+                           choices = names(DB$meta)[c(1, 3, 4, 6, 7, 8, 9)],
+                           selected = "Assembly Name")
+    }
+  })
+  
+  # MST node labels 
+  output$mst_node_label <- renderUI({
+    selectInput(
+      "mst_node_label",
+      label = "",
+      choices = names(DB$meta)[c(1, 3, 4, 6, 7, 8, 9)],
+      selected = "Assembly Name",
+      width = "100%"
+    )
+  })
+  
+  ### Plot Reactives ----
+  
+  #### MST ----
+  
+  mst_tree <- reactive({
+    data <- toVisNetworkData(Vis$ggraph_1)
+    data$nodes <- mutate(data$nodes, 
+                                label = label_mst(),
+                                value = mst_node_scaling(),
+                                opacity = node_opacity())
+    
+    ctxRendererJS <- htmlwidgets::JS("({ctx, id, x, y, state: { selected, hover }, style, font, label, metadata}) => {
+                            var pieData = JSON.parse(metadata);
+                            var radius = style.size;
+                            var centerX = x;
+                            var centerY = y;
+                            var total = pieData.reduce((sum, slice) => sum + slice.value, 0)
+                            var startAngle = 0;
+
+                            const drawNode = () => {
+                                // Set shadow properties
+                                if (style.shadow) {
+                                  var shadowSize = style.shadowSize;
+                                  ctx.shadowColor = style.shadowColor;
+                                  ctx.shadowBlur = style.shadowSize;
+                                  ctx.shadowOffsetX = style.shadowX;
+                                  ctx.shadowOffsetY = style.shadowY;
+                                  
+                                  ctx.beginPath();
+                                  ctx.arc(centerX, centerY, radius, 0, 2 * Math.PI);
+                                  ctx.fill();
+                                  
+                                  ctx.shadowColor = 'transparent';
+                                  ctx.shadowBlur = 0;
+                                  ctx.shadowOffsetX = 0;
+                                  ctx.shadowOffsetY = 0;
+                                }
+
+                                pieData.forEach(slice => {
+                                    var sliceAngle = 2 * Math.PI * (slice.value / total);
+                                    ctx.beginPath();
+                                    ctx.moveTo(centerX, centerY);
+                                    ctx.arc(centerX, centerY, radius, startAngle, startAngle + sliceAngle);
+                                    ctx.closePath();
+                                    ctx.fillStyle = slice.color;
+                                    ctx.fill();
+                                     if (pieData.length > 1) {
+                ctx.strokeStyle = 'black';
+                ctx.lineWidth = 1;
+                ctx.stroke();
+            }
+                                    startAngle += sliceAngle;
+                                });
+                    
+                                // Draw a border
+                                ctx.beginPath();
+                                ctx.arc(centerX, centerY, radius, 0, 2 * Math.PI);
+                                ctx.strokeStyle = 'black';
+                                ctx.lineWidth = 1;
+                                ctx.stroke();
+                            };
+                            drawLabel = () => {
+                              //Draw the label
+                              var lines = label.split(`\n`);
+                              var lineHeight = font.size;
+                              ctx.font = `${font.size}px ${font.face}`;
+                              ctx.fillStyle = font.color;
+                              ctx.textAlign = 'center';
+                              ctx.textBaseline = 'middle';
+                              lines.forEach((line, index) => {
+                                ctx.fillText(line, centerX, 
+                                centerY + radius + (index + 1) * lineHeight);
+                              })
+                            }
+                            
+                            return {
+                                drawNode,
+                                drawExternalLabel: drawLabel,
+                                nodeDimensions: { width: 2 * radius, height: 2 * radius },
+                            };
+                        }")
+    
+    Vis$var_cols <- NULL
+    
+    # Generate pie charts as nodes
+    if(input$mst_color_var == TRUE & (!is.null(input$mst_col_var))) {
+      
+      group <- character(nrow(data$nodes))
+      for (i in 1:length(unique(Vis$meta_mst[[input$mst_col_var]]))) {
+        group[i] <- unique(Vis$meta_mst[[input$mst_col_var]])[i]
+      }
+      
+      data$nodes <- cbind(data$nodes, data.frame(metadata = character(nrow(data$nodes))))
+      
+      if(length(which(data$nodes$group == "")) != 0) {
+        data$nodes$group[which(data$nodes$group == "")] <- data$nodes$group[1]
+      }
+      
+      if(is.null(input$mst_col_scale)) {
+        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
+                                      color = viridis(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
+      } else if (input$mst_col_scale == "Rainbow") {
+        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
+                                      color = rainbow(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
+      } else if (input$mst_col_scale == "Viridis") {
+        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
+                                      color = viridis(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
+      }
+      
+      for(i in 1:nrow(data$nodes)) {
+        
+        iso_subset <- strsplit(data$nodes$label[i], split = "\n")[[1]]
+        variable <- Vis$meta_mst[[input$mst_col_var]]
+        values <- variable[which(Vis$meta_mst$`Assembly Name` %in% iso_subset)]
+        
+        for(j in 1:length(unique(values))) {
+          
+          share <- sum(unique(values)[j] == values) / length(values) * 100
+          color <- Vis$var_cols$color[Vis$var_cols$value == unique(values)[j]]
+          
+          if(j == 1) {
+            pie_vec <- paste0('{"value":', share,',"color":"', color,'"}')
+          } else {
+            pie_vec <- paste0(pie_vec, ',{"value":', share,',"color":"', color,'"}')
+          }
+        }
+        
+        data$nodes$metadata[i] <- paste0('[', pie_vec, ']')
+      }
+    }
+    
+    data$edges <- mutate(data$edges,
+                                length = if(input$mst_scale_edges == FALSE) {
+                                  input$mst_edge_length
+                                } else {
+                                  data$edges$weight * input$mst_edge_length_scale
+                                },
+                                label = as.character(data$edges$weight),
+                                opacity = input$mst_edge_opacity)
+    
+    if (input$mst_show_clusters) {
+      clusters <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
+      if (input$mst_cluster_type == "Type 1") {
+        data$nodes$group <- clusters$group
+      }
+    }
+    
+    visNetwork_graph <- visNetwork(data$nodes, data$edges,
+                                   main = mst_title(),
+                                   background = mst_background_color(),
+                                   submain = mst_subtitle()) %>%
+      visNodes(size = mst_node_size(),
+               shape = input$mst_node_shape,
+               shadow = input$mst_shadow,
+               color = mst_color_node(),
+               ctxRenderer = ctxRendererJS,
+               scaling = list(min = mst_node_size_min(),
+                              max = mst_node_size_max()),
+               font = list(color = node_font_color(),
+                           size = input$node_label_fontsize)) %>%
+      visEdges(color = mst_color_edge(),
+               font = list(color = mst_edge_font_color(),
+                           size = mst_edge_font_size(),
+                           strokeWidth = 4)) %>%
+      visOptions(collapse = TRUE) %>%
+      visInteraction(hover = TRUE) %>%
+      visLayout(randomSeed = 1) %>%
+      visLegend(useGroups = FALSE,
+                zoom = TRUE,
+                width = legend_width(),
+                position = input$mst_legend_ori,
+                ncol = legend_col(),
+                addNodes = mst_legend())
+    
+    if (input$mst_show_clusters) {
+      if (input$mst_cluster_col_scale == "Viridis") {
+        color_palette <- viridis(length(unique(data$nodes$group)))
+      } else {
+        color_palette <- rainbow(length(unique(data$nodes$group)))
+      }
+      
+      if (input$mst_cluster_type == "Type 1") {
+        for (i in 1:length(unique(data$nodes$group))) {
+          visNetwork_graph <- visNetwork_graph %>% 
+            visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
+        }
+      } else {
+        thin_edges <- data$edges
+        thin_edges$width <- 1
+        thin_edges$color <- "black"
+        
+        thick_edges <- data$edges
+        thick_edges$width <- 24
+        
+        thick_edges$color <- rep("rgba(0, 0, 0, 0)", length(data$edges$from))
+        color_palette <- rainbow(length(unique(clusters$edges)))
+        for (i in 1:length(unique(clusters$edges))) {
+          print(clusters$edges)
+          if (unique(clusters$edges)[i] != "0") {
+            edge_color <- paste(col2rgb(color_palette[i]), collapse=", ")
+            thick_edges$color[clusters$edges == unique(clusters$edges)[i]] <- paste0("rgba(", edge_color, ", 0.5)")
+          }
+        }
+        merged_edges <- rbind(thick_edges, thin_edges)
+        data$edges <- merged_edges
+        visNetwork_graph <- visNetwork(data$nodes, data$edges,
+                                       main = mst_title(),
+                                       background = mst_background_color(),
+                                       submain = mst_subtitle()) %>%
+          visNodes(size = mst_node_size(),
+                   shape = input$mst_node_shape,
+                   shadow = input$mst_shadow,
+                   color = mst_color_node(),
+                   ctxRenderer = ctxRendererJS,
+                   scaling = list(min = mst_node_size_min(),
+                                  max = mst_node_size_max()),
+                   font = list(color = node_font_color(),
+                               size = input$node_label_fontsize)) %>%
+          visEdges(color = mst_color_edge(),
+                   font = list(color = mst_edge_font_color(),
+                               size = mst_edge_font_size(),
+                               strokeWidth = 4),
+                   smooth = FALSE,
+                   physics = FALSE) %>%
+          visOptions(collapse = TRUE) %>%
+          visInteraction(hover = TRUE) %>%
+          visLayout(randomSeed = 1) %>%
+          visLegend(useGroups = FALSE,
+                    zoom = TRUE,
+                    width = legend_width(),
+                    position = input$mst_legend_ori,
+                    ncol = legend_col(),
+                    addNodes = mst_legend())
+      }
+    }
+    visNetwork_graph
+  })
+  
+  # MST legend
+  legend_col <- reactive({
+    if(!is.null(Vis$var_cols)) {
+      if(nrow(Vis$var_cols) > 10) {
+        3
+      } else if(nrow(Vis$var_cols) > 5) {
+        2
+      } else {
+        1
+      }
+    } else {1}
+  })
+  
+  mst_legend <- reactive({
+    if(is.null(Vis$var_cols)) {
+      NULL
+    } else {
+      legend <- Vis$var_cols
+      names(legend)[1] <- "label"
+      mutate(legend, shape = "dot",
+             font.color = input$mst_legend_color,
+             size = input$mst_symbol_size,
+             font.size = input$mst_font_size)
+    }
+  })
+  
+  # Set MST legend width
+  legend_width <- reactive({
+    0.2
+  })
+  
+  # Set MST node shape
+  mst_node_shape <- reactive({
+    if(input$mst_node_shape == "Pie Nodes"){
+      "dot"
+    } else if(input$mst_node_shape %in% c("circle", "database", "box", "text")) {
+      shinyjs::disable('scale_nodes') 
+      updateCheckboxInput(session, "scale_nodes", value = FALSE)
+      shinyjs::disable('mst_node_size') 
+      shinyjs::disable('mst_node_scale')
+      input$mst_node_shape
+    } else {
+      shinyjs::enable('scale_nodes') 
+      shinyjs::enable('mst_node_size') 
+      shinyjs::enable('mst_node_scale')
+      input$mst_node_shape
+    }
+  })
+  
+  # Set MST label
+  label_mst <- reactive({
+    Vis$unique_meta[, colnames(Vis$unique_meta) %in% input$mst_node_label]
+  })
+  
+  # Set node color
+  mst_color_node <- reactive({
+    input$mst_color_node
+  })
+  
+  # Node Label Color
+  node_font_color <- reactive({
+    input$node_font_color
+  })
+  
+  
+  # Node Size Scaling
+  mst_node_scaling <- reactive({
+    if(input$scale_nodes == TRUE){
+      Vis$unique_meta$size
+    } else {NULL}
+  })
+  
+  # Node Size Min/May
+  mst_node_size_min <- reactive({
+    input$mst_node_scale[1]
+  })
+  
+  mst_node_size_max <- reactive({
+    input$mst_node_scale[2]
+  })
+  
+  # Node Size
+  mst_node_size <- reactive({
+    input$mst_node_size
+  })
+  
+  # Node Alpha/Opacity
+  node_opacity <- reactive({
+    input$node_opacity
+  })
+  
+  # Set Title
+  mst_title <- reactive({
+    if(!is.null(input$mst_title)) {
+      if(nchar(input$mst_title) < 1) {
+        list(text = "title",
+             style = paste0(
+               "font-family:Georgia, Times New Roman, Times, serif;",
+               "text-align:center;",
+               "font-size: ", as.character(input$mst_title_size), "px", 
+               "; color: ", as.character(mst_background_color()))
+        )
+      } else {
+        list(text = input$mst_title,
+             style = paste0(
+               "font-family:Georgia, Times New Roman, Times, serif;",
+               "text-align:center;",
+               "font-size: ", as.character(input$mst_title_size), "px", 
+               "; color: ", as.character(input$mst_title_color))
+        )
+      }
+    } else {
+      list(text = "title",
+           style = paste0(
+             "font-family:Georgia, Times New Roman, Times, serif;",
+             "text-align:center;",
+             "font-size: ", as.character(input$mst_title_size), "px", 
+             "; color: ", as.character(mst_background_color()))
+      )
+    }
+  })
+  
+  # Set Subtitle
+  mst_subtitle <- reactive({
+    list(text = input$mst_subtitle,
+         style = paste0(
+           "font-family:Georgia, Times New Roman, Times, serif;",
+           "text-align:center;",
+           "font-size: ", as.character(input$mst_subtitle_size), "px", 
+           "; color: ", as.character(input$mst_subtitle_color))
+    )
+  })
+  
+  # Background color
+  
+  mst_background_color <- reactive({
+    if(input$mst_background_transparent == TRUE) {
+      'rgba(0, 0, 0, 0)'
+    } else{
+      input$mst_background_color
+    }
+  })
+  
+  # Edge font color
+  mst_edge_font_color <- reactive({
+    input$mst_edge_font_color
+  })
+  
+  # Edge color
+  mst_color_edge <- reactive({
+    input$mst_color_edge
+  })
+  
+  # Edge font size
+  mst_edge_font_size <- reactive({
+    input$mst_edge_font_size
+  })
+  
+  #### NJ ----
+  
+  nj_tree <- reactive({
+    
+    # Convert negative edges 
+    Vis$nj[["edge.length"]] <- abs(Vis$nj[["edge.length"]])
+    
+    if(input$nj_nodelabel_show == TRUE) {
+      ggtree(Vis$nj, alpha = 0.2, layout = layout_nj()) + 
+        geom_nodelab(aes(label = node), color = "#29303A", size = nj_tiplab_size() + 1, hjust = 0.7) +
+        nj_limit() +
+        nj_inward() 
+    } else {
+      tree <- 
+        ggtree(Vis$nj, 
+               color = input$nj_color,
+               layout = layout_nj(),
+               ladderize = input$nj_ladder) %<+% Vis$meta_nj +
+        nj_clades() +
+        nj_tiplab() +
+        nj_tiplab_scale() + 
+        new_scale_color() +
+        nj_limit() +
+        nj_inward() +
+        nj_label_branch() +
+        nj_treescale() +
+        nj_nodepoint() +
+        nj_tippoint() +
+        nj_tippoint_scale() + 
+        new_scale_color() +
+        nj_clip_label() +
+        nj_rootedge() +
+        ggtitle(label = input$nj_title,
+                subtitle = input$nj_subtitle) +
+        theme_tree(bgcolor = input$nj_bg) +
+        theme(plot.title = element_text(colour = input$nj_title_color,
+                                        size = input$nj_title_size),
+              plot.subtitle = element_text(colour = input$nj_title_color,
+                                           size = input$nj_subtitle_size),
+              legend.background = element_rect(fill = input$nj_bg),
+              legend.direction = input$nj_legend_orientation,
+              legend.title = element_text(color = input$nj_color,
+                                          size = input$nj_legend_size*1.2),
+              legend.title.align = 0.5,
+              legend.position = nj_legend_pos(),
+              legend.text = element_text(color = input$nj_color, 
+                                         size = input$nj_legend_size),
+              legend.key = element_rect(fill = input$nj_bg),
+              legend.box.spacing = unit(1.5, "cm"),
+              legend.key.size = unit(0.05*input$nj_legend_size, 'cm'),
+              plot.background = element_rect(fill = input$nj_bg, color = input$nj_bg)) +
+        new_scale_fill() +
+        nj_fruit() +
+        nj_gradient() +
+        new_scale_fill() +
+        nj_fruit2() +
+        nj_gradient2() +
+        new_scale_fill() +
+        nj_fruit3() +
+        nj_gradient3() +
+        new_scale_fill() +
+        nj_fruit4() +
+        nj_gradient4() +
+        new_scale_fill() +
+        nj_fruit5() +
+        nj_gradient5() +
+        new_scale_fill() 
+      
+      # Add custom labels
+      if(length(Vis$custom_label_nj) > 0) {
+        
+        for(i in Vis$custom_label_nj[,1]) {
+          
+          if(!is.null(Vis$nj_label_pos_x[[i]])) {
+            x_pos <- Vis$nj_label_pos_x[[i]]
+          } else {
+            x_pos <- round(Vis$nj_max_x / 2, 0)
+          }
+          
+          if(!is.null(Vis$nj_label_pos_y[[i]])) {
+            y_pos <- Vis$nj_label_pos_y[[i]]
+          } else {
+            y_pos <- sum(DB$data$Include) / 2
+          }
+          
+          if(!is.null(Vis$nj_label_size[[i]])) {
+            size <- Vis$nj_label_size[[i]]
+          } else {
+            size <- 5
+          }
+          
+          tree <- tree + annotate("text",
+                                  x = x_pos,
+                                  y = y_pos, 
+                                  label = i,
+                                  size = size)
+        }
+      }
+      
+      # Add heatmap
+      if(input$nj_heatmap_show == TRUE & length(input$nj_heatmap_select) > 0) {
+        if (!(any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)) & 
+              any(!sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)))) {
+          tree <- gheatmap.mod(tree, 
+                               data = select(Vis$meta_nj, input$nj_heatmap_select),
+                               offset = nj_heatmap_offset(),
+                               width = nj_heatmap_width(),
+                               legend_title = input$nj_heatmap_title,
+                               colnames_angle = -nj_colnames_angle(),
+                               colnames_offset_y = nj_colnames_y(),
+                               colnames_color = input$nj_color) +
+            nj_heatmap_scale()
+        }
+      } 
+      
+      # Sizing control
+      Vis$nj_plot <- ggplotify::as.ggplot(tree, 
+                                          scale = input$nj_zoom,
+                                          hjust = input$nj_h,
+                                          vjust = input$nj_v)  
+      
+      Vis$nj_true <- TRUE
+      
+      # Correct background color if zoomed out
+      cowplot::ggdraw(Vis$nj_plot) + 
+        theme(plot.background = element_rect(fill = input$nj_bg, color = input$nj_bg))
+    }
+  })
+  
+  # Heatmap width
+  nj_heatmap_width <- reactive({
+    if(!is.null(input$nj_heatmap_width)) {
+      input$nj_heatmap_width
+    } else {
+      length_input <- length(input$nj_heatmap_select)
+      if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
+        if(length_input < 3) {
+          0.1
+        } else {
+          if (length_input >= 3 && length_input <= 50) {
+            min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+          } else {
+            1.5
+          }   
+        }
+      } else {
+        if(length_input < 3) {
+          0.3
+        } else if (length_input >= 3 && length_input <= 27) {
+          min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          3
+        }
+      }
+    }
+  })
+  
+  # Heatmap column titles position
+  nj_colnames_y <- reactive({
+    if(!is.null(input$nj_colnames_y)) {
+      input$nj_colnames_y
+    } else {
+      if(input$nj_layout == "inward" | input$nj_layout == "circular") {
+        0
+      } else {-1}
+    }
+  })
+  
+  # Heatmap column titles angle
+  nj_colnames_angle <- reactive({
+    if(!is.null(input$nj_colnames_angle)) {
+      input$nj_colnames_angle
+    } else {
+      if(!is.null(input$nj_layout)) {
+        if(input$nj_layout == "inward" | input$nj_layout == "circular") {
+          90
+        } else {-90}
+      } else {-90}
+    }
+  })
+  
+  # Heatmap scale
+  nj_heatmap_scale <- reactive({
+    if(!is.null(input$nj_heatmap_scale) & !is.null(input$nj_heatmap_div_mid)) {
+      if(input$nj_heatmap_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$nj_heatmap_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$nj_heatmap_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_heatmap_select]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_heatmap_select]), na.rm = TRUE)
+        }
+        scale_fill_gradient2(low = brewer.pal(3, input$nj_heatmap_scale)[1],
+                             mid = brewer.pal(3, input$nj_heatmap_scale)[2],
+                             high = brewer.pal(3, input$nj_heatmap_scale)[3],
+                             midpoint = midpoint,
+                             name = input$nj_heatmap_title)
+      } else {
+        if(input$nj_heatmap_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_nj[input$nj_heatmap_select])) == "numeric") {
+            if(input$nj_heatmap_scale == "magma") {
+              scale_fill_viridis(option = "A",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "inferno") {
+              scale_fill_viridis(option = "B",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "plasma") {
+              scale_fill_viridis(option = "C",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "viridis") {
+              scale_fill_viridis(option = "D",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "cividis") {
+              scale_fill_viridis(option = "E",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "rocket") {
+              scale_fill_viridis(option = "F",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "mako") {
+              scale_fill_viridis(option = "G",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "turbo") {
+              scale_fill_viridis(option = "H",
+                                 name = input$nj_heatmap_title)
+            } 
+          } else {
+            if(input$nj_heatmap_scale == "magma") {
+              scale_fill_viridis(discrete = TRUE, option = "A",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "inferno") {
+              scale_fill_viridis(discrete = TRUE, option = "B",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "plasma") {
+              scale_fill_viridis(discrete = TRUE, option = "C",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "viridis") {
+              scale_fill_viridis(discrete = TRUE, option = "D",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "cividis") {
+              scale_fill_viridis(discrete = TRUE, option = "E",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "rocket") {
+              scale_fill_viridis(discrete = TRUE, option = "F",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "mako") {
+              scale_fill_viridis(discrete = TRUE, option = "G",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "turbo") {
+              scale_fill_viridis(discrete = TRUE, option = "H",
+                                 name = input$nj_heatmap_title)
+            } 
+          }
+        } else {
+          scale_fill_brewer(palette = input$nj_heatmap_scale,
+                            name = input$nj_heatmap_title)
+        }
+      }
+    }
+  })
+  
+  # Tippoint Scale
+  nj_tippoint_scale <- reactive({
+    if(!is.null(input$nj_tippoint_scale) & !is.null(input$nj_tipcolor_mapping_div_mid)) {
+      if(input$nj_tippoint_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$nj_tipcolor_mapping_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$nj_tipcolor_mapping_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_tipcolor_mapping]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_tipcolor_mapping]), na.rm = TRUE)
+        }
+        scale_color_gradient2(low = brewer.pal(3, input$nj_tippoint_scale)[1],
+                              mid = brewer.pal(3, input$nj_tippoint_scale)[2],
+                              high = brewer.pal(3, input$nj_tippoint_scale)[3],
+                              midpoint = midpoint)
+      } else {
+        if(input$nj_tippoint_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_nj[input$nj_tipcolor_mapping])) == "numeric") {
+            if(input$nj_tippoint_scale == "magma") {
+              scale_color_viridis(option = "A")
+            } else if(input$nj_tippoint_scale == "inferno") {
+              scale_color_viridis(option = "B")
+            } else if(input$nj_tippoint_scale == "plasma") {
+              scale_color_viridis(option = "C")
+            } else if(input$nj_tippoint_scale == "viridis") {
+              scale_color_viridis(option = "D")
+            } else if(input$nj_tippoint_scale == "cividis") {
+              scale_color_viridis(option = "E")
+            } else if(input$nj_tippoint_scale == "rocket") {
+              scale_color_viridis(option = "F")
+            } else if(input$nj_tippoint_scale == "mako") {
+              scale_color_viridis(option = "G")
+            } else if(input$nj_tippoint_scale == "turbo") {
+              scale_color_viridis(option = "H")
+            } 
+          } else {
+            if(input$nj_tippoint_scale == "magma") {
+              scale_color_viridis(discrete = TRUE, option = "A")
+            } else if(input$nj_tippoint_scale == "inferno") {
+              scale_color_viridis(discrete = TRUE, option = "B")
+            } else if(input$nj_tippoint_scale == "plasma") {
+              scale_color_viridis(discrete = TRUE, option = "C")
+            } else if(input$nj_tippoint_scale == "viridis") {
+              scale_color_viridis(discrete = TRUE, option = "D")
+            } else if(input$nj_tippoint_scale == "cividis") {
+              scale_color_viridis(discrete = TRUE, option = "E")
+            } else if(input$nj_tippoint_scale == "rocket") {
+              scale_color_viridis(discrete = TRUE, option = "F")
+            } else if(input$nj_tippoint_scale == "mako") {
+              scale_color_viridis(discrete = TRUE, option = "G")
+            } else if(input$nj_tippoint_scale == "turbo") {
+              scale_color_viridis(discrete = TRUE, option = "H")
+            } 
+          }
+        } else {
+          scale_color_brewer(palette = input$nj_tippoint_scale)
+        }
+      }
+    }
+  })
+  
+  # Tiplab Scale
+  nj_tiplab_scale <- reactive({
+    if(!is.null(input$nj_tiplab_scale) & !is.null(input$nj_color_mapping_div_mid)) {
+      if(input$nj_tiplab_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$nj_color_mapping_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$nj_color_mapping_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_color_mapping]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_color_mapping]), na.rm = TRUE)
+        }
+        scale_color_gradient2(low = brewer.pal(3, input$nj_tiplab_scale)[1],
+                              mid = brewer.pal(3, input$nj_tiplab_scale)[2],
+                              high = brewer.pal(3, input$nj_tiplab_scale)[3],
+                              midpoint = midpoint)
+      } else {
+        if(input$nj_tiplab_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_nj[input$nj_color_mapping])) == "numeric") {
+            if(input$nj_tiplab_scale == "magma") {
+              scale_color_viridis(option = "A")
+            } else if(input$nj_tiplab_scale == "inferno") {
+              scale_color_viridis(option = "B")
+            } else if(input$nj_tiplab_scale == "plasma") {
+              scale_color_viridis(option = "C")
+            } else if(input$nj_tiplab_scale == "viridis") {
+              scale_color_viridis(option = "D")
+            } else if(input$nj_tiplab_scale == "cividis") {
+              scale_color_viridis(option = "E")
+            } else if(input$nj_tiplab_scale == "rocket") {
+              scale_color_viridis(option = "F")
+            } else if(input$nj_tiplab_scale == "mako") {
+              scale_color_viridis(option = "G")
+            } else if(input$nj_tiplab_scale == "turbo") {
+              scale_color_viridis(option = "H")
+            } 
+          } else {
+            if(input$nj_tiplab_scale == "magma") {
+              scale_color_viridis(discrete = TRUE, option = "A")
+            } else if(input$nj_tiplab_scale == "inferno") {
+              scale_color_viridis(discrete = TRUE, option = "B")
+            } else if(input$nj_tiplab_scale == "plasma") {
+              scale_color_viridis(discrete = TRUE, option = "C")
+            } else if(input$nj_tiplab_scale == "viridis") {
+              scale_color_viridis(discrete = TRUE, option = "D")
+            } else if(input$nj_tiplab_scale == "cividis") {
+              scale_color_viridis(discrete = TRUE, option = "E")
+            } else if(input$nj_tiplab_scale == "rocket") {
+              scale_color_viridis(discrete = TRUE, option = "F")
+            } else if(input$nj_tiplab_scale == "mako") {
+              scale_color_viridis(discrete = TRUE, option = "G")
+            } else if(input$nj_tiplab_scale == "turbo") {
+              scale_color_viridis(discrete = TRUE, option = "H")
+            } 
+          }
+        } else {
+          scale_color_brewer(palette = input$nj_tiplab_scale)
+        }
+      }
+    }
+  })
+  
+  # Clade Highlight
+  nj_clades <- reactive({
+    if(!is.null(input$nj_parentnode)) {
+      if(!length(input$nj_parentnode) == 0) {
+        if(length(input$nj_parentnode) == 1) {
+          fill <- input$nj_clade_scale
+        } else if (length(input$nj_parentnode) == 2) {
+          if(startsWith(input$nj_clade_scale, "#")) {
+            fill <- brewer.pal(3, "Set1")[1:2]
+          } else {
+            fill <- brewer.pal(3, input$nj_clade_scale)[1:2]
+          }
+        } else {
+          fill <- brewer.pal(length(input$nj_parentnode), input$nj_clade_scale)
+        }
+        geom_hilight(node = as.numeric(input$nj_parentnode),
+                     fill = fill,
+                     type = input$nj_clade_type,
+                     to.bottom = TRUE
+        )
+      } else {NULL}
+    }
+  })
+  
+  # Legend Position
+  nj_legend_pos <- reactive({
+    if(!is.null(input$nj_legend_x) & !is.null(input$nj_legend_y)) {
+      c(input$nj_legend_x, input$nj_legend_y)
+    } else {
+      c(0.1, 1)
+    }
+  })
+  
+  # Heatmap offset
+  nj_heatmap_offset <- reactive({
+    if(is.null(input$nj_heatmap_offset)) {
+      0
+    } else {input$nj_heatmap_offset}
+  })
+  
+  # Tiles fill color gradient
+  nj_gradient <- reactive({
+    if(!is.null(input$nj_tiles_show_1) & 
+       !is.null(input$nj_fruit_variable) & 
+       !is.null(input$nj_tiles_scale_1) & 
+       !is.null(input$nj_tiles_mapping_div_mid_1)) {
+      if(input$nj_tiles_show_1 == TRUE) {
+        if(input$nj_tiles_scale_1 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$nj_tiles_mapping_div_mid_1 == "Zero") {
+            midpoint <- 0
+          } else if(input$nj_tiles_mapping_div_mid_1 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable]), na.rm = TRUE)
+          }
+          scale_fill_gradient2(low = brewer.pal(3, input$nj_tiles_scale_1)[1],
+                               mid = brewer.pal(3, input$nj_tiles_scale_1)[2],
+                               high = brewer.pal(3, input$nj_tiles_scale_1)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$nj_tiles_scale_1 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
+              if(input$nj_tiles_scale_1 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$nj_tiles_scale_1 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$nj_tiles_scale_1 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$nj_tiles_scale_1 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$nj_tiles_scale_1 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$nj_tiles_scale_1 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$nj_tiles_scale_1 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$nj_tiles_scale_1 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$nj_tiles_scale_1 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$nj_tiles_scale_1 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$nj_tiles_scale_1 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$nj_tiles_scale_1 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$nj_tiles_scale_1 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$nj_tiles_scale_1 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$nj_tiles_scale_1 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$nj_tiles_scale_1 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$nj_tiles_scale_1)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_gradient2 <- reactive({
+    if(!is.null(input$nj_tiles_show_2) & 
+       !is.null(input$nj_fruit_variable_2) & 
+       !is.null(input$nj_tiles_scale_2) & 
+       !is.null(input$nj_tiles_mapping_div_mid_2)) {
+      if(input$nj_tiles_show_2 == TRUE) {
+        if(input$nj_tiles_scale_2 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$nj_tiles_mapping_div_mid_2 == "Zero") {
+            midpoint <- 0
+          } else if(input$nj_tiles_mapping_div_mid_2 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_2]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_2]), na.rm = TRUE)
+          }
+          scale_fill_gradient2(low = brewer.pal(3, input$nj_tiles_scale_2)[1],
+                               mid = brewer.pal(3, input$nj_tiles_scale_2)[2],
+                               high = brewer.pal(3, input$nj_tiles_scale_2)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$nj_tiles_scale_2 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_2])) == "numeric") {
+              if(input$nj_tiles_scale_2 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$nj_tiles_scale_2 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$nj_tiles_scale_2 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$nj_tiles_scale_2 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$nj_tiles_scale_2 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$nj_tiles_scale_2 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$nj_tiles_scale_2 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$nj_tiles_scale_2 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$nj_tiles_scale_2 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$nj_tiles_scale_2 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$nj_tiles_scale_2 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$nj_tiles_scale_2 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$nj_tiles_scale_2 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$nj_tiles_scale_2 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$nj_tiles_scale_2 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$nj_tiles_scale_2 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$nj_tiles_scale_2)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_gradient3 <- reactive({
+    if(!is.null(input$nj_tiles_show_3) & 
+       !is.null(input$nj_fruit_variable_3) & 
+       !is.null(input$nj_tiles_scale_3 & 
+                !is.null(input$nj_tiles_mapping_div_mid_3))) {
+      if(input$nj_tiles_show_3 == TRUE) {
+        if(input$nj_tiles_scale_3 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$nj_tiles_mapping_div_mid_3 == "Zero") {
+            midpoint <- 0
+          } else if(input$nj_tiles_mapping_div_mid_3 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_3]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_3]), na.rm = TRUE)
+          }
+          scale_fill_gradient3(low = brewer.pal(3, input$nj_tiles_scale_3)[1],
+                               mid = brewer.pal(3, input$nj_tiles_scale_3)[2],
+                               high = brewer.pal(3, input$nj_tiles_scale_3)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$nj_tiles_scale_3 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_3])) == "numeric") {
+              if(input$nj_tiles_scale_3 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$nj_tiles_scale_3 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$nj_tiles_scale_3 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$nj_tiles_scale_3 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$nj_tiles_scale_3 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$nj_tiles_scale_3 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$nj_tiles_scale_3 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$nj_tiles_scale_3 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$nj_tiles_scale_3 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$nj_tiles_scale_3 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$nj_tiles_scale_3 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$nj_tiles_scale_3 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$nj_tiles_scale_3 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$nj_tiles_scale_3 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$nj_tiles_scale_3 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$nj_tiles_scale_3 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$nj_tiles_scale_3)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_gradient4 <- reactive({
+    if(!is.null(input$nj_tiles_show_4) & 
+       !is.null(input$nj_fruit_variable_4) & 
+       !is.null(input$nj_tiles_scale_4) & 
+       !is.null(input$nj_tiles_mapping_div_mid_4)) {
+      if(input$nj_tiles_show_4 == TRUE) {
+        if(input$nj_tiles_scale_4 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$nj_tiles_mapping_div_mid_4 == "Zero") {
+            midpoint <- 0
+          } else if(input$nj_tiles_mapping_div_mid_4 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_4]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_4]), na.rm = TRUE)
+          }
+          scale_fill_gradient4(low = brewer.pal(3, input$nj_tiles_scale_4)[1],
+                               mid = brewer.pal(3, input$nj_tiles_scale_4)[2],
+                               high = brewer.pal(3, input$nj_tiles_scale_4)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$nj_tiles_scale_4 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
+              if(input$nj_tiles_scale_4 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$nj_tiles_scale_4 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$nj_tiles_scale_4 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$nj_tiles_scale_4 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$nj_tiles_scale_4 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$nj_tiles_scale_4 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$nj_tiles_scale_4 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$nj_tiles_scale_4 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$nj_tiles_scale_4 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$nj_tiles_scale_4 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$nj_tiles_scale_4 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$nj_tiles_scale_4 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$nj_tiles_scale_4 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$nj_tiles_scale_4 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$nj_tiles_scale_4 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$nj_tiles_scale_4 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$nj_tiles_scale_4)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_gradient5 <- reactive({
+    if(!is.null(input$nj_tiles_show_5) & 
+       !is.null(input$nj_fruit_variable_5) & 
+       !is.null(input$nj_tiles_scale_5) & 
+       !is.null(input$nj_tiles_mapping_div_mid_5)) {
+      if(input$nj_tiles_show_5 == TRUE) {
+        if(input$nj_tiles_scale_5 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$nj_tiles_mapping_div_mid_5 == "Zero") {
+            midpoint <- 0
+          } else if(input$nj_tiles_mapping_div_mid_5 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_5]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_5]), na.rm = TRUE)
+          }
+          scale_fill_gradient5(low = brewer.pal(3, input$nj_tiles_scale_5)[1],
+                               mid = brewer.pal(3, input$nj_tiles_scale_5)[2],
+                               high = brewer.pal(3, input$nj_tiles_scale_5)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$nj_tiles_scale_5 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_5])) == "numeric") {
+              if(input$nj_tiles_scale_5 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$nj_tiles_scale_5 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$nj_tiles_scale_5 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$nj_tiles_scale_5 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$nj_tiles_scale_5 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$nj_tiles_scale_5 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$nj_tiles_scale_5 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$nj_tiles_scale_5 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$nj_tiles_scale_5 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$nj_tiles_scale_5 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$nj_tiles_scale_5 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$nj_tiles_scale_5 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$nj_tiles_scale_5 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$nj_tiles_scale_5 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$nj_tiles_scale_5 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$nj_tiles_scale_5 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$nj_tiles_scale_5)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  # No label clip off for linear NJ tree
+  nj_clip_label <- reactive({
+    if(!(input$nj_layout == "circular" | input$nj_layout == "inward")) {
+      coord_cartesian(clip = "off")
+    } else {NULL}
+  })
+  
+  # Geom Fruit
+  nj_fruit <- reactive({
+    if((!is.null(input$nj_tiles_show_1)) & 
+       (!is.null(input$nj_fruit_variable)) & 
+       (!is.null(input$nj_layout)) & 
+       (!is.null(input$nj_fruit_offset_circ)) & 
+       (!is.null(input$nj_fruit_width_circ)) & 
+       (!is.null(input$nj_fruit_alpha))) {
+      if(input$nj_tiles_show_1 == TRUE) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
+            offset = input$nj_fruit_offset_circ,
+            width = input$nj_fruit_width_circ,
+            alpha = input$nj_fruit_alpha
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
+            offset = input$nj_fruit_offset_circ,
+            width = input$nj_fruit_width_circ,
+            alpha = input$nj_fruit_alpha
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$nj_tiles_show_1 == TRUE) {
+        if(!is.null(Vis$nj_max_x)) {
+          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
+            offset = 0,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
+            offset = 0,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  # Geom Fruit
+  nj_fruit2 <- reactive({
+    if((!is.null(input$nj_tiles_show_2)) & 
+       (!is.null(input$nj_fruit_variable_2)) & 
+       (!is.null(input$nj_layout)) & 
+       (!is.null(input$nj_fruit_offset_circ_2)) & 
+       (!is.null(input$nj_fruit_width_circ_2)) & 
+       (!is.null(input$nj_fruit_alpha_2))) {
+      if(input$nj_tiles_show_2 == TRUE) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_2)),
+            offset = input$nj_fruit_offset_circ_2,
+            width = input$nj_fruit_width_circ_2,
+            alpha = input$nj_fruit_alpha_2
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_2)),
+            offset = input$nj_fruit_offset_circ_2,
+            width = input$nj_fruit_width_circ_2,
+            alpha = input$nj_fruit_alpha_2
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$nj_tiles_show_2 == TRUE) {
+        if(!is.null(Vis$nj_max_x)) {
+          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_2)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_2)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_fruit3 <- reactive({
+    if((!is.null(input$nj_tiles_show_3)) & 
+       (!is.null(input$nj_fruit_variable_3)) & 
+       (!is.null(input$nj_layout)) & 
+       (!is.null(input$nj_fruit_offset_circ_3)) & 
+       (!is.null(input$nj_fruit_width_circ_3)) & 
+       (!is.null(input$nj_fruit_alpha_3))) {
+      if(input$nj_tiles_show_3 == TRUE) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_3)),
+            offset = input$nj_fruit_offset_circ_3,
+            width = input$nj_fruit_width_circ_3,
+            alpha = input$nj_fruit_alpha_3
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_3)),
+            offset = input$nj_fruit_offset_circ_3,
+            width = input$nj_fruit_width_circ_3,
+            alpha = input$nj_fruit_alpha_3
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$nj_tiles_show_3 == TRUE) {
+        if(!is.null(Vis$nj_max_x)) {
+          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_3)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_3)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_fruit4 <- reactive({
+    if((!is.null(input$nj_tiles_show_4)) & 
+       (!is.null(input$nj_fruit_variable_4)) & 
+       (!is.null(input$nj_layout)) & 
+       (!is.null(input$nj_fruit_offset_circ_4)) & 
+       (!is.null(input$nj_fruit_width_circ_4)) & 
+       (!is.null(input$nj_fruit_alpha_4))) {
+      if(input$nj_tiles_show_4 == TRUE) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_4)),
+            offset = input$nj_fruit_offset_circ_4,
+            width = input$nj_fruit_width_circ_4,
+            alpha = input$nj_fruit_alpha_4
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_4)),
+            offset = input$nj_fruit_offset_circ_4,
+            width = input$nj_fruit_width_circ_4,
+            alpha = input$nj_fruit_alpha_4
+          )
+        }
+      } else {
+        if(input$nj_tiles_show_4 == TRUE) {
+          if(!is.null(Vis$nj_max_x)) {
+            if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+              width <- 1
+            } else {
+              width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+            }
+          } else {
+            width <- 2
+          }
+          if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+            geom_fruit(
+              geom = geom_tile,
+              mapping = aes(fill= !!sym(input$nj_fruit_variable_4)),
+              offset = 0.15,
+              width = width * 3,
+              alpha = 1
+            )
+          } else {
+            geom_fruit(
+              geom = geom_tile,
+              mapping = aes(fill= !!sym(input$nj_fruit_variable_4)),
+              offset = 0.05,
+              width = width,
+              alpha = 1
+            )
+          }
+        } else {NULL}
+      }
+    }
+  })
+  
+  nj_fruit5 <- reactive({
+    if((!is.null(input$nj_tiles_show_5)) & 
+       (!is.null(input$nj_fruit_variable_5)) & 
+       (!is.null(input$nj_layout)) & 
+       (!is.null(input$nj_fruit_offset_circ_5)) & 
+       (!is.null(input$nj_fruit_width_circ_5)) & 
+       (!is.null(input$nj_fruit_alpha_5))) {
+      if(input$nj_tiles_show_5 == TRUE) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_5)),
+            offset = input$nj_fruit_offset_circ_5,
+            width = input$nj_fruit_width_circ_5,
+            alpha = input$nj_fruit_alpha_5
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_5)),
+            offset = input$nj_fruit_offset_circ_5,
+            width = input$nj_fruit_width_circ_5,
+            alpha = input$nj_fruit_alpha_5
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$nj_tiles_show_5 == TRUE) {
+        if(!is.null(Vis$nj_max_x)) {
+          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_5)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_5)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  # Xlim
+  nj_limit <- reactive({
+    if(input$nj_layout == "circular") {
+      xlim(input$nj_xlim, NA)
+    } else {NULL}
+  })
+  
+  # Treescale
+  nj_treescale <- reactive({
+    if(!input$nj_layout == "circular") {
+      if(input$nj_treescale_show == TRUE) {
+        geom_treescale(x = nj_treescale_x(),
+                       y = nj_treescale_y(),
+                       width = nj_treescale_width(),
+                       color = input$nj_color,
+                       fontsize = 4)
+      } else {NULL}
+    } else {NULL}
+  }) 
+  
+  # Treescale Y Position
+  nj_treescale_y <- reactive({
+    if(is.null(input$nj_treescale_y)) {
+      0
+    } else {input$nj_treescale_y}
+  })
+  
+  # Treescale X Position
+  nj_treescale_x <- reactive({
+    if(is.null(input$nj_treescale_x)) {
+      round(ceiling(Vis$nj_max_x) * 0.2, 0)
+    } else {input$nj_treescale_x}
+  })
+  
+  # Treescale width
+  nj_treescale_width <- reactive({
+    if(!is.null(input$nj_treescale_width)) {
+      input$nj_treescale_width
+    } else {
+      round(ceiling(Vis$nj_max_x) * 0.1, 0)
+    }
+  })
+  
+  # Label branches
+  nj_label_branch <- reactive({
+    if(!input$nj_layout == "circular" | !input$nj_layout == "inward") {
+      if(input$nj_show_branch_label == TRUE) {
+        geom_label(
+          aes(
+            x=!!sym("branch"), 
+            label= !!sym(input$nj_branch_label)),
+          fill = input$nj_branch_label_color,
+          size = nj_branch_size(),
+          label.r = unit(input$nj_branch_labelradius, "lines"),
+          nudge_x = input$nj_branch_x,
+          nudge_y = input$nj_branch_y,
+          fontface = input$nj_branchlab_fontface,
+          alpha = input$nj_branchlab_alpha
+        )
+      } else {NULL}
+    } else {NULL}
+  })
+  
+  # Branch label size
+  nj_branch_size <- reactive({
+    if(!is.null(input$nj_branch_size)) {
+      input$nj_branch_size
+    } else {
+      Vis$branch_size_nj
+    }
+  })
+  
+  # Rootedge
+  nj_rootedge <- reactive({
+    if(input$nj_rootedge_show == TRUE) {
+      if(is.null(input$nj_rootedge_length)) {
+        geom_rootedge(rootedge = round(ceiling(Vis$nj_max_x) * 0.05, 0),
+                      linetype = input$nj_rootedge_line)
+      } else {
+        geom_rootedge(rootedge = input$nj_rootedge_length,
+                      linetype = input$nj_rootedge_line)
+      }
+    } else {NULL}
+  })
+  
+  # Tippoints
+  nj_tippoint <- reactive({
+    if(input$nj_tippoint_show == TRUE | input$nj_tipcolor_mapping_show == TRUE | input$nj_tipshape_mapping_show == TRUE) {
+      if(input$nj_tipcolor_mapping_show == TRUE & input$nj_tipshape_mapping_show == FALSE) {
+        geom_tippoint(
+          aes(color = !!sym(input$nj_tipcolor_mapping)),
+          alpha = input$nj_tippoint_alpha,
+          shape = input$nj_tippoint_shape,
+          size = nj_tippoint_size()
+        )
+      } else if (input$nj_tipcolor_mapping_show == FALSE & input$nj_tipshape_mapping_show == TRUE) {
+        geom_tippoint(
+          aes(shape = !!sym(input$nj_tipshape_mapping)),
+          alpha = input$nj_tippoint_alpha,
+          color = input$nj_tippoint_color,
+          size = nj_tippoint_size()
+        )
+      } else if (input$nj_tipcolor_mapping_show == TRUE & input$nj_tipshape_mapping_show == TRUE) {
+        geom_tippoint(
+          aes(shape = !!sym(input$nj_tipshape_mapping),
+              color = !!sym(input$nj_tipcolor_mapping)),
+          alpha = input$nj_tippoint_alpha,
+          size = nj_tippoint_size()
+        )
+      } else {
+        geom_tippoint(
+          alpha = input$nj_tippoint_alpha,
+          colour = input$nj_tippoint_color,
+          fill = input$nj_tippoint_color,
+          shape = input$nj_tippoint_shape,
+          size = nj_tippoint_size()
+        )
+      } 
+    } else {NULL}
+  })
+  
+  # Nodepoints
+  nj_nodepoint <- reactive({
+    if(input$nj_nodepoint_show == TRUE) {
+      geom_nodepoint(
+        alpha = input$nj_nodepoint_alpha,
+        color = input$nj_nodepoint_color,
+        shape = input$nj_nodepoint_shape,
+        size = nj_nodepoint_size()
+      )
+    } else {NULL}
+  })
+  
+  # Nodepoint size
+  nj_nodepoint_size <- reactive({
+    if(!is.null(input$nj_nodepoint_size)) {
+      input$nj_nodepoint_size
+    } else {
+      Vis$nodepointsize_nj
+    }
+  })
+  
+  # NJ circular or not
+  nj_tiplab <- reactive({
+    if(input$nj_tiplab_show == TRUE) {
+      if(input$nj_layout == "circular") {
+        if(input$nj_mapping_show == TRUE) {
+          geom_tiplab(
+            nj_mapping_tiplab(), 
+            geom = "text",
+            size = nj_tiplab_size(),
+            alpha = input$nj_tiplab_alpha,
+            fontface = input$nj_tiplab_fontface,
+            align = as.logical(input$nj_align),
+            hjust = as.numeric(input$nj_tiplab_position),
+            check.overlap = input$nj_tiplab_overlap
+          )
+        } else {
+          geom_tiplab(
+            nj_mapping_tiplab(),
+            color = input$nj_tiplab_color,
+            geom = "text",
+            size = nj_tiplab_size(),
+            alpha = input$nj_tiplab_alpha,
+            fontface = input$nj_tiplab_fontface,
+            align = as.logical(input$nj_align),
+            hjust = as.numeric(input$nj_tiplab_position),
+            check.overlap = input$nj_tiplab_overlap
+          )
+        }
+      } else if (input$nj_layout == "inward") {
+        if(input$nj_mapping_show == TRUE) {
+          geom_tiplab(
+            nj_mapping_tiplab(), 
+            geom = "text",
+            size = nj_tiplab_size(),
+            alpha = input$nj_tiplab_alpha,
+            fontface = input$nj_tiplab_fontface,
+            align = as.logical(input$nj_align),
+            hjust = as.numeric(input$nj_tiplab_position_inw),
+            check.overlap = input$nj_tiplab_overlap
+          )
+        } else {
+          geom_tiplab(
+            nj_mapping_tiplab(),
+            color = input$nj_tiplab_color,
+            geom = "text",
+            size = nj_tiplab_size(),
+            alpha = input$nj_tiplab_alpha,
+            fontface = input$nj_tiplab_fontface,
+            align = as.logical(input$nj_align),
+            hjust = as.numeric(input$nj_tiplab_position_inw),
+            check.overlap = input$nj_tiplab_overlap
+          )
+        }
+      } else {
+        if(input$nj_mapping_show == TRUE) {
+          if(input$nj_geom == TRUE) {
+            geom_tiplab(
+              nj_mapping_tiplab(), 
+              geom = nj_geom(),
+              angle = input$nj_tiplab_angle,
+              size = nj_tiplab_size(),
+              alpha = input$nj_tiplab_alpha,
+              fontface = input$nj_tiplab_fontface,
+              align = as.logical(input$nj_align),
+              nudge_x = input$nj_tiplab_nudge_x,
+              check.overlap = input$nj_tiplab_overlap,
+              label.padding = unit(nj_tiplab_padding(), "lines"),
+              label.r = unit(input$nj_tiplab_labelradius, "lines"), 
+              fill = input$nj_tiplab_fill
+            )
+          } else {
+            geom_tiplab(
+              nj_mapping_tiplab(), 
+              geom = nj_geom(),
+              angle = input$nj_tiplab_angle,
+              size = nj_tiplab_size(),
+              alpha = input$nj_tiplab_alpha,
+              fontface = input$nj_tiplab_fontface,
+              align = as.logical(input$nj_align),
+              nudge_x = input$nj_tiplab_nudge_x,
+              check.overlap = input$nj_tiplab_overlap
+            )
+          }
+        } else {
+          if(input$nj_geom == TRUE) {
+            geom_tiplab(
+              nj_mapping_tiplab(), 
+              geom = nj_geom(),
+              color = input$nj_tiplab_color,
+              angle = input$nj_tiplab_angle,
+              size = nj_tiplab_size(),
+              alpha = input$nj_tiplab_alpha,
+              fontface = input$nj_tiplab_fontface,
+              align = as.logical(input$nj_align),
+              nudge_x = input$nj_tiplab_nudge_x,
+              check.overlap = input$nj_tiplab_overlap,
+              label.padding = unit(nj_tiplab_padding(), "lines"),
+              label.r = unit(input$nj_tiplab_labelradius, "lines"), 
+              fill = input$nj_tiplab_fill
+            )
+          } else {
+            geom_tiplab(
+              nj_mapping_tiplab(), 
+              geom = nj_geom(),
+              color = input$nj_tiplab_color,
+              angle = input$nj_tiplab_angle,
+              size = nj_tiplab_size(),
+              alpha = input$nj_tiplab_alpha,
+              fontface = input$nj_tiplab_fontface,
+              align = as.logical(input$nj_align),
+              nudge_x = input$nj_tiplab_nudge_x,
+              check.overlap = input$nj_tiplab_overlap
+            )
+          }
+        }
+      }
+    } else {NULL}
+  })
+  
+  # Tip panel size
+  nj_tiplab_padding <- reactive({
+    if(!is.null(input$nj_tiplab_padding)) {
+      input$nj_tiplab_padding
+    } else {
+      Vis$tiplab_padding_nj
+    }
+  })
+  
+  # Tiplab size
+  nj_tiplab_size <- reactive({
+    if(!is.null(input$nj_tiplab_size)) {
+      input$nj_tiplab_size
+    } else {
+      Vis$labelsize_nj
+    }
+  })
+  
+  # Tippoint size
+  nj_tippoint_size <- reactive({
+    if(!is.null(input$nj_tippoint_size)) {
+      input$nj_tippoint_size
+    } else {
+      Vis$tippointsize_nj
+    }
+  })
+  
+  # Show Label Panels?
+  nj_geom <- reactive({
+    if(input$nj_geom == TRUE) {
+      "label"
+    } else {"text"}
+  })
+  
+  # NJ Tiplab color
+  nj_mapping_tiplab <- reactive({
+    if(input$nj_mapping_show == TRUE) {
+      if(!is.null(input$nj_tiplab)) {
+        aes(label = !!sym(input$nj_tiplab),
+            color = !!sym(input$nj_color_mapping))
+      } else {
+        aes(label = !!sym("Assembly Name"),
+            color = !!sym(input$nj_color_mapping))
+      }
+    } else {
+      if(!is.null(input$nj_tiplab)) {
+        aes(label = !!sym(input$nj_tiplab))
+      } else {
+        aes(label = !!sym("Assembly Name"))
+      }
+    }
+  })
+  
+  # NJ Tree Layout
+  layout_nj <- reactive({
+    if(input$nj_layout == "inward") {
+      "circular"
+    } else {input$nj_layout}
+  })
+  
+  # NJ inward circular
+  nj_inward <- reactive({
+    if (input$nj_layout == "inward") {
+      layout_inward_circular(xlim = input$nj_inward_xlim)
+    } else {
+      NULL
+    }
+  })
+  
+  #### UPGMA ----
+  
+  upgma_tree <- reactive({
+    if(input$upgma_nodelabel_show == TRUE) {
+      ggtree(Vis$upgma, alpha = 0.2, layout = layout_upgma()) + 
+        geom_nodelab(aes(label = node), color = "#29303A", size = upgma_tiplab_size() + 1, hjust = 0.7) +
+        upgma_limit() +
+        upgma_inward() 
+    } else {
+      tree <-
+        ggtree(Vis$upgma, 
+               color = input$upgma_color,
+               layout = layout_upgma(),
+               ladderize = input$upgma_ladder) %<+% Vis$meta_upgma +
+        upgma_tiplab() +
+        upgma_tiplab_scale() + 
+        new_scale_color() +
+        upgma_limit() +
+        upgma_inward() +
+        upgma_label_branch() +
+        upgma_treescale() +
+        upgma_nodepoint() +
+        upgma_tippoint() +
+        upgma_tippoint_scale() + 
+        new_scale_color() +
+        upgma_clip_label() +
+        upgma_rootedge() +
+        upgma_clades() +
+        ggtitle(label = input$upgma_title,
+                subtitle = input$upgma_subtitle) +
+        theme_tree(bgcolor = input$upgma_bg) +
+        theme(plot.title = element_text(colour = input$upgma_title_color,
+                                        size = input$upgma_title_size),
+              plot.subtitle = element_text(colour = input$upgma_title_color,
+                                           size = input$upgma_subtitle_size),
+              legend.background = element_rect(fill = input$upgma_bg),
+              legend.direction = input$upgma_legend_orientation,
+              legend.title = element_text(color = input$upgma_color,
+                                          size = input$upgma_legend_size*1.2),
+              legend.title.align = 0.5,
+              legend.position = upgma_legend_pos(),
+              legend.text = element_text(color = input$upgma_color, 
+                                         size = input$upgma_legend_size),
+              legend.key = element_rect(fill = input$upgma_bg),
+              legend.box.spacing = unit(1.5, "cm"),
+              legend.key.size = unit(0.05*input$upgma_legend_size, 'cm'),
+              plot.background = element_rect(fill = input$upgma_bg, color = input$upgma_bg)) +
+        new_scale_fill() +
+        upgma_fruit() +
+        upgma_gradient() +
+        new_scale_fill() +
+        upgma_fruit2() +
+        upgma_gradient2() +
+        new_scale_fill() +
+        upgma_fruit3() +
+        upgma_gradient3() +
+        new_scale_fill() +
+        upgma_fruit4() +
+        upgma_gradient4() +
+        new_scale_fill() +
+        upgma_fruit5() +
+        upgma_gradient5() +
+        new_scale_fill() 
+      
+      # Add custom labels
+      if(length(Vis$custom_label_upgma) > 0) {
+        
+        for(i in Vis$custom_label_upgma[,1]) {
+          
+          if(!is.null(Vis$upgma_label_pos_x[[i]])) {
+            x_pos <- Vis$upgma_label_pos_x[[i]]
+          } else {
+            x_pos <- round(Vis$upgma_max_x / 2, 0)
+          }
+          
+          if(!is.null(Vis$upgma_label_pos_y[[i]])) {
+            y_pos <- Vis$upgma_label_pos_y[[i]]
+          } else {
+            y_pos <- sum(DB$data$Include) / 2
+          }
+          
+          if(!is.null(Vis$upgma_label_size[[i]])) {
+            size <- Vis$upgma_label_size[[i]]
+          } else {
+            size <- 5
+          }
+          
+          tree <- tree + annotate("text",
+                                  x = x_pos,
+                                  y = y_pos, 
+                                  label = i,
+                                  size = size)
+        }
+      }
+      
+      # Add heatmap
+      if(input$upgma_heatmap_show == TRUE & length(input$upgma_heatmap_select) > 0) {
+        if (!(any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)) & 
+              any(!sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)))) {
+          tree <- gheatmap.mod(tree, 
+                               data = select(Vis$meta_upgma, input$upgma_heatmap_select),
+                               offset = upgma_heatmap_offset(),
+                               width = upgma_heatmap_width(),
+                               legend_title = input$upgma_heatmap_title,
+                               colnames_angle = -upgma_colnames_angle(),
+                               colnames_offset_y = upgma_colnames_y(),
+                               colnames_color = input$upgma_color) +
+            upgma_heatmap_scale()
+        }
+      } 
+      
+      # Sizing control
+      Vis$upgma_plot <- ggplotify::as.ggplot(tree, 
+                                             scale = input$upgma_zoom,
+                                             hjust = input$upgma_h,
+                                             vjust = input$upgma_v)  
+      
+      # Correct background color if zoomed out
+      cowplot::ggdraw(Vis$upgma_plot) + 
+        theme(plot.background = element_rect(fill = input$upgma_bg, color = input$upgma_bg))
+    }
+  })
+  
+  # Heatmap width
+  upgma_heatmap_width <- reactive({
+    if(!is.null(input$upgma_heatmap_width)) {
+      input$upgma_heatmap_width
+    } else {
+      length_input <- length(input$upgma_heatmap_select)
+      if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
+        if(length_input < 3) {
+          0.1
+        } else {
+          if (length_input >= 3 && length_input <= 50) {
+            min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+          } else {
+            1.5
+          }   
+        }
+      } else {
+        if(length_input < 3) {
+          0.3
+        } else if (length_input >= 3 && length_input <= 27) {
+          min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          3
+        }
+      }
+    }
+  })
+  
+  # Heatmap column titles position
+  upgma_colnames_y <- reactive({
+    if(!is.null(input$upgma_colnames_y)) {
+      input$upgma_colnames_y
+    } else {
+      if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
+        0
+      } else {-1}
+    }
+  })
+  
+  # Heatmap column titles angle
+  upgma_colnames_angle <- reactive({
+    if(!is.null(input$upgma_colnames_angle)) {
+      input$upgma_colnames_angle
+    } else {
+      if(!is.null(input$upgma_layout)) {
+        if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
+          90
+        } else {-90}
+      } else {-90}
+    }
+  })
+  
+  # Heatmap scale
+  upgma_heatmap_scale <- reactive({
+    if(!is.null(input$upgma_heatmap_scale) & !is.null(input$upgma_heatmap_div_mid)) {
+      if(input$upgma_heatmap_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$upgma_heatmap_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$upgma_heatmap_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_heatmap_select]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_heatmap_select]), na.rm = TRUE)
+        }
+        scale_fill_gradient2(low = brewer.pal(3, input$upgma_heatmap_scale)[1],
+                             mid = brewer.pal(3, input$upgma_heatmap_scale)[2],
+                             high = brewer.pal(3, input$upgma_heatmap_scale)[3],
+                             midpoint = midpoint,
+                             name = input$upgma_heatmap_title)
+      } else {
+        if(input$upgma_heatmap_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_upgma[input$upgma_heatmap_select])) == "numeric") {
+            if(input$upgma_heatmap_scale == "magma") {
+              scale_fill_viridis(option = "A",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "inferno") {
+              scale_fill_viridis(option = "B",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "plasma") {
+              scale_fill_viridis(option = "C",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "viridis") {
+              scale_fill_viridis(option = "D",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "cividis") {
+              scale_fill_viridis(option = "E",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "rocket") {
+              scale_fill_viridis(option = "F",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "mako") {
+              scale_fill_viridis(option = "G",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "turbo") {
+              scale_fill_viridis(option = "H",
+                                 name = input$upgma_heatmap_title)
+            } 
+          } else {
+            if(input$upgma_heatmap_scale == "magma") {
+              scale_fill_viridis(discrete = TRUE, option = "A",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "inferno") {
+              scale_fill_viridis(discrete = TRUE, option = "B",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "plasma") {
+              scale_fill_viridis(discrete = TRUE, option = "C",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "viridis") {
+              scale_fill_viridis(discrete = TRUE, option = "D",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "cividis") {
+              scale_fill_viridis(discrete = TRUE, option = "E",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "rocket") {
+              scale_fill_viridis(discrete = TRUE, option = "F",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "mako") {
+              scale_fill_viridis(discrete = TRUE, option = "G",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "turbo") {
+              scale_fill_viridis(discrete = TRUE, option = "H",
+                                 name = input$upgma_heatmap_title)
+            } 
+          }
+        } else {
+          scale_fill_brewer(palette = input$upgma_heatmap_scale,
+                            name = input$upgma_heatmap_title)
+        }
+      }
+    }
+  })
+  
+  # Tippoint Scale
+  upgma_tippoint_scale <- reactive({
+    if(!is.null(input$upgma_tippoint_scale) & !is.null(input$upgma_tipcolor_mapping_div_mid)) {
+      if(input$upgma_tippoint_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$upgma_tipcolor_mapping_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$upgma_tipcolor_mapping_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_tipcolor_mapping]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_tipcolor_mapping]), na.rm = TRUE)
+        }
+        scale_color_gradient2(low = brewer.pal(3, input$upgma_tippoint_scale)[1],
+                              mid = brewer.pal(3, input$upgma_tippoint_scale)[2],
+                              high = brewer.pal(3, input$upgma_tippoint_scale)[3],
+                              midpoint = midpoint)
+      } else {
+        if(input$upgma_tippoint_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping])) == "numeric") {
+            if(input$upgma_tippoint_scale == "magma") {
+              scale_color_viridis(option = "A")
+            } else if(input$upgma_tippoint_scale == "inferno") {
+              scale_color_viridis(option = "B")
+            } else if(input$upgma_tippoint_scale == "plasma") {
+              scale_color_viridis(option = "C")
+            } else if(input$upgma_tippoint_scale == "viridis") {
+              scale_color_viridis(option = "D")
+            } else if(input$upgma_tippoint_scale == "cividis") {
+              scale_color_viridis(option = "E")
+            } else if(input$upgma_tippoint_scale == "rocket") {
+              scale_color_viridis(option = "F")
+            } else if(input$upgma_tippoint_scale == "mako") {
+              scale_color_viridis(option = "G")
+            } else if(input$upgma_tippoint_scale == "turbo") {
+              scale_color_viridis(option = "H")
+            } 
+          } else {
+            if(input$upgma_tippoint_scale == "magma") {
+              scale_color_viridis(discrete = TRUE, option = "A")
+            } else if(input$upgma_tippoint_scale == "inferno") {
+              scale_color_viridis(discrete = TRUE, option = "B")
+            } else if(input$upgma_tippoint_scale == "plasma") {
+              scale_color_viridis(discrete = TRUE, option = "C")
+            } else if(input$upgma_tippoint_scale == "viridis") {
+              scale_color_viridis(discrete = TRUE, option = "D")
+            } else if(input$upgma_tippoint_scale == "cividis") {
+              scale_color_viridis(discrete = TRUE, option = "E")
+            } else if(input$upgma_tippoint_scale == "rocket") {
+              scale_color_viridis(discrete = TRUE, option = "F")
+            } else if(input$upgma_tippoint_scale == "mako") {
+              scale_color_viridis(discrete = TRUE, option = "G")
+            } else if(input$upgma_tippoint_scale == "turbo") {
+              scale_color_viridis(discrete = TRUE, option = "H")
+            } 
+          }
+        } else {
+          scale_color_brewer(palette = input$upgma_tippoint_scale)
+        }
+      }
+    }
+  })
+  
+  # Tiplab Scale
+  upgma_tiplab_scale <- reactive({
+    if(!is.null(input$upgma_tiplab_scale) & !is.null(input$upgma_color_mapping_div_mid)) {
+      if(input$upgma_tiplab_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$upgma_color_mapping_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$upgma_color_mapping_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_color_mapping]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_color_mapping]), na.rm = TRUE)
+        }
+        scale_color_gradient2(low = brewer.pal(3, input$upgma_tiplab_scale)[1],
+                              mid = brewer.pal(3, input$upgma_tiplab_scale)[2],
+                              high = brewer.pal(3, input$upgma_tiplab_scale)[3],
+                              midpoint = midpoint)
+      } else {
+        if(input$upgma_tiplab_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_upgma[input$upgma_color_mapping])) == "numeric") {
+            if(input$upgma_tiplab_scale == "magma") {
+              scale_color_viridis(option = "A")
+            } else if(input$upgma_tiplab_scale == "inferno") {
+              scale_color_viridis(option = "B")
+            } else if(input$upgma_tiplab_scale == "plasma") {
+              scale_color_viridis(option = "C")
+            } else if(input$upgma_tiplab_scale == "viridis") {
+              scale_color_viridis(option = "D")
+            } else if(input$upgma_tiplab_scale == "cividis") {
+              scale_color_viridis(option = "E")
+            } else if(input$upgma_tiplab_scale == "rocket") {
+              scale_color_viridis(option = "F")
+            } else if(input$upgma_tiplab_scale == "mako") {
+              scale_color_viridis(option = "G")
+            } else if(input$upgma_tiplab_scale == "turbo") {
+              scale_color_viridis(option = "H")
+            } 
+          } else {
+            if(input$upgma_tiplab_scale == "magma") {
+              scale_color_viridis(discrete = TRUE, option = "A")
+            } else if(input$upgma_tiplab_scale == "inferno") {
+              scale_color_viridis(discrete = TRUE, option = "B")
+            } else if(input$upgma_tiplab_scale == "plasma") {
+              scale_color_viridis(discrete = TRUE, option = "C")
+            } else if(input$upgma_tiplab_scale == "viridis") {
+              scale_color_viridis(discrete = TRUE, option = "D")
+            } else if(input$upgma_tiplab_scale == "cividis") {
+              scale_color_viridis(discrete = TRUE, option = "E")
+            } else if(input$upgma_tiplab_scale == "rocket") {
+              scale_color_viridis(discrete = TRUE, option = "F")
+            } else if(input$upgma_tiplab_scale == "mako") {
+              scale_color_viridis(discrete = TRUE, option = "G")
+            } else if(input$upgma_tiplab_scale == "turbo") {
+              scale_color_viridis(discrete = TRUE, option = "H")
+            } 
+          }
+        } else {
+          scale_color_brewer(palette = input$upgma_tiplab_scale)
+        }
+      }
+    }
+  })
+  
+  # Clade Highlight
+  upgma_clades <- reactive({
+    if(!is.null(input$upgma_parentnode)) {
+      if(!length(input$upgma_parentnode) == 0) {
+        if(length(input$upgma_parentnode) == 1) {
+          fill <- input$upgma_clade_scale
+        } else if (length(input$upgma_parentnode) == 2) {
+          if(startsWith(input$upgma_clade_scale, "#")) {
+            fill <- brewer.pal(3, "Set1")[1:2]
+          } else {
+            fill <- brewer.pal(3, input$upgma_clade_scale)[1:2]
+          }
+        } else {
+          fill <- brewer.pal(length(input$upgma_parentnode), input$upgma_clade_scale)
+        }
+        geom_hilight(node = as.numeric(input$upgma_parentnode),
+                     fill = fill,
+                     type = input$upgma_clade_type,
+                     to.bottom = TRUE)
+      } else {NULL}
+    }
+  })
+  
+  # Legend Position
+  upgma_legend_pos <- reactive({
+    if(!is.null(input$upgma_legend_x) & !is.null(input$upgma_legend_y)) {
+      c(input$upgma_legend_x, input$upgma_legend_y)
+    } else {
+      c(0.1, 1)
+    }
+  })
+  
+  # Heatmap offset
+  upgma_heatmap_offset <- reactive({
+    if(is.null(input$upgma_heatmap_offset)) {
+      0
+    } else {input$upgma_heatmap_offset}
+  })
+  
+  # Tiles fill color gradient
+  upgma_gradient <- reactive({
+    if(!is.null(input$upgma_tiles_show_1) & 
+       !is.null(input$upgma_fruit_variable) & 
+       !is.null(input$upgma_tiles_scale_1) &
+       !is.null(input$upgma_tiles_mapping_div_mid_1)) {
+      if(input$upgma_tiles_show_1 == TRUE) {
+        if(input$upgma_tiles_scale_1 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$upgma_tiles_mapping_div_mid_1 == "Zero") {
+            midpoint <- 0
+          } else if(input$upgma_tiles_mapping_div_mid_1 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable]), na.rm = TRUE)
+          }
+          scale_fill_gradient2(low = brewer.pal(3, input$upgma_tiles_scale_1)[1],
+                               mid = brewer.pal(3, input$upgma_tiles_scale_1)[2],
+                               high = brewer.pal(3, input$upgma_tiles_scale_1)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$upgma_tiles_scale_1 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
+              if(input$upgma_tiles_scale_1 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$upgma_tiles_scale_1 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$upgma_tiles_scale_1 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$upgma_tiles_scale_1 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$upgma_tiles_scale_1 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$upgma_tiles_scale_1 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$upgma_tiles_scale_1 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$upgma_tiles_scale_1 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$upgma_tiles_scale_1 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$upgma_tiles_scale_1 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$upgma_tiles_scale_1 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$upgma_tiles_scale_1 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$upgma_tiles_scale_1 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$upgma_tiles_scale_1 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$upgma_tiles_scale_1 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$upgma_tiles_scale_1 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$upgma_tiles_scale_1)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_gradient2 <- reactive({
+    if(!is.null(input$upgma_tiles_show_2) & 
+       !is.null(input$upgma_fruit_variable_2) & 
+       !is.null(input$upgma_tiles_scale_2) &
+       !is.null(input$upgma_tiles_mapping_div_mid_2)) {
+      if(input$upgma_tiles_show_2 == TRUE) {
+        if(input$upgma_tiles_scale_2 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$upgma_tiles_mapping_div_mid_2 == "Zero") {
+            midpoint <- 0
+          } else if(input$upgma_tiles_mapping_div_mid_2 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_2]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_2]), na.rm = TRUE)
+          }
+          scale_fill_gradient2(low = brewer.pal(3, input$upgma_tiles_scale_2)[1],
+                               mid = brewer.pal(3, input$upgma_tiles_scale_2)[2],
+                               high = brewer.pal(3, input$upgma_tiles_scale_2)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$upgma_tiles_scale_2 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2])) == "numeric") {
+              if(input$upgma_tiles_scale_2 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$upgma_tiles_scale_2 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$upgma_tiles_scale_2 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$upgma_tiles_scale_2 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$upgma_tiles_scale_2 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$upgma_tiles_scale_2 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$upgma_tiles_scale_2 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$upgma_tiles_scale_2 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$upgma_tiles_scale_2 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$upgma_tiles_scale_2 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$upgma_tiles_scale_2 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$upgma_tiles_scale_2 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$upgma_tiles_scale_2 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$upgma_tiles_scale_2 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$upgma_tiles_scale_2 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$upgma_tiles_scale_2 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$upgma_tiles_scale_2)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_gradient3 <- reactive({
+    if(!is.null(input$upgma_tiles_show_3) & 
+       !is.null(input$upgma_fruit_variable_3) & 
+       !is.null(input$upgma_tiles_scale_3) &
+       !is.null(input$upgma_tiles_mapping_div_mid_3)) {
+      if(input$upgma_tiles_show_3 == TRUE) {
+        if(input$upgma_tiles_scale_3 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$upgma_tiles_mapping_div_mid_3 == "Zero") {
+            midpoint <- 0
+          } else if(input$upgma_tiles_mapping_div_mid_3 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_3]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_3]), na.rm = TRUE)
+          }
+          scale_fill_gradient3(low = brewer.pal(3, input$upgma_tiles_scale_3)[1],
+                               mid = brewer.pal(3, input$upgma_tiles_scale_3)[2],
+                               high = brewer.pal(3, input$upgma_tiles_scale_3)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$upgma_tiles_scale_3 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3])) == "numeric") {
+              if(input$upgma_tiles_scale_3 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$upgma_tiles_scale_3 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$upgma_tiles_scale_3 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$upgma_tiles_scale_3 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$upgma_tiles_scale_3 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$upgma_tiles_scale_3 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$upgma_tiles_scale_3 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$upgma_tiles_scale_3 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$upgma_tiles_scale_3 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$upgma_tiles_scale_3 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$upgma_tiles_scale_3 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$upgma_tiles_scale_3 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$upgma_tiles_scale_3 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$upgma_tiles_scale_3 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$upgma_tiles_scale_3 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$upgma_tiles_scale_3 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$upgma_tiles_scale_3)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_gradient4 <- reactive({
+    if(!is.null(input$upgma_tiles_show_4) & 
+       !is.null(input$upgma_fruit_variable_4) & 
+       !is.null(input$upgma_tiles_scale_4) &
+       !is.null(input$upgma_tiles_mapping_div_mid_4)) {
+      if(input$upgma_tiles_show_4 == TRUE) {
+        if(input$upgma_tiles_scale_4 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$upgma_tiles_mapping_div_mid_4 == "Zero") {
+            midpoint <- 0
+          } else if(input$upgma_tiles_mapping_div_mid_4 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_4]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_4]), na.rm = TRUE)
+          }
+          scale_fill_gradient4(low = brewer.pal(3, input$upgma_tiles_scale_4)[1],
+                               mid = brewer.pal(3, input$upgma_tiles_scale_4)[2],
+                               high = brewer.pal(3, input$upgma_tiles_scale_4)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$upgma_tiles_scale_4 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
+              if(input$upgma_tiles_scale_4 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$upgma_tiles_scale_4 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$upgma_tiles_scale_4 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$upgma_tiles_scale_4 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$upgma_tiles_scale_4 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$upgma_tiles_scale_4 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$upgma_tiles_scale_4 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$upgma_tiles_scale_4 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$upgma_tiles_scale_4 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$upgma_tiles_scale_4 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$upgma_tiles_scale_4 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$upgma_tiles_scale_4 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$upgma_tiles_scale_4 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$upgma_tiles_scale_4 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$upgma_tiles_scale_4 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$upgma_tiles_scale_4 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$upgma_tiles_scale_4)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_gradient5 <- reactive({
+    if(!is.null(input$upgma_tiles_show_5) & 
+       !is.null(input$upgma_fruit_variable_5) & 
+       !is.null(input$upgma_tiles_scale_5) &
+       !is.null(input$upgma_tiles_mapping_div_mid_5)) {
+      if(input$upgma_tiles_show_5 == TRUE) {
+        if(input$upgma_tiles_scale_5 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$upgma_tiles_mapping_div_mid_5 == "Zero") {
+            midpoint <- 0
+          } else if(input$upgma_tiles_mapping_div_mid_5 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_5]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_5]), na.rm = TRUE)
+          }
+          scale_fill_gradient5(low = brewer.pal(3, input$upgma_tiles_scale_5)[1],
+                               mid = brewer.pal(3, input$upgma_tiles_scale_5)[2],
+                               high = brewer.pal(3, input$upgma_tiles_scale_5)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$upgma_tiles_scale_5 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5])) == "numeric") {
+              if(input$upgma_tiles_scale_5 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$upgma_tiles_scale_5 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$upgma_tiles_scale_5 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$upgma_tiles_scale_5 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$upgma_tiles_scale_5 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$upgma_tiles_scale_5 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$upgma_tiles_scale_5 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$upgma_tiles_scale_5 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$upgma_tiles_scale_5 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$upgma_tiles_scale_5 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$upgma_tiles_scale_5 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$upgma_tiles_scale_5 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$upgma_tiles_scale_5 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$upgma_tiles_scale_5 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$upgma_tiles_scale_5 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$upgma_tiles_scale_5 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$upgma_tiles_scale_5)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  # No label clip off for linear upgma tree
+  upgma_clip_label <- reactive({
+    if(!(input$upgma_layout == "circular" | input$upgma_layout == "inward")) {
+      coord_cartesian(clip = "off")
+    } else {NULL}
+  })
+  
+  # Geom Fruit
+  upgma_fruit <- reactive({
+    if((!is.null(input$upgma_tiles_show_1)) & 
+       (!is.null(input$upgma_fruit_variable)) & 
+       (!is.null(input$upgma_layout)) & 
+       (!is.null(input$upgma_fruit_offset_circ)) & 
+       (!is.null(input$upgma_fruit_width_circ)) & 
+       (!is.null(input$upgma_fruit_alpha))) {
+      if(input$upgma_tiles_show_1 == TRUE) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
+            offset = input$upgma_fruit_offset_circ,
+            width = input$upgma_fruit_width_circ,
+            alpha = input$upgma_fruit_alpha
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
+            offset = input$upgma_fruit_offset_circ,
+            width = input$upgma_fruit_width_circ,
+            alpha = input$upgma_fruit_alpha
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$upgma_tiles_show_1 == TRUE) {
+        if(!is.null(Vis$upgma_max_x)) {
+          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
+            offset = 0,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
+            offset = 0,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  # Geom Fruit
+  upgma_fruit2 <- reactive({
+    if((!is.null(input$upgma_tiles_show_2)) & 
+       (!is.null(input$upgma_fruit_variable_2)) & 
+       (!is.null(input$upgma_layout)) & 
+       (!is.null(input$upgma_fruit_offset_circ_2)) & 
+       (!is.null(input$upgma_fruit_width_circ_2)) & 
+       (!is.null(input$upgma_fruit_alpha_2))) {
+      if(input$upgma_tiles_show_2 == TRUE) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_2)),
+            offset = input$upgma_fruit_offset_circ_2,
+            width = input$upgma_fruit_width_circ_2,
+            alpha = input$upgma_fruit_alpha_2
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_2)),
+            offset = input$upgma_fruit_offset_circ_2,
+            width = input$upgma_fruit_width_circ_2,
+            alpha = input$upgma_fruit_alpha_2
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$upgma_tiles_show_2 == TRUE) {
+        if(!is.null(Vis$upgma_max_x)) {
+          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_2)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_2)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_fruit3 <- reactive({
+    if((!is.null(input$upgma_tiles_show_3)) & 
+       (!is.null(input$upgma_fruit_variable_3)) & 
+       (!is.null(input$upgma_layout)) & 
+       (!is.null(input$upgma_fruit_offset_circ_3)) & 
+       (!is.null(input$upgma_fruit_width_circ_3)) & 
+       (!is.null(input$upgma_fruit_alpha_3))) {
+      if(input$upgma_tiles_show_3 == TRUE) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_3)),
+            offset = input$upgma_fruit_offset_circ_3,
+            width = input$upgma_fruit_width_circ_3,
+            alpha = input$upgma_fruit_alpha_3
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_3)),
+            offset = input$upgma_fruit_offset_circ_3,
+            width = input$upgma_fruit_width_circ_3,
+            alpha = input$upgma_fruit_alpha_3
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$upgma_tiles_show_3 == TRUE) {
+        if(!is.null(Vis$upgma_max_x)) {
+          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_3)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_3)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_fruit4 <- reactive({
+    if((!is.null(input$upgma_tiles_show_4)) & 
+       (!is.null(input$upgma_fruit_variable_4)) & 
+       (!is.null(input$upgma_layout)) & 
+       (!is.null(input$upgma_fruit_offset_circ_4)) & 
+       (!is.null(input$upgma_fruit_width_circ_4)) & 
+       (!is.null(input$upgma_fruit_alpha_4))) {
+      if(input$upgma_tiles_show_4 == TRUE) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_4)),
+            offset = input$upgma_fruit_offset_circ_4,
+            width = input$upgma_fruit_width_circ_4,
+            alpha = input$upgma_fruit_alpha_4
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_4)),
+            offset = input$upgma_fruit_offset_circ_4,
+            width = input$upgma_fruit_width_circ_4,
+            alpha = input$upgma_fruit_alpha_4
+          )
+        }
+      } else {
+        if(input$upgma_tiles_show_4 == TRUE) {
+          if(!is.null(Vis$upgma_max_x)) {
+            if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+              width <- 1
+            } else {
+              width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+            }
+          } else {
+            width <- 2
+          }
+          if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+            geom_fruit(
+              geom = geom_tile,
+              mapping = aes(fill= !!sym(input$upgma_fruit_variable_4)),
+              offset = 0.15,
+              width = width * 3,
+              alpha = 1
+            )
+          } else {
+            geom_fruit(
+              geom = geom_tile,
+              mapping = aes(fill= !!sym(input$upgma_fruit_variable_4)),
+              offset = 0.05,
+              width = width,
+              alpha = 1
+            )
+          }
+        } else {NULL}
+      }
+    }
+  })
+  
+  upgma_fruit5 <- reactive({
+    if((!is.null(input$upgma_tiles_show_5)) & 
+       (!is.null(input$upgma_fruit_variable_5)) & 
+       (!is.null(input$upgma_layout)) & 
+       (!is.null(input$upgma_fruit_offset_circ_5)) & 
+       (!is.null(input$upgma_fruit_width_circ_5)) & 
+       (!is.null(input$upgma_fruit_alpha_5))) {
+      if(input$upgma_tiles_show_5 == TRUE) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_5)),
+            offset = input$upgma_fruit_offset_circ_5,
+            width = input$upgma_fruit_width_circ_5,
+            alpha = input$upgma_fruit_alpha_5
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_5)),
+            offset = input$upgma_fruit_offset_circ_5,
+            width = input$upgma_fruit_width_circ_5,
+            alpha = input$upgma_fruit_alpha_5
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$upgma_tiles_show_5 == TRUE) {
+        if(!is.null(Vis$upgma_max_x)) {
+          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_5)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_5)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  # Xlim
+  upgma_limit <- reactive({
+    if(input$upgma_layout == "circular") {
+      xlim(input$upgma_xlim, NA)
+    } else {NULL}
+  })
+  
+  # Treescale
+  upgma_treescale <- reactive({
+    if(!input$upgma_layout == "circular") {
+      if(input$upgma_treescale_show == TRUE) {
+        geom_treescale(x = upgma_treescale_x(),
+                       y = upgma_treescale_y(),
+                       width = upgma_treescale_width(),
+                       color = input$upgma_color,
+                       fontsize = 4)
+      } else {NULL}
+    } else {NULL}
+  }) 
+  
+  # Treescale Y Position
+  upgma_treescale_y <- reactive({
+    if(is.null(input$upgma_treescale_y)) {
+      0
+    } else {input$upgma_treescale_y}
+  })
+  
+  # Treescale X Position
+  upgma_treescale_x <- reactive({
+    if(is.null(input$upgma_treescale_x)) {
+      round(ceiling(Vis$upgma_max_x) * 0.2, 0)
+    } else {input$upgma_treescale_x}
+  })
+  
+  # Treescale width
+  upgma_treescale_width <- reactive({
+    if(!is.null(input$upgma_treescale_width)) {
+      input$upgma_treescale_width
+    } else {
+      round(ceiling(Vis$upgma_max_x) * 0.1, 0)
+    }
+  })
+  
+  # Label branches
+  upgma_label_branch <- reactive({
+    if(!input$upgma_layout == "circular" | !input$upgma_layout == "inward") {
+      if(input$upgma_show_branch_label == TRUE) {
+        geom_label(
+          aes(
+            x=!!sym("branch"), 
+            label= !!sym(input$upgma_branch_label)),
+          fill = input$upgma_branch_label_color,
+          size = upgma_branch_size(),
+          label.r = unit(input$upgma_branch_labelradius, "lines"),
+          nudge_x = input$upgma_branch_x,
+          nudge_y = input$upgma_branch_y,
+          fontface = input$upgma_branchlab_fontface,
+          alpha = input$upgma_branchlab_alpha
+        )
+      } else {NULL}
+    } else {NULL}
+  })
+  
+  # Branch label size
+  upgma_branch_size <- reactive({
+    if(!is.null(input$upgma_branch_size)) {
+      input$upgma_branch_size
+    } else {
+      Vis$branch_size_upgma
+    }
+  })
+  
+  # Rootedge
+  upgma_rootedge <- reactive({
+    if(input$upgma_rootedge_show == TRUE) {
+      if(is.null(input$upgma_rootedge_length)) {
+        geom_rootedge(rootedge = round(ceiling(Vis$upgma_max_x) * 0.05, 0),
+                      linetype = input$upgma_rootedge_line)
+      } else {
+        geom_rootedge(rootedge = input$upgma_rootedge_length,
+                      linetype = input$upgma_rootedge_line)
+      }
+    } else {NULL}
+  })
+  
+  # Tippoints
+  upgma_tippoint <- reactive({
+    if(input$upgma_tippoint_show == TRUE | input$upgma_tipcolor_mapping_show == TRUE | input$upgma_tipshape_mapping_show == TRUE) {
+      if(input$upgma_tipcolor_mapping_show == TRUE & input$upgma_tipshape_mapping_show == FALSE) {
+        geom_tippoint(
+          aes(color = !!sym(input$upgma_tipcolor_mapping)),
+          alpha = input$upgma_tippoint_alpha,
+          shape = input$upgma_tippoint_shape,
+          size = upgma_tippoint_size()
+        )
+      } else if (input$upgma_tipcolor_mapping_show == FALSE & input$upgma_tipshape_mapping_show == TRUE) {
+        geom_tippoint(
+          aes(shape = !!sym(input$upgma_tipshape_mapping)),
+          alpha = input$upgma_tippoint_alpha,
+          color = input$upgma_tippoint_color,
+          size = upgma_tippoint_size()
+        )
+      } else if (input$upgma_tipcolor_mapping_show == TRUE & input$upgma_tipshape_mapping_show == TRUE) {
+        geom_tippoint(
+          aes(shape = !!sym(input$upgma_tipshape_mapping),
+              color = !!sym(input$upgma_tipcolor_mapping)),
+          alpha = input$upgma_tippoint_alpha,
+          size = upgma_tippoint_size()
+        )
+      } else {
+        geom_tippoint(
+          alpha = input$upgma_tippoint_alpha,
+          colour = input$upgma_tippoint_color,
+          fill = input$upgma_tippoint_color,
+          shape = input$upgma_tippoint_shape,
+          size = upgma_tippoint_size()
+        )
+      } 
+    } else {NULL}
+  })
+  
+  # Nodepoints
+  upgma_nodepoint <- reactive({
+    if(input$upgma_nodepoint_show == TRUE) {
+      geom_nodepoint(
+        alpha = input$upgma_nodepoint_alpha,
+        color = input$upgma_nodepoint_color,
+        shape = input$upgma_nodepoint_shape,
+        size = upgma_nodepoint_size()
+      )
+    } else {NULL}
+  })
+  
+  # Nodepoint size
+  upgma_nodepoint_size <- reactive({
+    if(!is.null(input$upgma_nodepoint_size)) {
+      input$upgma_nodepoint_size
+    } else {
+      Vis$nodepointsize_upgma
+    }
+  })
+  
+  # upgma circular or not
+  upgma_tiplab <- reactive({
+    if(input$upgma_tiplab_show == TRUE) {
+      if(input$upgma_layout == "circular") {
+        if(input$upgma_mapping_show == TRUE) {
+          geom_tiplab(
+            upgma_mapping_tiplab(), 
+            geom = "text",
+            size = upgma_tiplab_size(),
+            alpha = input$upgma_tiplab_alpha,
+            fontface = input$upgma_tiplab_fontface,
+            align = as.logical(input$upgma_align),
+            hjust = as.numeric(input$upgma_tiplab_position),
+            check.overlap = input$upgma_tiplab_overlap
+          )
+        } else {
+          geom_tiplab(
+            upgma_mapping_tiplab(),
+            color = input$upgma_tiplab_color,
+            geom = "text",
+            size = upgma_tiplab_size(),
+            alpha = input$upgma_tiplab_alpha,
+            fontface = input$upgma_tiplab_fontface,
+            align = as.logical(input$upgma_align),
+            hjust = as.numeric(input$upgma_tiplab_position),
+            check.overlap = input$upgma_tiplab_overlap
+          )
+        }
+      } else if (input$upgma_layout == "inward") {
+        if(input$upgma_mapping_show == TRUE) {
+          geom_tiplab(
+            upgma_mapping_tiplab(), 
+            geom = "text",
+            size = upgma_tiplab_size(),
+            alpha = input$upgma_tiplab_alpha,
+            fontface = input$upgma_tiplab_fontface,
+            align = as.logical(input$upgma_align),
+            hjust = as.numeric(input$upgma_tiplab_position_inw),
+            check.overlap = input$upgma_tiplab_overlap
+          )
+        } else {
+          geom_tiplab(
+            upgma_mapping_tiplab(),
+            color = input$upgma_tiplab_color,
+            geom = "text",
+            size = upgma_tiplab_size(),
+            alpha = input$upgma_tiplab_alpha,
+            fontface = input$upgma_tiplab_fontface,
+            align = as.logical(input$upgma_align),
+            hjust = as.numeric(input$upgma_tiplab_position_inw),
+            check.overlap = input$upgma_tiplab_overlap
+          )
+        }
+      } else {
+        if(input$upgma_mapping_show == TRUE) {
+          if(input$upgma_geom == TRUE) {
+            geom_tiplab(
+              upgma_mapping_tiplab(), 
+              geom = upgma_geom(),
+              angle = input$upgma_tiplab_angle,
+              size = upgma_tiplab_size(),
+              alpha = input$upgma_tiplab_alpha,
+              fontface = input$upgma_tiplab_fontface,
+              align = as.logical(input$upgma_align),
+              nudge_x = input$upgma_tiplab_nudge_x,
+              check.overlap = input$upgma_tiplab_overlap,
+              label.padding = unit(upgma_tiplab_padding(), "lines"),
+              label.r = unit(input$upgma_tiplab_labelradius, "lines"), 
+              fill = input$upgma_tiplab_fill
+            )
+          } else {
+            geom_tiplab(
+              upgma_mapping_tiplab(), 
+              geom = upgma_geom(),
+              angle = input$upgma_tiplab_angle,
+              size = upgma_tiplab_size(),
+              alpha = input$upgma_tiplab_alpha,
+              fontface = input$upgma_tiplab_fontface,
+              align = as.logical(input$upgma_align),
+              nudge_x = input$upgma_tiplab_nudge_x,
+              check.overlap = input$upgma_tiplab_overlap
+            )
+          }
+        } else {
+          if(input$upgma_geom == TRUE) {
+            geom_tiplab(
+              upgma_mapping_tiplab(), 
+              geom = upgma_geom(),
+              color = input$upgma_tiplab_color,
+              angle = input$upgma_tiplab_angle,
+              size = upgma_tiplab_size(),
+              alpha = input$upgma_tiplab_alpha,
+              fontface = input$upgma_tiplab_fontface,
+              align = as.logical(input$upgma_align),
+              nudge_x = input$upgma_tiplab_nudge_x,
+              check.overlap = input$upgma_tiplab_overlap,
+              label.padding = unit(upgma_tiplab_padding(), "lines"),
+              label.r = unit(input$upgma_tiplab_labelradius, "lines"), 
+              fill = input$upgma_tiplab_fill
+            )
+          } else {
+            geom_tiplab(
+              upgma_mapping_tiplab(), 
+              geom = upgma_geom(),
+              color = input$upgma_tiplab_color,
+              angle = input$upgma_tiplab_angle,
+              size = upgma_tiplab_size(),
+              alpha = input$upgma_tiplab_alpha,
+              fontface = input$upgma_tiplab_fontface,
+              align = as.logical(input$upgma_align),
+              nudge_x = input$upgma_tiplab_nudge_x,
+              check.overlap = input$upgma_tiplab_overlap
+            )
+          }
+        }
+      }
+    } else {NULL}
+  })
+  
+  # Tip panel size
+  upgma_tiplab_padding <- reactive({
+    if(!is.null(input$upgma_tiplab_padding)) {
+      input$upgma_tiplab_padding
+    } else {
+      Vis$tiplab_padding_upgma
+    }
+  })
+  
+  # Tiplab size
+  upgma_tiplab_size <- reactive({
+    if(!is.null(input$upgma_tiplab_size)) {
+      input$upgma_tiplab_size
+    } else {
+      Vis$labelsize_upgma
+    }
+  })
+  
+  # Tippoint size
+  upgma_tippoint_size <- reactive({
+    if(!is.null(input$upgma_tippoint_size)) {
+      input$upgma_tippoint_size
+    } else {
+      Vis$tippointsize_upgma
+    }
+  })
+  
+  # Show Label Panels?
+  upgma_geom <- reactive({
+    if(input$upgma_geom == TRUE) {
+      "label"
+    } else {"text"}
+  })
+  
+  # upgma Tiplab color
+  upgma_mapping_tiplab <- reactive({
+    if(input$upgma_mapping_show == TRUE) {
+      if(!is.null(input$upgma_tiplab)) {
+        aes(label = !!sym(input$upgma_tiplab),
+            color = !!sym(input$upgma_color_mapping))
+      } else {
+        aes(label = !!sym("Assembly Name"),
+            color = !!sym(input$upgma_color_mapping))
+      }
+    } else {
+      if(!is.null(input$upgma_tiplab)) {
+        aes(label = !!sym(input$upgma_tiplab))
+      } else {
+        aes(label = !!sym("Assembly Name"))
+      }
+    }
+  })
+  
+  # upgma Tree Layout
+  layout_upgma <- reactive({
+    if(input$upgma_layout == "inward") {
+      "circular"
+    } else {input$upgma_layout}
+  })
+  
+  # upgma inward circular
+  upgma_inward <- reactive({
+    if (input$upgma_layout == "inward") {
+      layout_inward_circular(xlim = input$upgma_inward_xlim)
+    } else {
+      NULL
+    }
+  })
+  
+  ### Save MST Plot ----
+  output$save_plot_html <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save MST;", paste0("MST_", Sys.Date(), ".html")))
+      paste0("MST_", Sys.Date(), ".html")
+    },
+    content = function(file) {
+      mst_tree() %>% visSave(file = file, background = mst_background_color())
+    }
+  )
+  
+  ### Save NJ Plot ----
+  
+  # Define download handler to save the plot
+  
+  output$download_nj <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save NJ;", paste0("NJ_", Sys.Date(), ".", input$filetype_nj)))
+      paste0("NJ_", Sys.Date(), ".", input$filetype_nj)
+    },
+    content = function(file) {
+      if (input$filetype_nj == "png") {
+        png(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale))
+        print(nj_tree())
+        dev.off()
+      } else if (input$filetype_nj == "jpeg") {
+        jpeg(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale), quality = 100)
+        print(nj_tree())
+        dev.off()
+      } else if (input$filetype_nj == "svg") {
+        plot <- print(nj_tree())
+        ggsave(file=file, plot=plot, device = svg(width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio))/96,
+                                                  height = as.numeric(input$nj_scale)/96))
+      } else if (input$filetype_nj == "bmp") {
+        bmp(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale))
+        print(nj_tree())
+        dev.off()
+      }
+    }
+  )
+  
+  ### Save UPGMA Plot ----
+  
+  # Define download handler to save the plot
+  
+  output$download_upgma <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save UPGMA;", paste0("UPGMA_", Sys.Date(), ".", input$filetype_upgma)))
+      paste0("UPGMA_", Sys.Date(), ".", input$filetype_upgma)
+    },
+    content = function(file) {
+      if (input$filetype_upgma == "png") {
+        png(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale))
+        print(upgma_tree())
+        dev.off()
+      } else if (input$filetype_upgma == "jpeg") {
+        jpeg(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale), quality = 100)
+        print(upgma_tree())
+        dev.off()
+      } else if (input$filetype_upgma == "svg") {
+        plot <- print(upgma_tree())
+        ggsave(file=file, plot=plot, device = svg(width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio))/96,
+                                                  height = as.numeric(input$upgma_scale)/96))
+      } else if (input$filetype_upgma == "bmp") {
+        bmp(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale))
+        print(upgma_tree())
+        dev.off()
+      }
+    }
+  )
+  
+  ### Reactive Events ----
+  
+  # MST cluster reset button
+  observeEvent(input$mst_cluster_reset, {
+    if(!is.null(DB$schemeinfo))
+    updateNumericInput(session, "mst_cluster_threshold", value = as.numeric(DB$schemeinfo[7, 2]))
+  })
+  
+  # Shut off "Align Labels" control for UPGMA trees
+  shinyjs::disable('upgma_align')
+  shinyjs::disable('upgma_tiplab_linesize')
+  shinyjs::disable('upgma_tiplab_linetype')
+  
+  # Conditional disabling of control elemenmts
+  observe({
+    
+    # Tiles for inward layout
+    if(input$nj_layout == "inward") {
+      shinyjs::disable('nj_tiles_show') 
+      shinyjs::disable('nj_tiles_show_2')
+      shinyjs::disable('nj_tiles_show_3') 
+      shinyjs::disable('nj_tiles_show_4')
+      shinyjs::disable('nj_tiles_show_5') 
+      shinyjs::disable('nj_fruit_variable')
+      shinyjs::disable('nj_fruit_variable_2')
+      shinyjs::disable('nj_fruit_variable_3')
+      shinyjs::disable('nj_fruit_variable_4')
+      shinyjs::disable('nj_fruit_variable_5')
+      shinyjs::disable('nj_fruit_width')
+      shinyjs::disable('nj_fruit_width_2')
+      shinyjs::disable('nj_fruit_width_3')
+      shinyjs::disable('nj_fruit_width_4')
+      shinyjs::disable('nj_fruit_width_5')
+      shinyjs::disable('nj_fruit_offset')
+      shinyjs::disable('nj_fruit_offset_2')
+      shinyjs::disable('nj_fruit_offset_3')
+      shinyjs::disable('nj_fruit_offset_4')
+      shinyjs::disable('nj_fruit_offset_5')
+    } else {
+      shinyjs::enable('nj_tiles_show') 
+      shinyjs::enable('nj_tiles_show_2')
+      shinyjs::enable('nj_tiles_show_3') 
+      shinyjs::enable('nj_tiles_show_4')
+      shinyjs::enable('nj_tiles_show_5') 
+      shinyjs::enable('nj_fruit_variable')
+      shinyjs::enable('nj_fruit_variable_2')
+      shinyjs::enable('nj_fruit_variable_3')
+      shinyjs::enable('nj_fruit_variable_4')
+      shinyjs::enable('nj_fruit_variable_5')
+      shinyjs::enable('nj_fruit_width')
+      shinyjs::enable('nj_fruit_width_2')
+      shinyjs::enable('nj_fruit_width_3')
+      shinyjs::enable('nj_fruit_width_4')
+      shinyjs::enable('nj_fruit_width_5')
+      shinyjs::enable('nj_fruit_offset')
+      shinyjs::enable('nj_fruit_offset_2')
+      shinyjs::enable('nj_fruit_offset_3')
+      shinyjs::enable('nj_fruit_offset_4')
+      shinyjs::enable('nj_fruit_offset_5')
+    }
+    
+    if(input$upgma_layout == "inward") {
+      shinyjs::disable('upgma_tiles_show') 
+      shinyjs::disable('upgma_tiles_show_2')
+      shinyjs::disable('upgma_tiles_show_3') 
+      shinyjs::disable('upgma_tiles_show_4')
+      shinyjs::disable('upgma_tiles_show_5') 
+      shinyjs::disable('upgma_fruit_variable')
+      shinyjs::disable('upgma_fruit_variable_2')
+      shinyjs::disable('upgma_fruit_variable_3')
+      shinyjs::disable('upgma_fruit_variable_4')
+      shinyjs::disable('upgma_fruit_variable_5')
+      shinyjs::disable('upgma_fruit_width')
+      shinyjs::disable('upgma_fruit_width_2')
+      shinyjs::disable('upgma_fruit_width_3')
+      shinyjs::disable('upgma_fruit_width_4')
+      shinyjs::disable('upgma_fruit_width_5')
+      shinyjs::disable('upgma_fruit_offset')
+      shinyjs::disable('upgma_fruit_offset_2')
+      shinyjs::disable('upgma_fruit_offset_3')
+      shinyjs::disable('upgma_fruit_offset_4')
+      shinyjs::disable('upgma_fruit_offset_5')
+    } else {
+      shinyjs::enable('upgma_tiles_show') 
+      shinyjs::enable('upgma_tiles_show_2')
+      shinyjs::enable('upgma_tiles_show_3') 
+      shinyjs::enable('upgma_tiles_show_4')
+      shinyjs::enable('upgma_tiles_show_5') 
+      shinyjs::enable('upgma_fruit_variable')
+      shinyjs::enable('upgma_fruit_variable_2')
+      shinyjs::enable('upgma_fruit_variable_3')
+      shinyjs::enable('upgma_fruit_variable_4')
+      shinyjs::enable('upgma_fruit_variable_5')
+      shinyjs::enable('upgma_fruit_width')
+      shinyjs::enable('upgma_fruit_width_2')
+      shinyjs::enable('upgma_fruit_width_3')
+      shinyjs::enable('upgma_fruit_width_4')
+      shinyjs::enable('upgma_fruit_width_5')
+      shinyjs::enable('upgma_fruit_offset')
+      shinyjs::enable('upgma_fruit_offset_2')
+      shinyjs::enable('upgma_fruit_offset_3')
+      shinyjs::enable('upgma_fruit_offset_4')
+      shinyjs::enable('upgma_fruit_offset_5')
+    }
+    
+    # Shut off branch labels for NJ and UPGMA plots for circular layout
+    if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+      shinyjs::disable('nj_show_branch_label')
+    } else {
+      shinyjs::enable('nj_show_branch_label')
+    }
+    
+    if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+      shinyjs::disable('upgma_show_branch_label')
+    } else {
+      shinyjs::enable('upgma_show_branch_label')
+    }
+  })
+  
+  #### Generate Plot ----
+  
+  hamming_nj <- reactive({
+    if(anyNA(DB$allelic_profile)) {
+      if(input$na_handling == "omit") {
+        allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
+        
+        allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
+        
+        compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
+        
+      } else if(input$na_handling == "ignore_na"){
+        compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
+        
+      } else {
+        compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
+      } 
+      
+    } else {compute.distMatrix(DB$allelic_profile_true, hamming.dist)}
+  })
+  
+  hamming_mst <- reactive({
+    if(anyNA(DB$allelic_profile)) {
+      if(input$na_handling == "omit") {
+        allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
+        
+        allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
+        
+        dist <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
+        
+      } else if (input$na_handling == "ignore_na") {
+        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
+      } else {
+        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
+      }
+    } else {
+      dist <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
+    }
+    
+    # Find indices of pairs with a distance of 0
+    zero_distance_pairs <- as.data.frame(which(as.matrix(dist) == 0, arr.ind = TRUE))
+    
+    zero_distance_pairs <- zero_distance_pairs[zero_distance_pairs$row != zero_distance_pairs$col, ]
+    
+    if(nrow(zero_distance_pairs) > 0) {
+      
+      # Sort each row so that x <= y
+      df_sorted <- t(apply(zero_distance_pairs, 1, function(row) sort(row)))
+      
+      # Remove duplicate rows
+      df_unique <- as.data.frame(unique(df_sorted))
+      
+      colnames(df_unique) <- c("col", "row")
+      
+      # get metadata in df
+      vector_col <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        vector_col[count] <- Vis$meta_mst$`Assembly Name`[i]
+        count <- count + 1
+      }
+      
+      vector_row <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        vector_row[count] <- Vis$meta_mst$`Assembly Name`[i]
+        count <- count + 1
+      }
+      
+      col_id <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_id[count] <- Vis$meta_mst$`Assembly ID`[i]
+        count <- count + 1
+      }
+      
+      row_id <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_id[count] <- Vis$meta_mst$`Assembly ID`[i]
+        count <- count + 1
+      }
+      
+      col_index <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_index[count] <- Vis$meta_mst$Index[i]
+        count <- count + 1
+      }
+      
+      row_index <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_index[count] <- Vis$meta_mst$Index[i]
+        count <- count + 1
+      }
+      
+      col_date <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_date[count] <- Vis$meta_mst$`Isolation Date`[i]
+        count <- count + 1
+      }
+      
+      row_date <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_date[count] <- Vis$meta_mst$`Isolation Date`[i]
+        count <- count + 1
+      }
+      
+      col_host <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_host[count] <- Vis$meta_mst$Host[i]
+        count <- count + 1
+      }
+      
+      row_host <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_host[count] <- Vis$meta_mst$Host[i]
+        count <- count + 1
+      }
+      
+      col_country <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_country[count] <- Vis$meta_mst$Country[i]
+        count <- count + 1
+      }
+      
+      row_country <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_country[count] <- Vis$meta_mst$Country[i]
+        count <- count + 1
+      }
+      
+      col_city <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_city[count] <- Vis$meta_mst$City[i]
+        count <- count + 1
+      }
+      
+      row_city <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_city[count] <- Vis$meta_mst$City[i]
+        count <- count + 1
+      }
+      
+      df_unique <- cbind(df_unique, col_name = vector_col, row_name = vector_row, 
+                         col_index = col_index, row_index = row_index, col_id = col_id,
+                         row_id = row_id, col_date = col_date, row_date = row_date,
+                         col_host = col_host, row_host = row_host, col_country = col_country,
+                         row_country = row_country, col_city = col_city, row_city = row_city)
+      
+      # Add groups
+      grouped_df <- df_unique %>%
+        group_by(col) %>%
+        mutate(group_id = cur_group_id())
+      
+      # Merge groups
+      name <- character(0)
+      index <- character(0)
+      id <- character(0)
+      count <- 1
+      for (i in grouped_df$group_id) {
+        name[count] <- paste(unique(append(grouped_df$col_name[which(grouped_df$group_id == i)], 
+                                           grouped_df$row_name[which(grouped_df$group_id == i)])), 
+                             collapse = "\n")
+        
+        id[count] <- paste(unique(append(grouped_df$col_id[which(grouped_df$group_id == i)], 
+                                         grouped_df$row_id[which(grouped_df$group_id == i)])), 
+                           collapse = "\n")
+        
+        index[count] <- paste(unique(append(grouped_df$col_index[which(grouped_df$group_id == i)], 
+                                            grouped_df$row_index[which(grouped_df$group_id == i)])), 
+                              collapse = "\n")
+        
+        count <- count + 1
+      }
+      
+      merged_names <- cbind(grouped_df, "Index" = index, "Assembly Name" = name, "Assembly ID" = id)
+      
+      # remove duplicate groups
+      
+      final <- merged_names[!duplicated(merged_names$group_id), ]
+      
+      final_cleaned <- final[!(final$col_name %in% final$row_name),]
+      
+      final_cleaned <- select(final_cleaned, 3, 17:20)
+      
+      # adapt metadata
+      Date_merged <- character(0)
+      for(j in 1:length(final_cleaned$Index)) {
+        Date <- character(0)
+        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
+          Date <- append(Date, Vis$meta_mst$`Isolation Date`[which(Vis$meta_mst$Index == i)])
+        }
+        Date_merged <- append(Date_merged, paste(Date, collapse = "\n"))
+      }
+      
+      Host_merged <- character(0)
+      for(j in 1:length(final_cleaned$Index)) {
+        Host <- character(0)
+        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
+          Host <- append(Host, Vis$meta_mst$Host[which(Vis$meta_mst$Index == i)])
+        }
+        Host_merged <- append(Host_merged, paste(Host, collapse = "\n"))
+      }
+      
+      Country_merged <- character(0)
+      for(j in 1:length(final_cleaned$Index)) {
+        Country <- character(0)
+        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
+          Country <- append(Country, Vis$meta_mst$Country[which(Vis$meta_mst$Index == i)])
+        }
+        Country_merged <- append(Country_merged, paste(Country, collapse = "\n"))
+      }
+      
+      City_merged <- character(0)
+      for(j in 1:length(final_cleaned$Index)) {
+        City <- character(0)
+        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
+          City <- append(City, Vis$meta_mst$City[which(Vis$meta_mst$Index == i)])
+        }
+        City_merged <- append(City_merged, paste(City, collapse = "\n"))
+      }
+      
+      final_meta <- cbind(final_cleaned, "Isolation Date" = Date_merged, 
+                          "Host" = Host_merged, "Country" = Country_merged, "City" = City_merged)
+      
+      
+      # Merging with original data frame / allelic profile
+      
+      allelic_profile_true <- DB$allelic_profile_true
+      meta_true <- Vis$meta_mst
+      
+      rownames(allelic_profile_true) <- Vis$meta_mst$`Assembly Name`
+      rownames(meta_true) <- Vis$meta_mst$`Assembly Name`
+      
+      omit <- unique(append(df_unique$col_name, df_unique$row_name)) %in% final_cleaned$col_name
+      
+      omit_id <- unique(append(df_unique$col_name, df_unique$row_name))[!omit]
+      
+      remove <- !(rownames(allelic_profile_true) %in% omit_id)
+      
+      allelic_profile_clean <- allelic_profile_true[remove, ]
+      
+      meta_clean <- meta_true[remove, ]
+      
+      # substitute meta assembly names with group names
+      
+      count <- 1
+      for(i in which(rownames(meta_clean) %in% final_meta$col_name)) {
+        meta_clean$Index[i] <- final_meta$Index[count]
+        meta_clean$`Assembly Name`[i] <- final_meta$`Assembly Name`[count]
+        meta_clean$`Assembly ID`[i] <- final_meta$`Assembly ID`[count]
+        meta_clean$`Isolation Date`[i] <- final_meta$`Isolation Date`[count]
+        meta_clean$Host[i] <- final_meta$Host[count]
+        meta_clean$Country[i] <- final_meta$Country[count]
+        meta_clean$City[i] <- final_meta$City[count]
+        count <- count + 1
+      }
+      
+      # Metadata completion
+      # get group size
+      
+      size_vector <- numeric(0)
+      for(i in 1:nrow(meta_clean)) {
+        if (str_count(meta_clean$`Assembly Name`[i], "\n") == 0) {
+          size_vector[i] <- 1
+        } else {
+          size_vector[i] <- str_count(meta_clean$`Assembly Name`[i], "\n") +1
+        }
+      }
+      
+      meta_clean <- mutate(meta_clean, size = size_vector)
+      
+      # get font size dependent on group size
+      
+      font_size <- numeric(nrow(meta_clean))
+      
+      for (i in 1:length(font_size)) {
+        if(meta_clean$size[i] < 3) {
+          font_size[i] <- 12
+        } else {
+          font_size[i] <- 11
+        }
+      }
+      
+      # get v-align dependent on group size
+      valign <- numeric(nrow(meta_clean))
+      
+      for (i in 1:length(valign)) {
+        if(meta_clean$size[i] == 1) {
+          valign[i] <- -30
+        } else if(meta_clean$size[i] == 2) {
+          valign[i] <- -38
+        } else if(meta_clean$size[i] == 3) {
+          valign[i] <- -46
+        } else if(meta_clean$size[i] == 4) {
+          valign[i] <- -54
+        } else if(meta_clean$size[i] == 5) {
+          valign[i] <- -62
+        } else if(meta_clean$size[i] > 5) {
+          valign[i] <- -70
+        }
+      }
+      
+      Vis$unique_meta <- meta_clean %>%
+        cbind(font_size = font_size, valign = valign)
+      
+      # final dist calculation
+      
+      if(anyNA(DB$allelic_profile)){
+        if(input$na_handling == "omit") {
+          allelic_profile_clean_noNA_names <- allelic_profile_clean[, colSums(is.na(allelic_profile_clean)) == 0]
+          compute.distMatrix(allelic_profile_clean_noNA_names, hamming.dist)
+        } else if (input$na_handling == "ignore_na") {
+          compute.distMatrix(allelic_profile_clean, hamming.distIgnore)
+        } else {
+          compute.distMatrix(allelic_profile_clean, hamming.distCategory)
+        }
+      } else {compute.distMatrix(allelic_profile_clean, hamming.dist)}
+      
+      
+    } else {
+      font_size <- rep(12, nrow(Vis$meta_mst))
+      valign <- rep(-30, nrow(Vis$meta_mst))
+      size <- rep(1, nrow(Vis$meta_mst))
+      Vis$unique_meta <- Vis$meta_mst %>%
+        cbind(size , font_size, valign)
+      
+      dist
+    }
+    
+  })
+  
+  observeEvent(input$create_tree, {
+    log_print("Input create_tree")
+    
+    if(is.null(DB$data)) {
+      log_print("Missing data")
+      
+      show_toast(
+        title = "Missing data",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if(nrow(DB$allelic_profile_true) < 3) {
+      log_print("Min. of 3 entries required for visualization")
+      
+      show_toast(
+        title = "Min. of 3 entries required for visualization",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      
+      if(any(duplicated(DB$meta$`Assembly Name`)) | any(duplicated(DB$meta$`Assembly ID`))) {
+        log_print("Duplicated assemblies")
+        
+        dup_name <- which(duplicated(DB$meta_true$`Assembly Name`))
+        dup_id <- which(duplicated(DB$meta_true$`Assembly ID`))
+        
+        showModal(
+          modalDialog(
+            if((length(dup_name) + length(dup_id)) == 1) {
+              if(length(dup_name) == 1) {
+                HTML(paste0("Entry #", dup_name,
+                            " contains a duplicated assembly name:", "<br><br>",
+                            DB$meta_true$`Assembly Name`[dup_name]))
+              } else {
+                HTML(paste0("Entry #", dup_id,
+                            " contains a duplicated assembly ID:", "<br><br>",
+                            DB$meta_true$`Assembly ID`[dup_id]))
+              }
+            } else {
+              if(length(dup_name) == 0) {
+                HTML(c("Entries contain duplicated IDs <br><br>",
+                       paste0(unique(DB$meta_true$`Assembly ID`[dup_id]), "<br>")))
+              } else if(length(dup_id) == 0) {
+                HTML(c("Entries contain duplicated names<br><br>",
+                       paste0(unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>")))
+              } else {
+                HTML(c("Entries contain duplicated names and IDs <br><br>",
+                       paste0("Name: ", unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>"),
+                       paste0("ID: ", unique(DB$meta_true$`Assembly ID`[dup_id]), "<br>")))
+              }
+            },
+            title = "Duplicate entries",
+            fade = TRUE,
+            easyClose = TRUE,
+            footer = tagList(
+              modalButton("Cancel"),
+              actionButton("change_entries", "Go to Entry Table", class = "btn btn-default")
+            )
+          )
+        )
+      } else {
+        
+        set.seed(1)
+        
+        if (input$tree_algo == "Neighbour-Joining") {
+          
+          log_print("Rendering NJ tree")
+          
+          output$nj_field <- renderUI({
+            addSpinner(
+              plotOutput("tree_nj", width = paste0(as.character(as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), "px"), height = paste0(as.character(input$nj_scale), "px")),
+              spin = "dots",
+              color = "#ffffff"
+            )
+          })
+          
+          Vis$meta_nj <- select(DB$meta_true, -2)
+          
+          if(length(unique(gsub(" ", "_", colnames(Vis$meta_nj)))) < length(gsub(" ", "_", colnames(Vis$meta_nj)))) {
+            show_toast(
+              title = "Conflicting Custom Variable Names",
+              type = "warning",
+              position = "bottom-end",
+              timer = 6000
+            )
+          } else {
+            
+            # Create phylogenetic tree data
+            Vis$nj <- ape::nj(hamming_nj())
+            
+            # Create phylogenetic tree meta data
+            Vis$meta_nj <- mutate(Vis$meta_nj, taxa = Index) %>%
+              relocate(taxa)
+            
+            # Get number of included entries calculate start values for tree 
+            if(!is.null(input$nj_layout)) {
+              if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+                if(sum(DB$data$Include) < 21) {
+                  Vis$labelsize_nj <- 5.5
+                  Vis$tippointsize_nj <- 5.5
+                  Vis$nodepointsize_nj <- 4
+                  Vis$tiplab_padding_nj <- 0.25
+                  Vis$branch_size_nj <- 4.5
+                } else if (between(sum(DB$data$Include), 21, 40)) {
+                  Vis$labelsize_nj <- 5
+                  Vis$tippointsize_nj <- 5
+                  Vis$nodepointsize_nj <- 3.5
+                  Vis$tiplab_padding_nj <- 0.2
+                  Vis$branch_size_nj <- 4
+                } else if (between(sum(DB$data$Include), 41, 60)) {
+                  Vis$labelsize_nj <- 4.5
+                  Vis$tippointsize_nj <- 4.5
+                  Vis$nodepointsize_nj <- 3
+                  Vis$tiplab_padding_nj <- 0.15
+                  Vis$branch_size_nj <- 3.5
+                } else if (between(sum(DB$data$Include), 61, 80)) {
+                  Vis$labelsize_nj <- 4
+                  Vis$tippointsize_nj <- 4
+                  Vis$nodepointsize_nj <- 2.5
+                  Vis$tiplab_padding_nj <- 0.1
+                  Vis$branch_size_nj <- 3
+                } else if (between(sum(DB$data$Include), 81, 100)) {
+                  Vis$labelsize_nj <- 3.5
+                  Vis$tippointsize_nj <- 3.5
+                  Vis$nodepointsize_nj <- 2
+                  Vis$tiplab_padding_nj <- 0.1
+                  Vis$branch_size_nj <- 2.5
+                } else {
+                  Vis$labelsize_nj <- 3
+                  Vis$tippointsize_nj <- 3
+                  Vis$nodepointsize_nj <- 1.5
+                  Vis$tiplab_padding_nj <- 0.05
+                  Vis$branch_size_nj <- 2
+                }
+              } else {
+                if(sum(DB$data$Include) < 21) {
+                  Vis$labelsize_nj <- 5
+                  Vis$tippointsize_nj <- 5
+                  Vis$nodepointsize_nj <- 4
+                  Vis$tiplab_padding_nj <- 0.25
+                  Vis$branch_size_nj <- 4.5
+                } else if (between(sum(DB$data$Include), 21, 40)) {
+                  Vis$labelsize_nj <- 4.5
+                  Vis$tippointsize_nj <- 4.5
+                  Vis$nodepointsize_nj <- 3.5
+                  Vis$tiplab_padding_nj <- 0.2
+                  Vis$branch_size_nj <- 4
+                } else if (between(sum(DB$data$Include), 41, 60)) {
+                  Vis$labelsize_nj <- 4
+                  Vis$tippointsize_nj <- 4
+                  Vis$nodepointsize_nj <- 3
+                  Vis$tiplab_padding_nj <- 0.15
+                  Vis$branch_size_nj <- 3.5
+                } else if (between(sum(DB$data$Include), 61, 80)) {
+                  Vis$labelsize_nj <- 3.5
+                  Vis$tippointsize_nj <- 3.5
+                  Vis$nodepointsize_nj <- 2.5
+                  Vis$tiplab_padding_nj <- 0.1
+                  Vis$branch_size_nj <- 3
+                } else if (between(sum(DB$data$Include), 81, 100)) {
+                  Vis$labelsize_nj <- 3
+                  Vis$tippointsize_nj <- 3
+                  Vis$nodepointsize_nj <- 2
+                  Vis$tiplab_padding_nj <- 0.1
+                  Vis$branch_size_nj <- 2.5
+                } else {
+                  Vis$labelsize_nj <- 2.5
+                  Vis$tippointsize_nj <- 2.5
+                  Vis$nodepointsize_nj <- 1.5
+                  Vis$tiplab_padding_nj <- 0.05
+                  Vis$branch_size_nj <- 2
+                }
+              }
+            } else {
+              Vis$labelsize_nj <- 4
+              Vis$tippointsize_nj <- 4
+              Vis$nodepointsize_nj <- 2.5
+              Vis$tiplab_padding_nj <- 0.2
+              Vis$branch_size_nj <- 3.5
+            }
+            
+            Vis$nj_tree <- ggtree(Vis$nj)
+            
+            # Get upper and lower end of x range
+            Vis$nj_max_x <- max(Vis$nj_tree$data$x)
+            Vis$nj_min_x <- min(Vis$nj_tree$data$x)
+            
+            # Get parent node numbers
+            Vis$nj_parentnodes <- Vis$nj_tree$data$parent
+            
+            # Update visualization control inputs
+            if(!is.null(input$nj_tiplab_size)) {
+              updateNumericInput(session, "nj_tiplab_size", value = Vis$labelsize_nj)
+            }
+            if(!is.null(input$nj_tippoint_size)) {
+              updateSliderInput(session, "nj_tippoint_size", value = Vis$tippointsize_nj)
+            }
+            if(!is.null(input$nj_nodepoint_size)) {
+              updateSliderInput(session, "nj_nodepoint_size", value = Vis$nodepointsize_nj)
+            }
+            if(!is.null(input$nj_tiplab_padding)) {
+              updateSliderInput(session, "nj_tiplab_padding", value = Vis$tiplab_padding_nj)
+            }
+            if(!is.null(input$nj_branch_size)) {
+              updateNumericInput(session, "nj_branch_size", value = Vis$branch_size_nj)
+            }
+            if(!is.null(input$nj_treescale_width)) {
+              updateNumericInput(session, "nj_treescale_width", value = round(ceiling(Vis$nj_max_x) * 0.1, 0))
+            }
+            if(!is.null(input$nj_rootedge_length)) {
+              updateSliderInput(session, "nj_rootedge_length", value = round(ceiling(Vis$nj_max_x) * 0.05, 0))
+            }
+            
+            output$tree_nj <- renderPlot({
+              nj_tree()
+            })
+            
+            Vis$nj_true <- TRUE
+          }
+        } else if (input$tree_algo == "UPGMA") {
+          
+          log_print("Rendering UPGMA tree")
+          
+          output$upgma_field <- renderUI({
+            addSpinner(
+              plotOutput("tree_upgma", width = paste0(as.character(as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), "px"), height = paste0(as.character(input$upgma_scale), "px")),
+              spin = "dots",
+              color = "#ffffff"
+            )
+          })
+          
+          Vis$meta_upgma <- select(DB$meta_true, -2)
+          
+          if(length(unique(gsub(" ", "_", colnames(Vis$meta_upgma)))) < length(gsub(" ", "_", colnames(Vis$meta_upgma)))) {
+            show_toast(
+              title = "Conflicting Custom Variable Names",
+              type = "warning",
+              position = "bottom-end",
+              timer = 6000
+            )
+          } else {
+            
+            # Create phylogenetic tree data
+            Vis$upgma <- phangorn::upgma(hamming_nj())
+            
+            # Create phylogenetic tree meta data
+            Vis$meta_upgma <- mutate(Vis$meta_upgma, taxa = Index) %>%
+              relocate(taxa)
+            
+            # Get number of included entries calculate start values for tree 
+            if(!is.null(input$upgma_layout)) {
+              if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+                if(sum(DB$data$Include) < 21) {
+                  Vis$labelsize_upgma <- 5.5
+                  Vis$tippointsize_upgma <- 5.5
+                  Vis$nodepointsize_upgma <- 4
+                  Vis$tiplab_padding_upgma <- 0.25
+                  Vis$branch_size_upgma <- 4.5
+                } else if (between(sum(DB$data$Include), 21, 40)) {
+                  Vis$labelsize_upgma <- 5
+                  Vis$tippointsize_upgma <- 5
+                  Vis$nodepointsize_upgma <- 3.5
+                  Vis$tiplab_padding_upgma <- 0.2
+                  Vis$branch_size_upgma <- 4
+                } else if (between(sum(DB$data$Include), 41, 60)) {
+                  Vis$labelsize_upgma <- 4.5
+                  Vis$tippointsize_upgma <- 4.5
+                  Vis$nodepointsize_upgma <- 3
+                  Vis$tiplab_padding_upgma <- 0.15
+                  Vis$branch_size_upgma <- 3.5
+                } else if (between(sum(DB$data$Include), 61, 80)) {
+                  Vis$labelsize_upgma <- 4
+                  Vis$tippointsize_upgma <- 4
+                  Vis$nodepointsize_upgma <- 2.5
+                  Vis$tiplab_padding_upgma <- 0.1
+                  Vis$branch_size_upgma <- 3
+                } else if (between(sum(DB$data$Include), 81, 100)) {
+                  Vis$labelsize_upgma <- 3.5
+                  Vis$tippointsize_upgma <- 3.5
+                  Vis$nodepointsize_upgma <- 2
+                  Vis$tiplab_padding_upgma <- 0.1
+                  Vis$branch_size_upgma <- 2.5
+                } else {
+                  Vis$labelsize_upgma <- 3
+                  Vis$tippointsize_upgma <- 3
+                  Vis$nodepointsize_upgma <- 1.5
+                  Vis$tiplab_padding_upgma <- 0.05
+                  Vis$branch_size_upgma <- 2
+                }
+              } else {
+                if(sum(DB$data$Include) < 21) {
+                  Vis$labelsize_upgma <- 5
+                  Vis$tippointsize_upgma <- 5
+                  Vis$nodepointsize_upgma <- 4
+                  Vis$tiplab_padding_upgma <- 0.25
+                  Vis$branch_size_upgma <- 4.5
+                } else if (between(sum(DB$data$Include), 21, 40)) {
+                  Vis$labelsize_upgma <- 4.5
+                  Vis$tippointsize_upgma <- 4.5
+                  Vis$nodepointsize_upgma <- 3.5
+                  Vis$tiplab_padding_upgma <- 0.2
+                  Vis$branch_size_upgma <- 4
+                } else if (between(sum(DB$data$Include), 41, 60)) {
+                  Vis$labelsize_upgma <- 4
+                  Vis$tippointsize_upgma <- 4
+                  Vis$nodepointsize_upgma <- 3
+                  Vis$tiplab_padding_upgma <- 0.15
+                  Vis$branch_size_upgma <- 3.5
+                } else if (between(sum(DB$data$Include), 61, 80)) {
+                  Vis$labelsize_upgma <- 3.5
+                  Vis$tippointsize_upgma <- 3.5
+                  Vis$nodepointsize_upgma <- 2.5
+                  Vis$tiplab_padding_upgma <- 0.1
+                  Vis$branch_size_upgma <- 3
+                } else if (between(sum(DB$data$Include), 81, 100)) {
+                  Vis$labelsize_upgma <- 3
+                  Vis$tippointsize_upgma <- 3
+                  Vis$nodepointsize_upgma <- 2
+                  Vis$tiplab_padding_upgma <- 0.1
+                  Vis$branch_size_upgma <- 2.5
+                } else {
+                  Vis$labelsize_upgma <- 2.5
+                  Vis$tippointsize_upgma <- 2.5
+                  Vis$nodepointsize_upgma <- 1.5
+                  Vis$tiplab_padding_upgma <- 0.05
+                  Vis$branch_size_upgma <- 2
+                }
+              }
+            } else {
+              Vis$labelsize_upgma <- 4
+              Vis$tippointsize_upgma <- 4
+              Vis$nodepointsize_upgma <- 2.5
+              Vis$tiplab_padding_upgma <- 0.2
+              Vis$branch_size_upgma <- 3.5
+            }
+            
+            Vis$upgma_tree <- ggtree(Vis$upgma)
+            
+            # Get upper and lower end of x range
+            Vis$upgma_max_x <- max(Vis$upgma_tree$data$x)
+            Vis$upgma_min_x <- min(Vis$upgma_tree$data$x)
+            
+            # Get parent node numbers
+            Vis$upgma_parentnodes <- Vis$upgma_tree$data$parent
+            
+            # Update visualization control inputs
+            if(!is.null(input$upgma_tiplab_size)) {
+              updateNumericInput(session, "upgma_tiplab_size", value = Vis$labelsize_upgma)
+            }
+            if(!is.null(input$upgma_tippoint_size)) {
+              updateSliderInput(session, "upgma_tippoint_size", value = Vis$tippointsize_upgma)
+            }
+            if(!is.null(input$upgma_nodepoint_size)) {
+              updateSliderInput(session, "upgma_nodepoint_size", value = Vis$nodepointsize_upgma)
+            }
+            if(!is.null(input$upgma_tiplab_padding)) {
+              updateSliderInput(session, "upgma_tiplab_padding", value = Vis$tiplab_padding_upgma)
+            }
+            if(!is.null(input$upgma_branch_size)) {
+              updateNumericInput(session, "upgma_branch_size", value = Vis$branch_size_upgma)
+            }
+            if(!is.null(input$upgma_treescale_width)) {
+              updateNumericInput(session, "upgma_treescale_width", value = round(ceiling(Vis$upgma_max_x) * 0.1, 0))
+            }
+            if(!is.null(input$upgma_rootedge_length)) {
+              updateSliderInput(session, "upgma_rootedge_length", value = round(ceiling(Vis$upgma_max_x) * 0.05, 0))
+            }
+            
+            output$tree_upgma <- renderPlot({
+              upgma_tree()
+            })
+            
+            Vis$upgma_true <- TRUE
+          }
+        } else {
+          
+          log_print("Rendering MST graph")
+          
+          output$mst_field <- renderUI({
+            if(input$mst_background_transparent == TRUE) {
+              visNetworkOutput("tree_mst", width = paste0(as.character(as.numeric(input$mst_scale) * as.numeric(input$mst_ratio)), "px"), height = paste0(as.character(input$mst_scale), "px"))
+            } else {
+              addSpinner(
+                visNetworkOutput("tree_mst", width = paste0(as.character(as.numeric(input$mst_scale) * as.numeric(input$mst_ratio)), "px"), height = paste0(as.character(input$mst_scale), "px")),
+                spin = "dots",
+                color = "#ffffff"
+              )
+            }
+          })
+          
+          if(nrow(DB$meta_true) > 100) {
+            
+            log_print("Over 100 isolates in MST graph")
+            
+            show_toast(
+              title = "Computation might take a while",
+              type = "warning",
+              position = "bottom-end",
+              timer = 10000
+            )
+          }
+          
+          meta_mst <- DB$meta_true
+          Vis$meta_mst <- meta_mst
+          
+          # prepare igraph object
+          Vis$ggraph_1 <- hamming_mst() |>
+            as.matrix() |>
+            graph.adjacency(weighted = TRUE) |>
+            igraph::mst() 
+          
+          output$tree_mst <- renderVisNetwork({
+            mst_tree()
+          })
+          
+          Vis$mst_true <- TRUE
+        }
+      }
+    }
+  })
+  
+  # _______________________ ####
+  
+  ## Report ----
+  
+  observe({
+    if(!is.null(DB$data)) {
+      if(!is.null(input$tree_algo)) {
+        if(input$tree_algo == "Minimum-Spanning") {
+          shinyjs::disable("rep_plot_report")
+          updateCheckboxInput(session, "rep_plot_report", value = FALSE)
+        } else {
+          shinyjs::enable("rep_plot_report")
+        }
+      }
+    }
+  })
+  
+  ### Report creation UI ----
+  
+  observeEvent(input$create_rep, {
+    
+    if((input$tree_algo == "Minimum-Spanning" & isTRUE(Vis$mst_true)) |
+       (input$tree_algo == "UPGMA" & isTRUE(Vis$upgma_true)) |
+       (input$tree_algo == "Neighbour-Joining" & isTRUE(Vis$nj_true))) {
+      # Get currently selected missing value handling option
+      if(input$na_handling == "ignore_na") {
+        na_handling <- "Ignore missing values for pairwise comparison"
+      } else if(input$na_handling == "omit") {
+        na_handling <- "Omit loci with missing values for all assemblies"
+      } else if(input$na_handling == "category") {
+        na_handling <- "Treat missing values as allele variant"
+      }
+      
+      extra_var <- character()
+      if(input$tree_algo == "Minimum-Spanning") {
+        shinyjs::runjs("mstReport();")
+        if(isTRUE(input$mst_color_var)) {
+          extra_var <- c(extra_var, input$mst_col_var)
+        }
+      } else if(input$tree_algo == "Neighbour-Joining") {
+        if(isTRUE(input$nj_mapping_show)) {
+          extra_var <- c(extra_var, input$nj_color_mapping)
+        }
+        if(isTRUE(input$nj_tipcolor_mapping_show)) {
+          extra_var <- c(extra_var, input$nj_tipcolor_mapping)
+        }
+        if(isTRUE(input$nj_tipshape_mapping_show)) {
+          extra_var <- c(extra_var, input$nj_tipshape_mapping)
+        }
+        if(isTRUE(input$nj_tiles_show_1)) {
+          extra_var <- c(extra_var, input$nj_fruit_variable)
+        }
+        if(isTRUE(input$nj_tiles_show_2)) {
+          extra_var <- c(extra_var, input$nj_fruit_variable_2)
+        }
+        if(isTRUE(input$nj_tiles_show_3)) {
+          extra_var <- c(extra_var, input$nj_fruit_variable_3)
+        }
+        if(isTRUE(input$nj_tiles_show_4)) {
+          extra_var <- c(extra_var, input$nj_fruit_variable_4)
+        }
+        if(isTRUE(input$nj_tiles_show_5)) {
+          extra_var <- c(extra_var, input$nj_fruit_variable_5)
+        }
+        if(isTRUE(input$nj_heatmap_show)) {
+          extra_var <- c(extra_var, input$nj_heatmap_select)
+        }
+      } else if(input$tree_algo == "UPGMA") {
+        if(isTRUE(input$UPGMA_mapping_show)) {
+          extra_var <- c(extra_var, input$UPGMA_color_mapping)
+        }
+        if(isTRUE(input$UPGMA_tipcolor_mapping_show)) {
+          extra_var <- c(extra_var, input$UPGMA_tipcolor_mapping)
+        }
+        if(isTRUE(input$UPGMA_tipshape_mapping_show)) {
+          extra_var <- c(extra_var, input$UPGMA_tipshape_mapping)
+        }
+        if(isTRUE(input$UPGMA_tiles_show_1)) {
+          extra_var <- c(extra_var, input$UPGMA_fruit_variable)
+        }
+        if(isTRUE(input$UPGMA_tiles_show_2)) {
+          extra_var <- c(extra_var, input$UPGMA_fruit_variable_2)
+        }
+        if(isTRUE(input$UPGMA_tiles_show_3)) {
+          extra_var <- c(extra_var, input$UPGMA_fruit_variable_3)
+        }
+        if(isTRUE(input$UPGMA_tiles_show_4)) {
+          extra_var <- c(extra_var, input$UPGMA_fruit_variable_4)
+        }
+        if(isTRUE(input$UPGMA_tiles_show_5)) {
+          extra_var <- c(extra_var, input$UPGMA_fruit_variable_5)
+        }
+        if(isTRUE(input$UPGMA_heatmap_show)) {
+          extra_var <- c(extra_var, input$UPGMA_heatmap_select)
+        }
+      }
+      
+      showModal(
+        modalDialog(
+          fluidRow(
+            column(
+              width = 12,
+              fluidRow(
+                column(
+                  width = 4,
+                  align = "left",
+                  HTML(
+                    paste(
+                      tags$span(style='color:black; font-size: 15px; font-weight: 900', 'General')
+                    )
+                  )
+                ),
+                column(
+                  width = 3,
+                  align = "left",
+                  checkboxInput(
+                    "rep_general",
+                    label = "",
+                    value = TRUE
+                  )
+                )
+              ),
+              fluidRow(
+                column(
+                  width = 12,
+                  align = "left",
+                  fluidRow(
+                    column(
+                      width = 3,
+                      checkboxInput(
+                        "rep_date_general", 
+                        label = h5("Date", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 7,
+                      dateInput(
+                        "mst_date_general_select",
+                        "",
+                        max = Sys.Date()
+                      )
+                    )
+                  ),
+                  fluidRow(
+                    column(
+                      width = 3,
+                      checkboxInput(
+                        "rep_operator_general", 
+                        label = h5("Operator", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 8,
+                      textInput(
+                        "mst_operator_general_select",
+                        ""
+                      ) 
+                    )
+                  ),
+                  fluidRow(
+                    column(
+                      width = 3,
+                      checkboxInput(
+                        "rep_institute_general", 
+                        label = h5("Institute", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 8,
+                      textInput(
+                        "mst_institute_general_select",
+                        ""
+                      ) 
+                    )
+                  ),
+                  fluidRow(
+                    column(
+                      width = 3,
+                      checkboxInput(
+                        "rep_comm_general", 
+                        label = h5("Comment", style = "color:black;")
+                      )
+                    ),
+                    column(
+                      width = 8,
+                      textAreaInput(
+                        inputId = "mst_comm_general_select",
+                        label = "",
+                        width = "100%",
+                        height = "60px",
+                        cols = NULL,
+                        rows = NULL,
+                        placeholder = NULL,
+                        resize = "vertical"
+                      ) 
+                    )
+                  )
+                )
+              ),
+              hr(),
+              fluidRow(
+                column(
+                  width = 4,
+                  align = "left",
+                  HTML(
+                    paste(
+                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Isolate Table')
+                    )
+                  )
+                ),
+                column(
+                  width = 3,
+                  align = "left",
+                  checkboxInput(
+                    "rep_entrytable",
+                    label = "",
+                    value = TRUE
+                  )
+                ),
+                column(
+                  width = 4,
+                  align = "left",
+                  HTML(
+                    paste(
+                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Include Plot')
+                    )
+                  )
+                ),
+                column(
+                  width = 1,
+                  align = "left",
+                  checkboxInput(
+                    "rep_plot_report",
+                    label = "",
+                    value = TRUE
+                  )
+                )
+              ),
+              fluidRow(
+                column(
+                  width = 6,
+                  align = "left",
+                  div(
+                    class = "rep_tab_sel",
+                    pickerInput("select_rep_tab",
+                                label = "",
+                                choices = names(DB$meta)[-2],
+                                selected = c("Assembly Name", "Scheme", "Isolation Date",
+                                             "Host", "Country", "City", extra_var),
+                                options = list(
+                                  size = 10,
+                                  `actions-box` = TRUE,
+                                  style = "background-color: white; border-radius: 5px;"
+                                ),
+                                multiple = TRUE)
+                  )
+                )
+              ),
+              hr(),
+              fluidRow(
+                column(
+                  width = 4,
+                  align = "left",
+                  HTML(
+                    paste(
+                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Analysis Parameter')
+                    )
+                  )
+                ),
+                column(
+                  width = 3,
+                  align = "left",
+                  checkboxInput(
+                    "rep_analysis",
+                    label = "",
+                    value = TRUE
+                  )
+                )
+              ),
+              fluidRow(
+                column(
+                  width = 6,
+                  align = "left",
+                  fluidRow(
+                    column(
+                      width = 4,
+                      checkboxInput(
+                        "rep_cgmlst_analysis",
+                        label = h5("Scheme", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 8,
+                      align = "right",
+                      HTML(
+                        paste(
+                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', DB$scheme)
+                        )
+                      )
+                    )
+                  ),
+                  fluidRow(
+                    column(
+                      width = 4,
+                      checkboxInput(
+                        "rep_tree_analysis",
+                        label = h5("Tree", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 8,
+                      align = "right",
+                      HTML(
+                        paste(
+                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', input$tree_algo)
+                        )
+                      )
+                    )
+                  )
+                ),
+                column(
+                  width = 6,
+                  align = "left",
+                  fluidRow(
+                    column(2),
+                    column(
+                      width = 4,
+                      checkboxInput(
+                        "rep_distance",
+                        label = h5("Distance", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 5,
+                      align = "right",
+                      HTML(
+                        paste(
+                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', 'Hamming')
+                        )
+                      )
+                    )
+                  ),
+                  fluidRow(
+                    column(2),
+                    column(
+                      width = 4,
+                      checkboxInput(
+                        "rep_version",
+                        label = h5("Version", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 5,
+                      align = "right",
+                      HTML(
+                        paste(
+                          tags$span(style='color:black; position: relative; top: 17px; font-style: italic', phylotraceVersion)
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              fluidRow(
+                column(
+                  width = 3,
+                  align = "left",
+                  checkboxInput(
+                    "rep_missval",
+                    label = h5("NA handling", style = "color:black;"),
+                    value = TRUE
+                  )
+                ),
+                column(
+                  width = 7,
+                  align = "right",
+                  HTML(
+                    paste(
+                      tags$span(style='color: black; position: relative; top: 17px; font-style: italic; right: 35px;', na_handling)
+                    )
+                  )
+                )
+              )
+            )
+          ),
+          title = "cgMLST Report Generation",
+          easyClose = TRUE,
+          footer = tagList(
+            modalButton("Cancel"),
+            downloadBttn(
+              "download_report",
+              style = "simple",
+              label = "Save",
+              size = "sm",
+              icon = icon("download")
+            )
+          )
+        )
+      )
+    } else {
+      show_toast(
+        title = "No tree created",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    }
+  })
+  
+  observe({
+    if(!is.null(input$rep_general)) {
+      if(isFALSE(input$rep_general)) {
+        shinyjs::disable('rep_date_general') 
+        shinyjs::disable('rep_operator_general') 
+        shinyjs::disable('rep_institute_general') 
+        shinyjs::disable('rep_comm_general') 
+        shinyjs::disable('mst_date_general_select') 
+        shinyjs::disable('mst_operator_general_select') 
+        shinyjs::disable('mst_institute_general_select') 
+        shinyjs::disable('mst_comm_general_select') 
+      } else {
+        shinyjs::enable('rep_date_general') 
+        shinyjs::enable('rep_operator_general') 
+        shinyjs::enable('rep_institute_general') 
+        shinyjs::enable('rep_comm_general')
+        shinyjs::enable('mst_date_general_select') 
+        shinyjs::enable('mst_operator_general_select') 
+        shinyjs::enable('mst_institute_general_select') 
+        shinyjs::enable('mst_comm_general_select') 
+      }
+    }
+    
+    if(!is.null(input$rep_analysis)) {
+      if(isFALSE(input$rep_analysis)) {
+        shinyjs::disable('rep_cgmlst_analysis') 
+        shinyjs::disable('rep_tree_analysis') 
+        shinyjs::disable('rep_distance') 
+        shinyjs::disable('rep_missval') 
+        shinyjs::disable('rep_version') 
+      } else {
+        shinyjs::enable('rep_cgmlst_analysis') 
+        shinyjs::enable('rep_tree_analysis') 
+        shinyjs::enable('rep_distance') 
+        shinyjs::enable('rep_missval') 
+        shinyjs::enable('rep_version') 
+      }
+    }
+    
+    if(length(input$select_rep_tab) > 0) {
+      updateCheckboxInput(session, "rep_entrytable", value = TRUE)
+    } else {
+      updateCheckboxInput(session, "rep_entrytable", value = FALSE)
+    }
+  })
+  
+  ### Save Report ----
+  
+  #### Get Report elements ----
+  
+  observe({
+    if(!is.null(DB$data)){
+      if(!is.null(input$tree_algo)) {
+        req(c(input$rep_entrytable, input$rep_general,
+              input$rep_date_general, input$rep_operator_general,
+              input$rep_institute_general, input$rep_comm_general,
+              input$rep_analysis, input$rep_cgmlst_analysis,
+              input$rep_tree_analysis, input$rep_distance,
+              input$rep_missval, input$rep_version,
+              input$rep_plot_report, input$select_rep_tab))
+        Report$report_df <- data.frame(Element = c("entry_table", "general_show",
+                                                   "general_date", "operator",
+                                                   "institute", "comment",
+                                                   "analysis_show", "scheme",
+                                                   "tree", "distance", "na_handling", "version",
+                                                   "plot"),
+                                       Include = c(input$rep_entrytable, input$rep_general,
+                                                   input$rep_date_general, input$rep_operator_general,
+                                                   input$rep_institute_general, input$rep_comm_general,
+                                                   input$rep_analysis, input$rep_cgmlst_analysis,
+                                                   input$rep_tree_analysis, input$rep_distance,
+                                                   input$rep_missval, input$rep_version,
+                                                   input$rep_plot_report))
+      }
+    }
+  })
+  
+  #### Get Report values ----
+  
+  observeEvent(input$create_tree, {
+    if(input$tree_algo == "Minimum-Spanning") {
+      Report$report_list_mst <- list(entry_table = DB$meta_true,
+                                     scheme = DB$schemeinfo, 
+                                     tree = input$tree_algo,
+                                     na_handling = if(anyNA(DB$allelic_profile_true)){input$na_handling} else {NULL},
+                                     distance = "Hamming Distances",
+                                     version = c(phylotraceVersion, "2.5.1"),
+                                     plot = "MST")
+    } else if(input$tree_algo == "Neighbour-Joining") {
+      Report$report_list_nj <- list(entry_table = DB$meta_true,
+                                    scheme = DB$schemeinfo, 
+                                    tree = input$tree_algo,
+                                    na_handling = input$na_handling,
+                                    distance = "Hamming Distances",
+                                    version = c(phylotraceVersion, "2.5.1"),
+                                    plot = "NJ")
+    } else {
+      Report$report_list_upgma <- list(entry_table = DB$meta_true,
+                                       scheme = DB$schemeinfo, 
+                                       tree = input$tree_algo,
+                                       na_handling = input$na_handling,
+                                       distance = "Hamming Distances",
+                                       version = c(phylotraceVersion, "2.5.1"),
+                                       plot = "UPGMA")
+    }
+  })
+  
+  # Save plot for Report
+  plot.report <- reactive({
+    if(input$tree_algo == "Neighbour-Joining") {
+      jpeg(paste0(getwd(), "/Report/NJ.jpeg"), width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale), quality = 100)
+      print(nj_tree())
+      dev.off()
+    } else if(input$tree_algo == "UPGMA") {
+      jpeg(paste0(getwd(), "/Report/UPGMA.jpeg"), width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale), quality = 100)
+      print(upgma_tree())
+      dev.off()
+    } else if (input$tree_algo == "Minimum-Spanning") {
+      shinyjs::runjs("mstReport();")
+      decoded_data <- base64enc::base64decode(input$canvas_data)
+      writeBin(decoded_data, paste0(getwd(), "/Report/MST.jpg"))
+    }
+  })
+  
+  #### Event Save Report ----
+  output$download_report <- downloadHandler(
+    filename = function() {
+      if(input$tree_algo == "Minimum-Spanning") {
+        paste0("MST_Report_", Sys.Date(), ".html")
+      } else if(input$tree_algo == "Neighbour-Joining") {
+        paste0("NJ_Report_", Sys.Date(), ".html")
+      } else {paste0("UPGMA_Report_", Sys.Date(), ".html")}
+    },
+    content = function(file) {
+      if(input$tree_algo == "Minimum-Spanning") {
+        plot.report()
+        
+        report <- c(Report$report_list_mst, 
+                    "general_date" = as.character(input$mst_date_general_select),
+                    "operator" = input$mst_operator_general_select,
+                    "institute" = input$mst_institute_general_select,
+                    "comment" = input$mst_comm_general_select,
+                    "report_df" = Report$report_df)
+        
+        report[["table_columns"]] <- input$select_rep_tab
+        
+        # Save data to an RDS file if any elements were selected
+        if (!is.null(report)) {
+          
+          log_print("Creating MST report")
+          
+          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
+          
+          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
+          
+          file.copy(paste0(getwd(), "/Report/Report.html"), file)
+        } else {
+          log_print("Creating MST report failed (report is null)")
+        }
+      } else if(input$tree_algo == "Neighbour-Joining") {
+        plot.report()
+        report <- c(Report$report_list_nj, 
+                    "general_date" = as.character(input$mst_date_general_select),
+                    "operator" = input$mst_operator_general_select,
+                    "institute" = input$mst_institute_general_select,
+                    "comment" = input$mst_comm_general_select,
+                    "report_df" = Report$report_df)
+        
+        report[["table_columns"]] <- input$select_rep_tab
+        
+        # Save data to an RDS file if any elements were selected
+        if (!is.null(report)) {
+          log_print("Creating NJ report")
+          
+          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
+          
+          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
+          
+          file.copy(paste0(getwd(), "/Report/Report.html"), file)
+        } else {
+          log_print("Creating NJ report failed (report is null)")
+        }
+        
+      } else {
+        plot.report()
+        report <- c(Report$report_list_upgma, 
+                    "general_date" = as.character(input$mst_date_general_select),
+                    "operator" = input$mst_operator_general_select,
+                    "institute" = input$mst_institute_general_select,
+                    "comment" = input$mst_comm_general_select,
+                    "report_df" = Report$report_df)
+        
+        report[["table_columns"]] <- input$select_rep_tab
+        
+        # Save data to an RDS file if any elements were selected
+        if (!is.null(report)) {
+          log_print("Creating UPGMA report")
+          
+          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
+          
+          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
+          
+          file.copy(paste0(getwd(), "/Report/Report.html"), file)
+        } else {
+          log_print("Creating UPGMA report failed (report is null)")
+        }
+        
+      }
+      removeModal()
+    }
+  )
+  
+  
+  # _______________________ ####
+  
+  ## Gene Screening  ----
+  
+  ### Render UI Elements ----
+  
+  # Rendering results table
+  output$gs_results_table <- renderUI({
+    req(DB$data)
+    if(!is.null(Screening$selected_isolate)) {
+      if(length(Screening$selected_isolate) > 0) {
+        fluidRow(
+          div(class = "loci_table",
+              DT::dataTableOutput("gs_profile_table")),
+          br(),
+          HTML(
+            paste0("<span style='color: white; font-size: 12px'>", 
+                   '<strong>RSL</strong> = <em>Reference Sequence Length</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>%CRS</strong> = <em>% Coverage of Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>%IRS</strong> = <em>% Identity to Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>ACS</strong> = <em>Accession of Closest Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>NCS</strong> = <em>Name of Closest Sequence</em>')
+            
+          )
+        )
+      } else {
+        fluidRow(
+          br(), br(),
+          p(
+            HTML(
+              paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
+                     'Select entry from the table to display resistance profile')
+              
+            )
+          )
+        )
+      }
+    } else {
+      fluidRow(
+        br(), br(),
+        p(
+          HTML(
+            paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
+                   'Select entry from the table to display resistance profile')
+            
+          )
+        )
+      )
+    }
+  })
+  
+  # Gene screening download button
+  output$gs_download <- renderUI({
+    req(DB$data)
+    if(!is.null(Screening$selected_isolate)) {
+      if(length(Screening$selected_isolate) > 0) {
+        fluidRow(
+          downloadBttn(
+            "download_resistance_profile",
+            style = "simple",
+            label = "Profile Table",
+            size = "sm",
+            icon = icon("download"),
+            color = "primary"
+          ),
+          bsTooltip("download_resistance_profile_bttn", 
+                    HTML(paste0("Save resistance profile table for</br>",
+                                Screening$selected_isolate)), 
+                    placement = "bottom", trigger = "hover")
+        )
+      } else {NULL}
+    } else {NULL}
+  })
+  
+  # Conditionally render table selectiom interface
+  output$gs_table_selection <- renderUI({
+    req(DB$data, input$gs_view)
+    if(input$gs_view == "Table") {
+      fluidRow(
+        column(1),
+        column(
+          width = 10,
+          div(class = "loci_table",
+              dataTableOutput("gs_isolate_table"))
+        )
+      )
+    } else {NULL}
+  })
+  
+  # Resistance profile table output display
+  output$gs_profile_display <- renderUI({
+    req(DB$data)
+    if(!is.null(DB$meta_gs) & !is.null(input$gs_view)) {
+      if(input$gs_view == "Table") {
+        column(
+          width = 10,
+          hr(), 
+          fluidRow(
+            column(
+              width = 4,
+              p(
+                HTML(
+                  paste0("<span style='color: white; font-size: 18px'>", 
+                         "Gene Screening Results</br>",
+                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
+                         "Comprising genes for resistance, virulence, stress, etc.")
+                )
+              )
+            ),
+            column(
+              width = 4,
+              uiOutput("gs_download")
+            )
+          ),
+          br(),
+          uiOutput("gs_results_table")
+        )
+      } else {
+        column(
+          width = 10,
+          fluidRow(
+            column(
+              width = 4,
+              p(
+                HTML(
+                  paste0("<span style='color: white; font-size: 18px'>", 
+                         "Gene Screening Results</br>",
+                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
+                         "Comprising genes for resistance, virulence, stress, etc.")
+                )
+              )
+            ),
+            column(
+              width = 4,
+              div(
+                class = "gs-picker",
+                pickerInput(
+                  "gs_profile_select",
+                  "",
+                  choices = list(
+                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+                    },
+                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
+                    },
+                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
+                    }
+                  ),
+                  choicesOpt = list(
+                    disabled = c(
+                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
+                    )
+                  ),
+                  options = list(
+                    `live-search` = TRUE,
+                    size = 10,
+                    style = "background-color: white; border-radius: 5px;"
+                  )
+                )
+              )
+            ),
+            column(
+              width = 3,
+              uiOutput("gs_download")
+            )
+          ),
+          br(),
+          uiOutput("gs_results_table")
+        )
+      }
+    } else {NULL}
+  })
+  
+  # Screening sidebar
+  output$screening_sidebar <- renderUI({
+    req(DB$data)
+    if(!is.null(DB$meta_gs)) {
+      column(
+        width = 12,
+        align = "center",
+        br(), br(),
+        p(
+          HTML(
+            paste(
+              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Toggle View')
+            )
+          )
+        ),
+        radioGroupButtons(
+          inputId = "gs_view",
+          choices = c("Picker", "Table"),
+          selected = "Picker",
+          checkIcon = list(
+            yes = icon("square-check"),
+            no = icon("square")
+          )
+        ),
+        br()
+      )
+    } else {NULL}
+  })
+  
+  # Resistance profile table
+  observe({
+    req(DB$meta_gs, Screening$selected_isolate, DB$database, DB$scheme, DB$data)
+    
+    if(length(Screening$selected_isolate) > 0 & any(Screening$selected_isolate %in% DB$data$`Assembly ID`)) {
+      iso_select <- Screening$selected_isolate
+      iso_path <- file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
+                            iso_select, "resProfile.tsv")
+      
+      res_profile <- read.delim(iso_path)
+      
+      colnames(res_profile) <- c(
+        "Protein Identifier",	"Contig ID", "Start", "Stop", "Strand", "Gene Symbol", 
+        "Sequence Name", "Scope", "Element Type",  "Element Subtype", "Class", 
+        "Subclass", "Method", "Target Length", "RSL",	"%CRS", "%IRS", 
+        "Alignment Length", "ACS", "Name of Closest Sequence", "HMM ID", "HMM Description")
+      
+      Screening$res_profile <- res_profile %>%
+        relocate(c("Gene Symbol", "Sequence Name", "Element Subtype", "Class", 
+                   "Subclass", "Scope", "Contig ID", "Target Length", "Alignment Length",
+                   "Start", "Stop", "Strand"))
+      
+      # Generate gene profile table
+      output$gs_profile_table <- DT::renderDataTable(
+        Screening$res_profile,
+        selection = "single",
+        rownames= FALSE,
+        options = list(pageLength = 10, scrollX = TRUE,
+                       autoWidth = TRUE,
+                       columnDefs = list(list(width = '400px', targets = c("Sequence Name",
+                                                                           "Name of Closest Sequence"))),
+                       columnDefs = list(list(width = 'auto', targets = "_all")),
+                       columnDefs = list(list(searchable = TRUE,
+                                              targets = "_all")),
+                       initComplete = DT::JS(
+                         "function(settings, json) {",
+                         "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                         "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                         # "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                         # "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                         "}"
+                       ),
+                       drawCallback = DT::JS(
+                         "function(settings) {",
+                         # "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                         # "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                         "}"
+                       ))
+      )
+    } else {
+      output$gs_profile_table <- NULL
+    }
+  })
+
+  #Resistance profile selection table
+  observe({
+    req(DB$meta, DB$data)
+    output$gs_isolate_table <- renderDataTable(
+      select(DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ], -c(3, 4, 10, 11, 12)),
+      selection = "single",
+      rownames= FALSE,
+      options = list(pageLength = 10,
+                     columnDefs = list(list(searchable = TRUE,
+                                            targets = "_all")),
+                     initComplete = DT::JS(
+                       "function(settings, json) {",
+                       "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                       "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                       "}"
+                     ),
+                     drawCallback = DT::JS(
+                       "function(settings) {",
+                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                       "}"
+                     ))
+    )
+  })
+  
+  observe({
+    req(input$screening_res_sel, DB$database, DB$scheme, DB$data)
+    if(!is.null(Screening$status_df) &
+       !is.null(input$screening_res_sel) & 
+       !is.null(Screening$status_df$status) & 
+       !is.null(Screening$status_df$isolate)) {
+      if(length(input$screening_res_sel) > 0) {
+        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
+          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
+            results <- read.delim(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
+                                            input$screening_res_sel, "resProfile.tsv"))
+            
+            output$screening_table <- renderDataTable(
+              select(results, c(6, 7, 8, 9, 11)),
+              selection = "single",
+              options = list(pageLength = 10,
+                             columnDefs = list(list(searchable = TRUE,
+                                                    targets = "_all")),
+                             initComplete = DT::JS(
+                               "function(settings, json) {",
+                               "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                               "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                               "}"
+                             ),
+                             drawCallback = DT::JS(
+                               "function(settings) {",
+                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                               "}"
+                             )))
+          } else {output$screening_table <- NULL}
+        }
+      } else {
+        output$screening_table <- NULL
+      }
+    } else {
+      output$screening_table <- NULL
+    }
+      
+  })
+  
+  # Availablity feedback
+  output$gene_screening_info <- renderUI({
+    req(DB$data)
+    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
+          )
+        )
+      )
+    } else {
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
+          )
+        )
+      )
+    }
+  })
+  
+  output$gene_resistance_info <- renderUI({
+    req(DB$data)
+    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
+          )
+        )
+      )
+    } else {
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
+          )
+        )
+      )
+    }
+  })
+  
+  # Screening Interface
+  
+  output$screening_interface <- renderUI({
+    req(DB$data)
+    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
+      column(
+        width = 12,
+        fluidRow(
+          column(1),
+          column(
+            width = 3,
+            align = "center",
+            br(), br(),
+            p(
+              HTML(
+                paste(
+                  tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Isolates for Screening')
+                )
+              )
+            ),
+            if(Screening$picker_status) {
+              div(
+                class = "screening_div",
+                pickerInput(
+                  "screening_select",
+                  "",
+                  choices = list(
+                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
+                    },
+                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+                    },
+                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
+                    }
+                  ),
+                  choicesOpt = list(
+                    disabled = c(
+                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
+                    )
+                  ),
+                  options = list(
+                    `live-search` = TRUE,
+                    `actions-box` = TRUE,
+                    size = 10,
+                    style = "background-color: white; border-radius: 5px;"
+                  ),
+                  multiple = TRUE
+                )
+              )
+            } else {
+              div(
+                class = "screening_div",
+                pickerInput(
+                  "screening_select",
+                  "",
+                  choices = Screening$picker_choices,
+                  selected = Screening$picker_selected,
+                  options = list(
+                    `live-search` = TRUE,
+                    `actions-box` = TRUE,
+                    size = 10,
+                    style = "background-color: white; border-radius: 5px;"
+                  ),
+                  multiple = TRUE
+                ) 
+              )
+            },
+            br(), br(),
+            uiOutput("genome_path_gs")
+          ),
+          column(
+            width = 3,
+            uiOutput("screening_start")
+          ),
+          column(
+            width = 3,
+            align = "center",
+            br(), br(),
+            uiOutput("screening_result_sel")
+          ),
+          column(1)
+        ),
+        fluidRow(
+          column(1),
+          column(
+            width = 10,
+            br(), br(), 
+            uiOutput("screening_result"),
+            br(), br(), br(), br()
+          )
+        )
+      )
+    }
+  })
+  
+  ### Screening Events ----
+  
+  observe({
+    req(DB$data, input$gs_view)
+    if(input$gs_view == "Table") {
+      meta_gs <- DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ]
+      Screening$selected_isolate <- meta_gs$`Assembly ID`[input$gs_isolate_table_rows_selected]
+    } else if(input$gs_view == "Picker") {
+      Screening$selected_isolate <- input$gs_profile_select
+    }
+  })
+  
+  output$download_resistance_profile <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save resistance profile table ", Screening$selected_isolate, "_Profile.csv"))
+      
+      paste0(format(Sys.Date()), "_", Screening$selected_isolate, "_Profile.csv")
+    },
+    content = function(file) {
+      write.table(
+        Screening$res_profile,
+        file, 
+        sep = ";",
+        row.names = FALSE, 
+        quote = FALSE
+      ) 
+    }
+  )
+  
+  # Reset screening 
+  observeEvent(input$screening_reset_bttn, {
+    log_print("Reset gene screening")
+    
+    # reset status file
+    sapply(Screening$status_df$isolate, remove.screening.status)
+    
+    # set feedback variables
+    Screening$status <- "idle"
+    Screening$status_df <- NULL
+    Screening$choices <- NULL
+    Screening$picker_status <- TRUE
+    Screening$first_result <- NULL
+    
+    # change reactive UI
+    output$screening_table <- NULL
+    output$screening_result <- NULL
+    output$screening_fail <- NULL
+    
+    updatePickerInput(session, "screening_select", selected = character(0))
+    
+    # disable isolate picker
+    shinyjs::runjs("$('#screening_select').prop('disabled', false);")
+    shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
+  })
+  
+  # Cancel screening
+  observeEvent(input$screening_cancel, {
+    showModal(
+      modalDialog(
+        paste0(
+          "Gene screening is still pending. Stopping this process will cancel the screening."
+        ),
+        title = "Reset Multi Typing",
+        fade = TRUE,
+        easyClose = TRUE,
+        footer = tagList(
+          modalButton("Cancel"),
+          actionButton("conf_screening_cancel", "Stop", class = "btn btn-danger")
+        )
+      )
+    )
+  })
+  
+  observeEvent(input$conf_screening_cancel, {
+    log_print("Cancelled gene screening")
+    removeModal()
+    
+    show_toast(
+      title = "Gene Screening Terminated",
+      type = "warning",
+      position = "bottom-end",
+      timer = 6000
+    )
+    
+    # terminate screening
+    system(paste("kill $(pgrep -f 'execute/screening.sh')"), wait = FALSE)
+    system(paste("killall -TERM tblastn"), wait = FALSE)
+    
+    # reset status file
+    sapply(Screening$status_df$isolate, remove.screening.status)
+    
+    # set feedback variables
+    Screening$status <- "idle"
+    Screening$status_df <- NULL
+    Screening$choices <- NULL
+    Screening$picker_status <- TRUE
+    Screening$first_result <- NULL
+    
+    # change reactive UI
+    output$screening_table <- NULL
+    output$screening_result <- NULL
+    
+    updatePickerInput(session, "screening_select", selected = character(0))
+    
+    # disable isolate picker
+    shinyjs::runjs("$('#screening_select').prop('disabled', false);")
+    shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
+  })
+  
+  # Get selected assembly
+  observe({
+    req(DB$data, Screening$status)
+    if (length(input$screening_select) < 1) {
+      output$genome_path_gs <- renderUI(HTML(
+        paste("<span style='color: white; font-style:italic'>", length(input$screening_select), " isolate(s) queried for screening")
+      ))
+      
+      output$screening_start <- NULL
+      
+    } else if (length(input$screening_select) > 0) {
+      
+      output$screening_start <- renderUI({
+        
+        fluidRow(
+          column(
+            width = 12,
+            br(), br(), 
+            if(length(input$screening_select) < 1) {
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+                    paste("<span style='color: white; font-style:italic'>", 
+                          "&nbsp Select Isolate(s) for Screening")))
+                )
+              )
+            } else if(Screening$status == "finished") {
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:white"></i>',
+                    paste("<span style='color: white; font-style:italic'>", 
+                          "&nbsp Reset to Perform Screening Again")))
+                ),
+                actionButton(
+                  "screening_reset_bttn",
+                  "Reset",
+                  icon = icon("arrows-rotate")
+                ),
+                if(!is.null(Screening$status_df)) {
+                  p(
+                    HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
+                               sum(Screening$status_df$status != "unfinished"), "/",
+                               nrow(Screening$status_df), " Isolate(s) screened"))
+                  )
+                }
+              )
+            } else if(Screening$status == "idle") {
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
+                    paste("<span style='color: white;'>",
+                          "&nbsp Screening Ready")))
+                ),
+                actionButton(
+                  inputId = "screening_start_button",
+                  label = "Start",
+                  icon = icon("circle-play")
+                )
+              )
+            } else if(Screening$status == "started") {
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-clock" style="font-size:15px;color:white"></i>',
+                    paste("<span style='color: white;'>",
+                          "&nbsp Running Screening ...")))
+                ),
+                fluidRow(
+                  column(3),
+                  column(
+                    width = 3,
+                    actionButton(
+                      inputId = "screening_cancel",
+                      label = "Terminate",
+                      icon = icon("ban")
+                    )
+                  ),
+                  column(
+                    width = 3,
+                    HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:22px;color:white;margin-top:27px;position:relative;left:20px"></i>'))
+                  )
+                ),
+                if(!is.null(Screening$status_df)) {
+                  p(
+                    HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
+                               sum(Screening$status_df$status != "unfinished"), "/",
+                               nrow(Screening$status_df), " isolate(s) screened"))
+                  )
+                }
+              )
+            }
+          )
+        )
+      })
+    } else {NULL}
+  })
+  
+  #### Running Screening ----
+  
+  observeEvent(input$screening_start_button, {
+    
+    if(tail(readLogFile(), 1) != "0") {
+      show_toast(
+        title = "Pending Multi Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      
+      log_print("Started gene screening")
+      
+      Screening$status <- "started"
+      Screening$picker_choices <- list(
+        Unscreened = if (sum(DB$data$Screened == "No") == 1) {
+          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
+        } else {
+          DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
+        },
+        Screened =  if (sum(DB$data$Screened == "Yes") == 1) {
+          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
+        } else {
+          DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+        },
+        `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
+          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
+        } else {
+          DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
+        }
+      )
+      Screening$picker_selected <- input$screening_select
+      Screening$picker_status <- FALSE
+      
+      show_toast(
+        title = "Gene screening started",
+        type = "success",
+        position = "bottom-end",
+        timer = 6000
+      )
+      
+      Screening$meta_df <- data.frame(wd = getwd(),
+                                 selected = paste(
+                                   file.path(DB$database, gsub(" ", "_", DB$scheme),
+                                             "Isolates", input$screening_select,
+                                             paste0(input$screening_select, ".zip")), 
+                                   collapse = " "),
+                                 species = gsub(" ", "_", DB$scheme))
+      
+      Screening$status_df <- data.frame(isolate = basename(gsub(".zip", "", str_split_1(Screening$meta_df$selected, " "))), 
+                                        status = "unfinished")
+      
+       # Reset screening status
+      sapply(Screening$status_df$isolate, remove.screening.status)
+      
+      saveRDS(Screening$meta_df, paste0(getwd(), "/execute/screening_meta.rds"))
+      
+      # Disable pickerInput
+      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').prop('disabled', true);"))
+      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').selectpicker('refresh');"))
+    
+      # System execution screening.sh
+      system(paste("bash", paste0(getwd(), "/execute/screening.sh")), wait = FALSE)
+    }
+  })
+  
+  observe({
+    req(DB$data, Screening$status, input$screening_res_sel, Screening$status_df)
+    if(!is.null(Screening$status_df) &
+       !is.null(Screening$status_df$status) & 
+       !is.null(Screening$status_df$isolate) &
+       !is.null(input$screening_res_sel)) {
+      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
+        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
+          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
+            output$screening_result <- renderUI(
+              column(
+                width = 12,
+                hr(), br(),
+                dataTableOutput("screening_table") 
+              )
+            )
+          } else {
+            output$screening_result <- renderUI(
+              column(
+                width = 12,
+                hr(), br(),
+                verbatimTextOutput("screening_fail")
+              )
+            )
+          }
+        }
+      } else {
+        output$screening_result <- NULL
+      }
+    } else {
+      output$screening_result <- NULL
+    }
+  })
+  
+  observe({
+    req(DB$data, Screening$status, input$screening_res_sel)
+    if(!is.null(Screening$status_df) &
+       !is.null(Screening$status_df$status) & 
+       !is.null(Screening$status_df$isolate) &
+       !is.null(input$screening_res_sel)) {
+      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
+        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
+          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "fail") {
+            output$screening_fail <- renderPrint({
+              cat(paste(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
+                                            "Isolates", input$screening_res_sel, "status.txt")),"\n"))
+            })
+          }
+        }
+      } else {
+        output$screening_fail <- NULL
+      }
+    } else {
+      output$screening_fail <- NULL
+    }
+  })
+  
+  observe({
+    req(DB$data)
+    if(!is.null(Screening$status)) {
+      if(Screening$status != "idle") {
+        
+        # start status screening for user feedback
+        check_screening()
+        
+        if(isTRUE(Screening$first_result)) {
+          output$screening_result_sel <- renderUI(
+            column(
+              width = 12,
+              align = "center",
+              selectInput(
+                "screening_res_sel",
+                label = h5("Select Result", style = "color:white; margin-bottom: 28px; margin-top: -10px;"),
+                choices = ""
+              ),
+              if(!is.null(Screening$status_df)) {
+                p(HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
+                             if(sum(Screening$status_df$status == "success") == 1) {
+                               "1 success &nbsp / &nbsp"
+                             } else {
+                               paste0(sum(Screening$status_df$status == "success"), " successes &nbsp / &nbsp")
+                             },
+                             if(sum(Screening$status_df$status == "fail") == 1) {
+                               "1 failure"
+                             } else {
+                               paste0(sum(Screening$status_df$status == "fail"), " failures")
+                             })))
+              }
+            )
+          )
+          
+          Screening$first_result <- FALSE
+        }
+      } else if(Screening$status == "idle") {
+        output$screening_result_sel <- NULL
+      }
+    }
+  }) 
+    
+  check_screening <- reactive({
+    invalidateLater(500, session)
+    
+    req(Screening$status_df)
+    
+    if(Screening$status == "started") {
+      
+      Screening$status_df$status <- sapply(Screening$status_df$isolate, check_status)
+      
+      if(any("unfinished" != Screening$status_df$status) &
+         !identical(Screening$choices, Screening$status_df$isolate[which(Screening$status_df$status != "unfinished")])) {
+        
+        status_df <- Screening$status_df[which(Screening$status_df$status != "unfinished"),]
+        
+        Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
+                                                                 Screening$status_df$status == "fail")]
+        
+        if(sum(Screening$status_df$status != "unfinished") > 0) {
+          if(is.null(Screening$first_result)) {
+            Screening$first_result <- TRUE
+          }
+        }
+        
+        if(tail(status_df$status, 1) == "success") {
+          
+          # Changing "Screened" metadata variable in database
+          Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+          
+          Database[["Typing"]]$Screened[which(Database[["Typing"]]["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
+
+          saveRDS(Database, file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+
+          DB$data$Screened[which(DB$data["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
+          
+          DB$meta_gs <- select(DB$data, c(1, 3:13))
+          DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+          DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+          
+          show_toast(
+            title = paste("Successful screening of", tail(Screening$choices, 1)),
+            type = "success",
+            position = "bottom-end",
+            timer = 6000)
+          
+          updateSelectInput(session = session,
+                            inputId = "screening_res_sel",
+                            choices = Screening$choices,
+                            selected = tail(Screening$choices, 1))
+          
+        } else if(tail(status_df$status, 1) == "fail") {
+          
+          show_toast(
+            title = paste("Failed screening of", tail(status_df$isolate, 1)),
+            type = "error",
+            position = "bottom-end",
+            timer = 6000)
+          
+          updateSelectInput(session = session,
+                            inputId = "screening_res_sel",
+                            choices = Screening$choices,
+                            selected = tail(Screening$choices, 1))
+        }
+        
+        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+          Screening$status <- "finished"
+        }
+      } else {
+        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+          Screening$status <- "finished"
+        }
+      }
+      
+      if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+        Screening$status <- "finished"
+      }
+    }
+  }) 
+  
+  
+  # _______________________ ####
+  
+  ## Typing  ----
+  
+  # Render Single/Multi Switch
+  
+  readLogFile <- reactive({
+    invalidateLater(5000, session)
+    readLines(paste0(getwd(), "/logs/script_log.txt"))
+  })
+  
+  # Render sidebar dependent on data presence
+  # No sidebar
+  output$typing_sidebar <- renderUI({
+    if(!is.null(DB$exist)) {
+      if(DB$exist) {
+        NULL
+      } else {
+        column(
+          width = 12,
+          align = "center",
+          br(), br(),
+          p(
+            HTML(
+              paste(
+                tags$span(style='color: white; font-size: 18px; margin-bottom: 0px', 'Typing Mode')
+              )
+            )
+          ),
+          radioGroupButtons(
+            inputId = "typing_mode",
+            choices = c("Single", "Multi"),
+            selected = "Single",
+            checkIcon = list(
+              yes = icon("square-check"),
+              no = icon("square")
+            )
+          ),
+          br()
+        )
+      }
+    }
+    
+  })
+  
+  # No db typing message
+  output$typing_no_db <- renderUI({
+    if(!is.null(DB$exist)) {
+      if(DB$exist) {
+        column(
+          width = 4,
+          align = "left",
+          br(),
+          br(),
+          br(),
+          br(),
+          p(
+            HTML(
+              paste0(
+                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 50px', 'To initiate allelic typing, a cgMLST scheme must be downloaded first.'
+                )
+              )
+            )
+          )
+        )
+      } else {NULL}
+    } else {NULL}
+  })
+  
+  ### Single Typing ----
+  
+  #### Render UI Elements ----
+  
+  # Render single typing naming issues
+  output$single_select_issues <- renderUI({
+    req(input$assembly_id)
+    
+    if(nchar(trimws(input$assembly_id)) < 1) {
+      ass_id <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
+    } else {
+      ass_id <- trimws(input$assembly_id)
+    }
+    
+    if(ass_id %in% unlist(DB$data["Assembly ID"])) {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Assembly ID already present in database.")))
+    } else if (ass_id == "") {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Empty Assembly ID.")))
+    } else if (grepl("[()/\\:*?\"<>|]", ass_id)) {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Invalid Assembly ID. Avoid special characters.")))
+    } else if(grepl(" ", ass_id)) {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Invalid Assembly ID. Avoid empty spaces.")))
+    } else {HTML(paste(
+      '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
+      paste("<span style='color: white; font-style:italic'>",
+            "&nbsp Assembly ID compatible with local database.")))}
+  })
+  
+  # Render Typing Results if finished
+  observe({
+    if(Typing$progress_format_end == 999999) {
+      if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
+        if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
+          output$typing_result_table <- renderRHandsontable({
+            Typing$typing_result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
+            Typing$typing_result_table <- mutate_all(Typing$typing_result_table, as.character)
+            if(nrow(Typing$typing_result_table) > 0) {
+              if(nrow(Typing$typing_result_table) > 15) {
+                rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
+                              stretchH = "all", height = 500, readOnly = TRUE,
+                              contextMenu = FALSE) %>%
+                  hot_cols(columnSorting = TRUE) %>%
+                  hot_rows(rowHeights = 25) %>%
+                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter",
+                          cellWidths = list(100, 160, NULL)) %>%
+                  hot_col("Value", renderer=htmlwidgets::JS(
+                    "function(instance, td, row, col, prop, value, cellProperties) {
+                      if (value.length > 8) {
+                        value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                      }
+                      td.innerHTML = value;
+                      td.style.textAlign = 'center';
+                      return td;
+                     }"
+                  ))
+              } else {
+                rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
+                              stretchH = "all", readOnly = TRUE,
+                              contextMenu = FALSE,) %>%
+                  hot_cols(columnSorting = TRUE) %>%
+                  hot_rows(rowHeights = 25) %>%
+                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter",
+                          cellWidths = list(100, 160, NULL)) %>%
+                  hot_col("Value", renderer=htmlwidgets::JS(
+                    "function(instance, td, row, col, prop, value, cellProperties) {
+                      if (value.length > 8) {
+                        value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                      }
+                      td.innerHTML = value;
+                      td.style.textAlign = 'center';
+                      return td;
+                     }"
+                  ))
+              }
+            }
+          })
+          
+          output$single_typing_results <- renderUI({
+            result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
+            number_events <- nrow(result_table)
+            
+            n_new <- length(grep("New Variant", result_table$Event))
+            
+            n_missing <- number_events - n_new
+            
+            # Show results table only if successful typing 
+            if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
+              if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
+                if(number_events > 0) {
+                  column(
+                    width = 12,
+                    HTML(paste("<span style='color: white;'>", 
+                               length(Typing$scheme_loci_f) - number_events,
+                               "loci were assigned a variant from local scheme.")),
+                    br(), 
+                    HTML(paste("<span style='color: white;'>", 
+                               n_missing,
+                               if(n_missing == 1) " locus not assigned (<i>NA</i>)." else " loci not assigned (<i>NA</i>).")),
+                    br(),
+                    HTML(paste("<span style='color: white;'>", 
+                               n_new,
+                               if(n_new == 1) " locus with new variant."  else " loci with new variants.")),
+                    br(), br(),
+                    rHandsontableOutput("typing_result_table")
+                  )
+                } else {
+                  column(
+                    width = 12,
+                    HTML(paste("<span style='color: white;'>", 
+                               length(Typing$scheme_loci_f),
+                               "successfully assigned from local scheme."))
+                  )
+                }
+              }
+            }
+          })
+          
+        } else {
+          
+          output$single_typing_results <- NULL
+          
+        }
+      } else {
+        output$single_typing_results <- NULL
+      }
+    }
+    
+  })
+  
+  # Render Initiate Typing UI
+  output$initiate_typing_ui <- renderUI({
+    column(
+      width = 4,
+      align = "center",
+      br(),
+      br(),
+      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+      br(),
+      br(),
+      p(
+        HTML(
+          paste(
+            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File (FASTA)')
+          )
+        )
+      ),
+      fluidRow(
+        column(1),
+        column(
+          width = 11,
+          align = "center",
+          shinyFilesButton(
+            "genome_file",
+            "Browse" ,
+            icon = icon("file"),
+            title = "Select the assembly in .fasta/.fna/.fa format:",
+            multiple = FALSE,
+            buttonType = "default",
+            class = NULL,
+            root = path_home()
+          ),
+          br(),
+          br(),
+          uiOutput("genome_path"),
+          br()
+        )
+      )
+    )
+  })
+  
+  # Render Declare Metadata UI
+  
+  observe({
+    if (nrow(Typing$single_path) < 1) {
+      output$genome_path <- renderUI(HTML(
+        paste("<span style='color: white; margin-left:-30px'>", "No file selected.")
+      ))
+      
+      # dont show subsequent metadata declaration and typing start UI
+      output$metadata_single_box <- NULL
+      output$start_typing_ui <- NULL
+      
+    } else if (nrow(Typing$single_path) > 0) {
+      
+      if (str_detect(str_sub(Typing$single_path$name, start = -6), ".fasta") | 
+          str_detect(str_sub(Typing$single_path$name, start = -6), ".fna") | 
+          str_detect(str_sub(Typing$single_path$name, start = -6), ".fa")) {
+        
+        # Render selected assembly path
+        output$genome_path <- renderUI({
+          HTML(
+            paste(
+              "<span style='color: white; margin-left:-30px; font-weight: bolder'>",
+              as.character(Typing$single_path$name)
+            )
+          )
+        })
+        
+        # Render metadata declaration box
+        output$metadata_single_box <- renderUI({
+          
+          # Render placeholder 
+          updateTextInput(session, "assembly_id", value = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
+          updateTextInput(session, "assembly_name", value = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
+          
+          column(
+            width = 3,
+            align = "center",
+            br(), br(),
+            h3(p("Declare Metadata"), style = "color:white; margin-left:-40px"),
+            br(), br(),
+            div(
+              class = "multi_meta_box",
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "90%",
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("assembly_id",
+                                value = "",
+                                label = "",
+                                width = "80%")
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 12,
+                    uiOutput("single_select_issues")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("assembly_name",
+                                label = "",
+                                width = "80%")
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      dateInput("append_isodate",
+                                label = "",
+                                width = "80%",
+                                max = Sys.Date())
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("append_host",
+                                label = "",
+                                width = "80%")
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table_country",
+                      pickerInput(
+                        "append_country",
+                        label = "",
+                        choices = list("Common" = sel_countries,
+                                       "All Countries" = country_names),
+                        options = list(
+                          `live-search` = TRUE,
+                          `actions-box` = TRUE,
+                          size = 10,
+                          style = "background-color: white; border-radius: 5px;"
+                        ),
+                        width = "90%"
+                      )
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput(
+                        "append_city",
+                        label = "",
+                        width = "80%"
+                      )
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 12,
+                    align = "center",
+                    br(), br(),
+                    actionButton(
+                      inputId = "conf_meta_single",
+                      label = "Confirm"
+                    ),
+                    br()
+                  )
+                ),
+                br()
+              )
+            )
+          )
+        })
+      } else {
+        show_toast(
+          title = "Wrong file type (only fasta/fna/fa)",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+      }
+    }
+  })
+  
+  # Get genome datapath
+  
+  observe({
+    # Get selected Genome in Single Mode
+    shinyFileChoose(input,
+                    "genome_file",
+                    roots = c(Home = path_home(), Root = "/"),
+                    defaultRoot = "Home",
+                    session = session,
+                    filetypes = c('', 'fasta', 'fna', 'fa'))
+    Typing$single_path <- parseFilePaths(roots = c(Home = path_home(), Root = "/"), input$genome_file)
+    
+  })
+  
+  #### Run blat ----
+  
+  observeEvent(input$typing_start, {
+    
+    log_print("Input typing_start")
+    
+    if(tail(readLogFile(), 1) != "0") {
+      show_toast(
+        title = "Pending Multi Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if (Screening$status == "started") {
+      show_toast(
+        title = "Pending Gene Screening",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      
+      if(!is.null(DB$data)) {
+        if(sum(apply(DB$data, 1, anyNA)) >= 1) {
+          DB$no_na_switch <- TRUE
+        } else {
+          DB$no_na_switch <- FALSE
+        }
+      }
+      
+      # Activate entry detection
+      DB$check_new_entries <- TRUE
+      
+      Typing$single_end <- FALSE
+      
+      Typing$progress_format_start <- 0
+      Typing$progress_format_end <- 0
+      
+      # Remove Initiate Typing UI 
+      output$initiate_typing_ui <- NULL
+      output$metadata_single_box <- NULL
+      output$start_typing_ui <- NULL
+      
+      # status feedback
+      Typing$status <- "Processing"
+      
+      # Locate folder containing cgMLST scheme
+      search_string <- paste0(gsub(" ", "_", DB$scheme), "_alleles")
+      
+      scheme_folders <- dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme)))
+      
+      if (any(grepl(search_string, scheme_folders))) {
+        
+        # reset results file 
+        if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
+          unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
+        }
+        
+        # blat initiate index
+        scheme_select <- as.character(scheme_folders[which(grepl(search_string, scheme_folders))])
+        
+        show_toast(
+          title = "Typing Initiated",
+          type = "success",
+          position = "bottom-end",
+          timer = 6000
+        )
+        
+        log_print("Initiated single typing")
+        
+        ### Run blat Typing
+        
+        single_typing_df <- data.frame(
+          db_path = DB$database,
+          wd = getwd(),
+          save = input$save_assembly_st,
+          scheme = paste0(gsub(" ", "_", DB$scheme)),
+          genome = Typing$single_path$datapath,
+          alleles = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", search_string)
+        )
+        
+        saveRDS(single_typing_df, "execute/single_typing_df.rds")
+        
+        # Execute single typing script
+        system(paste("bash", paste0(getwd(), "/execute/single_typing.sh")), 
+               wait = FALSE)
+        
+        scheme_loci <- list.files(path = scheme_select, full.names = TRUE)
+        
+        # Filter the files that have FASTA extensions
+        Typing$scheme_loci_f <-
+          scheme_loci[grep("\\.(fasta|fa|fna)$", scheme_loci, ignore.case = TRUE)]
+        
+        output$single_typing_progress <- renderUI({
+          fluidRow(
+            br(), br(), 
+            column(width = 1),
+            column(
+              width = 3,
+              h3(p("Pending Single Typing ..."), style = "color:white")
+            ),
+            br(), br(), br(), 
+            fluidRow(
+              column(width = 1),
+              column(
+                width = 4,
+                br(), br(), br(),
+                fluidRow(
+                  column(
+                    width = 12,
+                    uiOutput("reset_single_typing"),
+                    HTML(
+                      paste(
+                        "<span style='color: white; font-weight: bolder'>",
+                        as.character(Typing$single_path$name)
+                      )
+                    ),
+                    br(), br(),
+                    progressBar(
+                      "progress_bar",
+                      value = 0,
+                      display_pct = TRUE,
+                      title = ""
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 12,
+                    uiOutput("typing_formatting"),
+                    uiOutput("typing_fin")
+                  )
+                )
+              ),
+              column(1),
+              column(
+                width = 5,
+                br(), br(), br(),
+                uiOutput("single_typing_results")
+              )
+            )
+          )
+        })
+      } else {
+        log_print("Folder containing cgMLST alleles not in working directory")
+        
+        show_alert(
+          title = "Error",
+          text = paste0(
+            "Folder containing cgMLST alleles not in working directory.",
+            "\n",
+            "Download cgMLST Scheme for selected Organism first."
+          ),
+          type = "error"
+        )
+      }
+    }
+  })
+  
+  # Function to update Progress Bar
+  update <- reactive({
+    invalidateLater(3000, session)
+    
+    # write progress in process tracker
+    cat(
+      c(length(list.files(paste0(getwd(), "/execute/blat_single/results"))),
+        readLines(paste0(getwd(), "/logs/progress.txt"))[-1]), 
+      file = paste0(getwd(), "/logs/progress.txt"),
+      sep = "\n"
+    )
+    
+    progress <- readLines(paste0(getwd(), "/logs/progress.txt"))
+    
+    # if typing with blat is finished -> "attaching" phase started
+    if(!is.na(progress[1])) {
+      if(!is.na(progress[2])) {
+        if(progress[2] == "888888") {
+          Typing$progress_format_start <- progress[2]
+          Typing$pending_format <- progress[2]
+          Typing$status <- "Attaching"
+        }
+      }
+      # "attaching" phase completed
+      if(!is.na(progress[3])) {
+        if(progress[3] == "999999") {
+          Typing$progress_format_end <- progress[3]
+          Typing$entry_added <- progress[3]
+          Typing$status <- "Finalized"
+        }
+      }
+      Typing$progress <- as.numeric(progress[1])
+      floor((Typing$progress / length(Typing$scheme_loci_f)) * 100)
+    } else {
+      floor((Typing$progress / length(Typing$scheme_loci_f)) * 100)
+    }
+  })
+  
+  # Observe Typing Progress
+  observe({
+    
+    if(readLogFile()[1] == "0") {
+      # Update Progress Bar
+      updateProgressBar(
+        session = session,
+        id = "progress_bar",
+        value = update(),
+        total = 100,
+        title = paste0(as.character(Typing$progress), "/", length(Typing$scheme_loci_f), " loci screened")
+      )
+    }
+    
+    if (Typing$progress_format_start == 888888) {
+      output$typing_formatting <- renderUI({
+        column(
+          width = 12,
+          align = "center",
+          br(),
+          fluidRow(
+            column(
+              width = 6,
+              HTML(paste("<span style='color: white;'>", "Transforming data ..."))
+            ),
+            column(
+              width = 3,
+              align = "left",
+              HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px;color:white"></i>'))
+            )
+          )
+        )
+      })
+    } else {
+      output$typing_formatting <- NULL
+    }
+    
+    # Render when finalized  
+    if (Typing$progress_format_end == 999999) {
+      
+      output$typing_formatting <- NULL
+      
+      output$typing_fin <- renderUI({
+        fluidRow(
+          column(
+            width = 12,
+            align = "center",
+            br(), br(),
+            if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
+              if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
+                req(Typing$scheme_loci_f, Typing$typing_result_table)
+                if(sum(Typing$typing_result_table$Event != "New Variant") >  (0.5 * length(Typing$scheme_loci_f))){
+                  HTML(
+                    paste("<span style='color: white;'>", 
+                          sub(".*Successful", "Finished", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
+                          paste("<span style='color: orange;'>", "Warning: Isolate contains large number of failed allele assignments."),
+                          paste("<span style='color: white;'>", "Reset to start another typing process."),
+                          sep = '<br/>\n'))                    
+                } else {
+                  HTML(paste("<span style='color: white;'>", 
+                             sub(".*Successful", "Successful", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
+                             "Reset to start another typing process.", sep = '<br/>'))
+                }
+              } else {
+                HTML(paste("<span style='color: white;'>", 
+                           sub(".*typing", "Typing", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
+                           "Reset to start another typing process.", sep = '<br/>'))
+              }
+            },
+            br(), br(),
+            actionButton(
+              "reset_single_typing",
+              "Reset",
+              icon = icon("arrows-rotate")
+            )
+          )
+        )
+      })
+    } else {
+      output$typing_fin <- NULL
+      output$single_typing_results <- NULL
+    }
+    
+  })
+  
+  #### Declare Metadata  ----
+  
+  observeEvent(input$conf_meta_single, {
+    
+    if(nchar(trimws(input$assembly_id)) < 1) {
+      ass_id <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
+    } else {
+      ass_id <- trimws(input$assembly_id)
+    }
+    
+    if(nchar(trimws(input$assembly_name)) < 1) {
+      ass_name <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
+    } else {
+      ass_name <- trimws(input$assembly_name)
+    }
+    
+    if(ass_id %in% unlist(DB$data["Assembly ID"])) {
+      show_toast(
+        title = "Assembly ID already present",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (isFALSE(Typing$reload)) {
+      show_toast(
+        title = "Reload Database first",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if (ass_id == "") {
+    show_toast(
+      title = "Empty Assembly ID",
+      type = "error",
+      position = "bottom-end",
+      timer = 3000
+      )
+    } else if (grepl("[()/\\:*?\"<>|]", ass_id)) {
+      show_toast(
+        title = "Invalid Assembly ID. No special characters allowed: ()/\\:*?\"<>|",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if(grepl(" ", ass_id)) {
+      show_toast(
+        title = "Empty spaces in Assembly ID not allowed",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if(Screening$status == "started") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      
+      log_print("Single typing metadata confirmed")
+      
+      meta_info <- data.frame(assembly_id = ass_id,
+                              assembly_name = ass_name,
+                              cgmlst_typing = DB$scheme,
+                              append_isodate = input$append_isodate,
+                              append_host = trimws(input$append_host),
+                              append_country = trimws(input$append_country),
+                              append_city = trimws(input$append_city),
+                              append_analysisdate = Sys.Date(),
+                              db_directory = getwd()) 
+      
+      saveRDS(meta_info, paste0(
+        getwd(),
+        "/execute/meta_info_single.rds"
+      ))
+      
+      show_toast(
+        title = "Metadata declared",
+        type = "success",
+        position = "bottom-end",
+        timer = 3000
+      )
+      
+      # Render Start Typing UI
+      output$start_typing_ui <- renderUI({
+        div(
+          class = "multi_start_col",
+          column(
+            width = 3,
+            align = "center",
+            br(),
+            br(),
+            h3(p("Start Typing"), style = "color:white"),
+            br(),
+            br(),
+            HTML(
+              paste(
+                "<span style='color: white;'>",
+                "Typing by <strong>",
+                DB$scheme,
+                "</strong> scheme."
+              )
+            ),
+            br(), br(), br(), br(),
+            div(
+              class = "save-assembly",
+              materialSwitch(
+                "save_assembly_st",
+                h5(p("Save Assemblies in Local Database"), style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
+                value = TRUE,
+                right = TRUE)
+            ),
+            HTML(
+              paste(
+                "<span style='color: orange;'>",
+                "Isolates with unsaved assembly files can NOT be applied to screening for resistance genes."
+              )
+            ),
+            br(), br(), br(), br(),
+            actionButton(
+              inputId = "typing_start",
+              label = "Start",
+              icon = icon("circle-play")
+            )
+          )
+        )
+      })
+    }
+  })
+  
+  ####  Events Single Typing ----
+  
+  observeEvent(input$reset_single_typing, {
+    log_print("Reset single typing")
+    
+    Typing$status <- "Inactive"
+    
+    Typing$progress <- 0
+    
+    Typing$progress_format <- 900000
+    
+    output$single_typing_progress <- NULL
+    
+    output$typing_fin <- NULL
+    
+    output$single_typing_results <- NULL
+    
+    output$typing_formatting <- NULL
+    
+    Typing$single_path <- data.frame()
+    
+    # reset results file 
+    if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
+      unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
+      # Resetting single typing progress logfile bar 
+      con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
+      
+      cat("0\n", file = con)   
+      
+      close(con)
+    }
+    
+    output$initiate_typing_ui <- renderUI({
+      column(
+        width = 4,
+        align = "center",
+        br(),
+        br(),
+        h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+        br(),
+        br(),
+        p(
+          HTML(
+            paste(
+              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File (FASTA)')
+            )
+          )
+        ),
+        fluidRow(
+          column(1),
+          column(
+            width = 11,
+            align = "center",
+            shinyFilesButton(
+              "genome_file",
+              "Browse" ,
+              icon = icon("file"),
+              title = "Select the assembly in .fasta/.fna/.fa format:",
+              multiple = FALSE,
+              buttonType = "default",
+              class = NULL,
+              root = path_home()
+            ),
+            br(),
+            br(),
+            uiOutput("genome_path"),
+            br()
+          )
+        )
+      )
+    })
+  })
+  
+  # Notification for finalized Single typing
+  Typing$single_end <- TRUE
+  Typing$progress_format_end <- 0
+  
+  observe({
+    if(Typing$single_end == FALSE) {
+      if (Typing$progress_format_end == 999999) {
+        show_toast(
+          title = "Single Typing finalized",
+          type = "success",
+          position = "bottom-end",
+          timer = 8000
+        )
+        Typing$single_end <- TRUE
+      }
+    }
+  })
+  
+  ### Multi Typing ----
+  
+  #### Render Multi Typing UI Elements ----
+  output$initiate_multi_typing_ui <- renderUI({
+    column(
+      width = 4,
+      align = "center",
+      br(),
+      br(),
+      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+      br(), br(),
+      p(
+        HTML(
+          paste(
+            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+          )
+        )
+      ),
+      fluidRow(
+        column(1),
+        column(
+          width = 11,
+          align = "center",
+          shinyDirButton(
+            "genome_file_multi",
+            "Browse",
+            icon = icon("folder-open"),
+            title = "Select the folder containing the genome assemblies (FASTA)",
+            buttonType = "default",
+            root = path_home()
+          ),
+          br(),
+          br(),
+          uiOutput("multi_select_info"),
+          br()
+        )
+      ),
+      uiOutput("multi_select_tab_ctrls"),
+      br(),
+      fluidRow(
+        column(1),
+        column(
+          width = 11,
+          align = "left",
+          rHandsontableOutput("multi_select_table")
+        )
+      )
+    )
+  })
+  
+  # Render selection info
+  output$multi_select_info <- renderUI({
+    
+    if(!is.null(Typing$multi_path)) {
+      if(length(Typing$multi_path) < 1) {
+        HTML(paste("<span style='color: white; margin-left:-30px'>", 
+                   "No files selected."))
+      } else {
+        HTML(paste("<span style='color: white; margin-left:-30px'>",
+                   sum(hot_to_r(input$multi_select_table)$Include == TRUE),
+                   " files selected."))
+      }
+    }
+  })
+  
+  # Render multi selection table issues
+  output$multi_select_issues <- renderUI({
+    req(Typing$multi_sel_table, input$multi_select_table)
+    if(any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
+       any(duplicated(hot_to_r(input$multi_select_table)$Files))){
+      HTML(
+        paste(
+          paste("<span style='color: orange;'>",
+                "Some name(s) are already present in local database.<br/>"),
+          paste("<span style='color: #ff7334;'>",
+                "Duplicated name(s). <br/>")
+        )
+      )
+    } else if (any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
+               !any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
+      HTML(
+        paste("<span style='color: #e0b300;'>",
+              "Some name(s) are already present in local database.<br/>")
+      )
+    } else if (!any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
+               any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
+      HTML(
+        paste("<span style='color: #ff7334;'>",
+              "Duplicated name(s). <br/>")
+      )
+    }
+  })
+  
+  output$multi_select_issue_info <- renderUI({
+    req(Typing$multi_sel_table, input$multi_select_table)
+    
+    multi_select_table <- hot_to_r(input$multi_select_table)
+    
+    if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
+       any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)])) |
+       any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
+      
+      if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)])))  {
+        
+        if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
+           any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
+          HTML(paste(
+            paste(
+              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+              paste("<span style='color: white; font-style:italic'>",
+                  "&nbspRename highlighted isolates or deselect them.</br>")),
+            paste(
+              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+              paste("<span style='color: white; font-style:italic'>",
+                  "&nbspFilename(s) contain(s) empty spaces."))
+          ))
+        } else {
+          HTML(paste(
+            '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+            paste("<span style='color: white; font-style:italic'>",
+                     "&nbspFilename(s) contain(s) empty spaces.")))
+        }
+      } else {
+        HTML(paste(
+          '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+          paste("<span style='color: white; font-style:italic'>", 
+                   "&nbspRename highlighted isolates or deselect them.")))
+      }
+    } else {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
+        paste("<span style='color: white; font-style:italic'>",
+              "&nbspFiles ready for allelic typing.")))
+    }
+  })
+  
+  # Render Metadata Select Box after Folder selection
+  observe({
+    if(!is.null(Typing$multi_sel_table)) {
+      if (nrow(Typing$multi_sel_table) > 0) {
+        
+        output$multi_select_tab_ctrls <- renderUI(
+          fluidRow(
+            column(1),
+            column(
+              width = 2,
+              align = "left",
+              actionButton(
+                "sel_all_mt",
+                "All",
+                icon = icon("check")
+              )
+            ),
+            column(
+              width = 2,
+              align = "left",
+              actionButton(
+                "desel_all_mt",
+                "None",
+                icon = icon("xmark")
+              )
+            ),
+            column(2),
+            column(
+              width = 5,
+              align = "right",
+              br(),
+              uiOutput("multi_select_issues")
+            )
+          )
+        )
+        
+        output$metadata_multi_box <- renderUI({
+          column(
+            width = 3,
+            align = "center",
+            br(),
+            br(),
+            h3(p("Declare Metadata"), style = "color:white;margin-left:-40px"),
+            br(), br(),
+            div(
+              class = "multi_meta_box",
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "90%",
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      dateInput("append_isodate_multi",
+                                label = "",
+                                width = "80%",
+                                max = Sys.Date())
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("append_host_multi",
+                                label = "",
+                                width = "80%")
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table_country",
+                      pickerInput(
+                        "append_country_multi",
+                        label = "",
+                        choices = list("Common" = sel_countries,
+                                       "All Countries" = country_names),
+                        options = list(
+                          `live-search` = TRUE,
+                          `actions-box` = TRUE,
+                          size = 10,
+                          style = "background-color: white; border-radius: 5px;"
+                        ),
+                        width = "90%"
+                      )
+                    )  
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("append_city_multi",
+                                label = "",
+                                width = "80%")
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 12,
+                    align = "center",
+                    br(), br(),
+                    actionButton(
+                      inputId = "conf_meta_multi",
+                      label = "Confirm"
+                    ),
+                    br(), br(),
+                    uiOutput("multi_select_issue_info")
+                  )
+                )
+              )    
+            )
+          )
+        }) 
+      } else {
+        output$metadata_multi_box <- NULL
+      }
+    }
+  })
+  
+  # Check if ongoing Multi Typing - Render accordingly
+  observe({
+    # Get selected Genome in Multi Mode
+    shinyDirChoose(input,
+                   "genome_file_multi",
+                   roots = c(Home = path_home(), Root = "/"),
+                   defaultRoot = "Home",
+                   session = session,
+                   filetypes = c('', 'fasta', 'fna', 'fa'))
+    
+    Typing$multi_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)
+    
+    files_selected <- list.files(as.character(Typing$multi_path))
+    Typing$files_filtered <- files_selected[which(!endsWith(files_selected, ".gz") &
+                                                    grepl("\\.fasta|\\.fna|\\.fa", files_selected))]
+    
+    Typing$multi_sel_table <- data.frame(
+      Include = rep(TRUE, length(Typing$files_filtered)),
+      Files = gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", 
+                   Typing$files_filtered),
+      Type = sub(".*(\\.fasta|\\.fasta\\.gz|\\.fna|\\.fna\\.gz|\\.fa|\\.fa\\.gz)$",
+                 "\\1", Typing$files_filtered, perl = F))
+    
+    if(nrow(Typing$multi_sel_table) > 0) {
+      output$multi_select_tab_ctrls <- renderUI(
+        fluidRow(
+          column(1),
+          column(
+            width = 2,
+            align = "left",
+            actionButton(
+              "sel_all_mt",
+              "All",
+              icon = icon("check")
+            )
+          ),
+          column(
+            width = 2,
+            align = "left",
+            actionButton(
+              "desel_all_mt",
+              "None",
+              icon = icon("xmark")
+            )
+          ),
+          column(2),
+          column(
+            width = 5,
+            align = "right",
+            br(),
+            uiOutput("multi_select_issues")
+          )
+        )
+      )
+    } else {
+      output$multi_select_tab_ctrls <- NULL
+    }
+    
+    if(between(nrow(Typing$multi_sel_table), 1, 15)) {
+      output$multi_select_table <- renderRHandsontable({
+        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
+                             stretchH = "all", contextMenu = FALSE
+        ) %>%
+          hot_cols(columnSorting = FALSE) %>%
+          hot_rows(rowHeights = 25) %>%
+          hot_col(2, readOnly = FALSE,
+                  valign = "htBottom") %>%
+          hot_col(3, readOnly = TRUE) %>%
+          hot_col(1,
+                  halign = "htCenter",
+                  valign = "htTop", 
+                  colWidths = 60)
+        
+        htmlwidgets::onRender(rht, sprintf(
+          "function(el, x) {
+        var hot = this.hot;
+        
+        var columnData = hot.getDataAtCol(1); // Change column index if needed
+        var duplicates = {};
+          
+        var highlightInvalidAndDuplicates = function(invalidValues) {
+          
+          var columnData = hot.getDataAtCol(1); // Change column index if needed
+          var duplicates = {};
+
+          // Find all duplicate values
+          for (var i = 0; i < columnData.length; i++) {
+            var value = columnData[i];
+            if (value !== null && value !== undefined) {
+              if (duplicates[value]) {
+                duplicates[value].push(i);
+              } else {
+                duplicates[value] = [i];
+              }
+            }
+          }
+
+          // Reset all cell backgrounds in the column
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            if (cell) {
+              cell.style.background = 'white';
+            }
+          }
+
+          // Highlight duplicates and invalid values
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            var value = columnData[i];
+            if (cell) {
+              if (invalidValues.includes(value)) {
+                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
+              } else if (duplicates[value] && duplicates[value].length > 1) {
+                cell.style.background = '#FF7334'; // Highlight color for duplicates
+              }
+            }
+          }
+        };
+
+        var changefn = function(changes, source) {
+          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
+            highlightInvalidAndDuplicates(%s);
+          }
+        };
+
+        hot.addHook('afterChange', changefn);
+        hot.addHook('afterLoadData', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+        hot.addHook('afterRender', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+
+        highlightInvalidAndDuplicates(%s); // Initial highlight on load
+        
+        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
+          var colData = hot.getDataAtCol(0);
+          for (var i = 0; i < colData.length; i++) {
+            hot.setDataAtCell(i, 0, message.value);
+          }
+          hot.render(); // Re-render the table
+        });
+      }", 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id())))
+      })
+      
+    } else if(nrow(Typing$multi_sel_table) > 15) {
+      output$multi_select_table <- renderRHandsontable({
+        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
+                             stretchH = "all", height = 500,
+                             contextMenu = FALSE
+        ) %>%
+          hot_cols(columnSorting = FALSE) %>%
+          hot_rows(rowHeights = 25) %>%
+          hot_col(2,
+                  readOnly = FALSE,
+                  valign = "htBottom") %>%
+          hot_col(3, readOnly = TRUE) %>%
+          hot_col(1,
+                  halign = "htCenter",
+                  valign = "htTop", 
+                  colWidths = 60)
+        
+        htmlwidgets::onRender(rht, sprintf(
+          "function(el, x) {
+        var hot = this.hot;
+        
+        var columnData = hot.getDataAtCol(1); // Change column index if needed
+        var duplicates = {};
+          
+        var highlightInvalidAndDuplicates = function(invalidValues) {
+          
+          var columnData = hot.getDataAtCol(1); // Change column index if needed
+          var duplicates = {};
+
+          // Find all duplicate values
+          for (var i = 0; i < columnData.length; i++) {
+            var value = columnData[i];
+            if (value !== null && value !== undefined) {
+              if (duplicates[value]) {
+                duplicates[value].push(i);
+              } else {
+                duplicates[value] = [i];
+              }
+            }
+          }
+
+          // Reset all cell backgrounds in the column
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            if (cell) {
+              cell.style.background = 'white';
+            }
+          }
+
+          // Highlight duplicates and invalid values
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            var value = columnData[i];
+            if (cell) {
+              if (invalidValues.includes(value)) {
+                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
+              } else if (duplicates[value] && duplicates[value].length > 1) {
+                cell.style.background = '#FF7334'; // Highlight color for duplicates
+              }
+            }
+          }
+        };
+
+        var changefn = function(changes, source) {
+          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
+            highlightInvalidAndDuplicates(%s);
+          }
+        };
+
+        hot.addHook('afterChange', changefn);
+        hot.addHook('afterLoadData', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+        hot.addHook('afterRender', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+
+        highlightInvalidAndDuplicates(%s); // Initial highlight on load
+        
+        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
+          var colData = hot.getDataAtCol(0);
+          for (var i = 0; i < colData.length; i++) {
+            hot.setDataAtCell(i, 0, message.value);
+          }
+          hot.render(); // Re-render the table
+        });
+      }", 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id())))
+        
+      })
+      
+    } else {
+      output$multi_select_table <- NULL
+    } 
+  })
+  
+  observeEvent(input$conf_meta_multi, {
+    
+    multi_select_table <- hot_to_r(input$multi_select_table)[hot_to_r(input$multi_select_table)$Include == TRUE,]
+    
+    if(any(unlist(gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", multi_select_table$Files)) %in% unlist(DB$data["Assembly ID"]))) {
+      show_toast(
+        title = "Assembly ID(s) already present",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (any(duplicated(multi_select_table$Files))) {
+      show_toast(
+        title = "Duplicated filename(s)",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (any(multi_select_table$Files == "")) {
+      show_toast(
+        title = "Empty filename(s)",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (any(grepl("[()/\\:*?\"<>|]", multi_select_table$Files))) {
+      show_toast(
+        title = "Invalid filename(s). No special characters allowed: ()/\\:*?\"<>|",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (!any(multi_select_table$Include == TRUE)) {
+      show_toast(
+        title = "No files selected",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
+      show_toast(
+        title = "Empty spaces in filename(s) not allowed",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (isFALSE(Typing$reload)) {
+      show_toast(
+        title = "Reload Database first",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if(Screening$status == "started") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      
+      log_print("Multi typing metadata confirmed")
+      
+      meta_info <- data.frame(cgmlst_typing = DB$scheme,
+                              append_isodate = trimws(input$append_isodate_multi),
+                              append_host = trimws(input$append_host_multi),
+                              append_country = trimws(input$append_country_multi),
+                              append_city = trimws(input$append_city_multi),
+                              append_analysisdate = Sys.Date(),
+                              db_directory = getwd())
+      
+      saveRDS(meta_info, paste0(getwd(), "/execute/meta_info.rds"))
+      
+      show_toast(
+        title = "Metadata declared",
+        type = "success",
+        position = "bottom-end",
+        timer = 3000
+      )
+      
+      output$start_multi_typing_ui <- renderUI({
+        div(
+          class = "multi_start_col",
+          column(
+            width = 3,
+            align = "center",
+            br(),
+            br(),
+            h3(p("Start Typing"), style = "color:white"),
+            br(),
+            br(),
+            HTML(
+              paste(
+                "<span style='color: white;'>",
+                "Typing by <strong>",
+                DB$scheme,
+                "</strong> scheme."
+              )
+            ),
+            br(), br(), br(), br(),
+            div(
+              class = "save-assembly",
+              materialSwitch(
+                "save_assembly_mt",
+                h5(p("Save Assemblies in Local Database"), style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
+                value = TRUE,
+                right = TRUE)
+            ),
+            HTML(
+              paste(
+                "<span style='color: orange;font-style:italic'>",
+                "Isolates with unsaved assembly files can NOT be applied to screening for resistance genes."
+              )
+            ),
+            br(), br(), br(), br(),
+            actionButton(
+              "start_typ_multi",
+              "Start",
+              icon = icon("circle-play")
+            )
+          )
+        )
+      })
+    }
+  })
+  
+  #### Events Multi Typing ----
+  
+  observeEvent(input$sel_all_mt, {
+    session$sendCustomMessage(type = "setColumnValue", message = list(value = TRUE))
+  })
+  
+  observeEvent(input$desel_all_mt, {
+    session$sendCustomMessage(type = "setColumnValue", message = list(value = FALSE))
+  })
+  
+  # Print Log
+  output$print_log <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save multi typing log ", paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")))
+      paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")
+    },
+    content = function(file) {
+      writeLines(readLines(paste0(getwd(), "/logs/script_log.txt")), file)
+    }
+  )
+  
+  # Reset Multi Typing
+  observeEvent(input$reset_multi, {
+    if(!grepl("Multi Typing", tail(readLines(paste0(getwd(),"/logs/script_log.txt")), n = 1))) {
+      showModal(
+        modalDialog(
+          paste0(
+            "A Multi Typing process is still pending. Stopping this process will cancel the processing."
+          ),
+          title = "Reset Multi Typing",
+          fade = TRUE,
+          easyClose = TRUE,
+          footer = tagList(
+            modalButton("Cancel"),
+            actionButton("conf_multi_kill", "Stop", class = "btn btn-danger")
+          )
+        )
+      )
+    } else {
+      
+      log_print("Reset multi typing")
+      
+      # Reset multi typing result list
+      saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
+      multi_help <- FALSE
+      Typing$result_list <- NULL
+      
+      # Null logfile
+      writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
+      
+      # Reset User Feedback variable
+      Typing$pending_format <- 0
+      Typing$multi_started <- FALSE
+      
+      output$initiate_multi_typing_ui <- renderUI({
+        column(
+          width = 4,
+          align = "center",
+          br(),
+          br(),
+          h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+          br(), br(),
+          p(
+            HTML(
+              paste(
+                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+              )
+            )
+          ),
+          fluidRow(
+            column(1),
+            column(
+              width = 11,
+              align = "center",
+              shinyDirButton(
+                "genome_file_multi",
+                "Browse",
+                icon = icon("folder-open"),
+                title = "Select the folder containing the genome assemblies (FASTA)",
+                buttonType = "default",
+                root = path_home()
+              ),
+              br(),
+              br(),
+              uiOutput("multi_select_info"),
+              br()
+            )
+          ),
+          uiOutput("multi_select_tab_ctrls"),
+          br(),
+          fluidRow(
+            column(1),
+            column(
+              width = 11,
+              align = "left",
+              rHandsontableOutput("multi_select_table")
+            )
+          )
+        )
+      })
+      
+      output$pending_typing <- NULL
+      output$multi_typing_results <- NULL
+    }
+  })
+  
+  # Confirm Reset after 
+  observeEvent(input$conf_multi_kill, {
+    removeModal()
+    
+    log_print("Kill multi typing")
+    
+    # Kill multi typing and reset logfile  
+    system(paste("bash", paste0(getwd(), "/execute/kill_multi.sh")), 
+           wait = TRUE)
+    
+    show_toast(
+      title = "Execution cancelled",
+      type = "warning",
+      position = "bottom-end",
+      timer = 6000
+    )
+    
+    # Kill multi typing and reset logfile  
+    writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
+    
+    #Reset multi typing result list
+    saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
+    multi_help <- FALSE
+    Typing$result_list <- NULL
+    
+    # Reset User Feedback variable
+    Typing$pending_format <- 0
+    output$pending_typing <- NULL
+    output$multi_typing_results <- NULL
+    Typing$failures <- 0
+    Typing$successes <- 0
+    Typing$multi_started <- FALSE
+    
+    output$initiate_multi_typing_ui <- renderUI({
+      column(
+        width = 4,
+        align = "center",
+        br(),
+        br(),
+        h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+        br(), br(),
+        p(
+          HTML(
+            paste(
+              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+            )
+          )
+        ),
+        fluidRow(
+          column(1),
+          column(
+            width = 11,
+            align = "center",
+            shinyDirButton(
+              "genome_file_multi",
+              "Browse",
+              icon = icon("folder-open"),
+              title = "Select the folder containing the genome assemblies (FASTA)",
+              buttonType = "default",
+              root = path_home()
+            ),
+            br(),
+            br(),
+            uiOutput("multi_select_info"),
+            br()
+          )
+        ),
+        uiOutput("multi_select_tab_ctrls"),
+        br(),
+        fluidRow(
+          column(1),
+          column(
+            width = 11,
+            align = "left",
+            rHandsontableOutput("multi_select_table")
+          )
+        )
+      )
+    })
+    
+  })
+  
+  observeEvent(input$start_typ_multi, {
+    log_print("Initiate multi typing")
+    
+    if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if (Screening$status == "started") {
+      show_toast(
+        title = "Pending Gene Screening",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      removeModal()
+      
+      show_toast(
+        title = "Multi Typing started",
+        type = "success",
+        position = "bottom-end",
+        timer = 10000
+      )
+      
+      Typing$new_table <- NULL
+      
+      # Remove Allelic Typing Controls
+      output$initiate_multi_typing_ui <- NULL
+      output$metadata_multi_box <- NULL
+      output$start_multi_typing_ui <- NULL
+      
+      # Activate entry detection
+      DB$check_new_entries <- TRUE
+      
+      # Initiate Feedback variables
+      Typing$multi_started <- TRUE
+      Typing$pending <- TRUE
+      Typing$failures <- 0
+      Typing$successes <- 0
+      
+      # get selected file table
+      multi_select_table <- hot_to_r(input$multi_select_table)
+      
+      filenames <- paste(multi_select_table$Files[which(multi_select_table$Include == TRUE)], collapse = " ")
+      
+      files <- Typing$multi_sel_table$Files[which(multi_select_table$Include == TRUE)]
+      type <- Typing$multi_sel_table$Type[which(multi_select_table$Include == TRUE)]
+      genome_names <- paste(paste0(gsub(" ", "~", files), type), collapse = " ")
+      
+      # Start Multi Typing Script
+      multi_typing_df <- data.frame(
+        db_path = DB$database,
+        wd = getwd(),
+        save = input$save_assembly_mt,
+        scheme = paste0(gsub(" ", "_", DB$scheme)),
+        genome_folder = as.character(parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)),
+        filenames = paste0(filenames, collapse= " "),
+        genome_names = genome_names,
+        alleles = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")
+      )
+      
+      saveRDS(multi_typing_df, "execute/multi_typing_df.rds")
+      
+      # Execute multi blat script  
+      system(paste("bash", paste0(getwd(), "/execute/multi_typing.sh")), wait = FALSE)
+    }
+  })
+  
+  
+  #### User Feedback ----
+  
+  observe({
+    if(file.exists(paste0(getwd(), "/logs/script_log.txt"))) {
+      if(Typing$multi_started == TRUE) {
+        check_multi_status()
+      } else {
+        Typing$status <- "Inactive"
+      }
+    }
+  })
+  
+  check_multi_status <- reactive({
+    
+    invalidateLater(3000, session)
+    
+    log <- readLines(paste0(getwd(), "/logs/script_log.txt"))
+    
+    # Determine if Single or Multi Typing
+    if(str_detect(log[1], "Multi")) {
+      Typing$pending_mode <- "Multi"
+    } else {
+      Typing$pending_mode <- "Single"
+    }
+    
+    # Check typing status
+    if(str_detect(tail(log, 1), "Attaching")) {
+      Typing$status <- "Attaching"
+    } else if(str_detect(tail(log, 1), "Successful")) {
+      Typing$multi_help <- TRUE
+      Typing$status <- "Successful"
+      show_toast(
+        title = paste0("Successful", sub(".*Successful", "", tail(log, 1))),
+        type = "success",
+        position = "bottom-end",
+        timer = 8000
+      )
+    } else if(str_detect(tail(log, 1), "failed")) {
+      Typing$status <- "Failed"
+      show_toast(
+        title = sub(".* - ", "", tail(log, 1)),
+        type = "error",
+        position = "bottom-end",
+        timer = 8000
+      )
+    } else if(str_detect(tail(log, 1), "Processing")) {
+      Typing$status <- "Processing"
+      
+      if(any(str_detect(tail(log, 2), "Successful"))) {
+        
+        if(!identical(Typing$last_success, tail(log, 2)[1])) {
+          Typing$multi_help <- TRUE
+          show_toast(
+            title = paste0("Successful", sub(".*Successful", "", tail(log, 2)[1])),
+            type = "success",
+            position = "bottom-end",
+            timer = 8000
+          )
+          
+          Typing$last_success <- tail(log, 2)[1]
+        }
+      } else if(any(str_detect(tail(log, 2), "failed"))) {
+        
+        if(!identical(Typing$last_failure, tail(log, 2)[1])) {
+          
+          show_toast(
+            title = sub(".* - ", "", tail(log, 2)[1]),
+            type = "error",
+            position = "bottom-end",
+            timer = 8000
+          )
+          
+          Typing$last_failure <- tail(log, 2)[1]
+        }
+      }
+    } else if(str_detect(tail(log, 1), "finalized")) {
+      Typing$multi_help <- TRUE
+      Typing$status <- "Finalized"
+      
+      if(Typing$pending == TRUE) {
+        show_toast(
+          title = "Typing finalized",
+          type = "success",
+          position = "bottom-end",
+          timer = 8000
+        )
+        
+        Typing$pending <- FALSE
+      }
+    }
+  })
+  
+  ##### Render Multi Typing UI Feedback ----
+  
+  observe({
+    if(!is.null(input$multi_results_picker)) {
+      Typing$multi_table_length <- nrow(Typing$result_list[[input$multi_results_picker]])
+    } else {
+      Typing$multi_table_length <- NULL
+    }
+  })
+  
+  observe({
+    if(!is.null(Typing$result_list)) {
+      if(length(Typing$result_list) > 0) {
+        if(is.null(Typing$multi_table_length)) {
+          output$multi_typing_result_table <- renderRHandsontable({
+            rhandsontable(Typing$result_list[[input$multi_results_picker]], 
+                          rowHeaders = NULL, stretchH = "all",
+                          readOnly = TRUE, contextMenu = FALSE) %>%
+              hot_rows(rowHeights = 25) %>%
+              hot_col(1:3, valign = "htMiddle", halign = "htCenter",
+                      cellWidths = list(100, 160, NULL)) %>%
+              hot_col("Value", renderer=htmlwidgets::JS(
+                "function(instance, td, row, col, prop, value, cellProperties) {
+                  if (value.length > 8) {
+                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                  }
+                  td.innerHTML = value;
+                  td.style.textAlign = 'center';
+                  return td;
+                 }"
+              ))
+            })
+          
+        } else {
+          if(Typing$multi_table_length > 15) {
+            output$multi_typing_result_table <- renderRHandsontable({
+              rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
+                            stretchH = "all", height = 500,
+                            readOnly = TRUE, contextMenu = FALSE) %>%
+                hot_rows(rowHeights = 25) %>%
+                hot_col(1:3, valign = "htMiddle", halign = "htCenter",
+                        cellWidths = list(100, 160, NULL)) %>%
+                hot_col("Value", renderer=htmlwidgets::JS(
+                  "function(instance, td, row, col, prop, value, cellProperties) {
+                  if (value.length > 8) {
+                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                  }
+                  td.innerHTML = value;
+                  td.style.textAlign = 'center';
+                  return td;
+                 }"
+                ))
+              })
+          } else {
+            output$multi_typing_result_table <- renderRHandsontable({
+              rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
+                            stretchH = "all", readOnly = TRUE,
+                            contextMenu = FALSE) %>%
+                hot_rows(rowHeights = 25) %>%
+                hot_col(1:3, valign = "htMiddle", halign = "htCenter",
+                        cellWidths = list(100, 160, NULL)) %>%
+                hot_col("Value", renderer=htmlwidgets::JS(
+                  "function(instance, td, row, col, prop, value, cellProperties) {
+                  if (value.length > 8) {
+                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                  }
+                  td.innerHTML = value;
+                  td.style.textAlign = 'center';
+                  return td;
+                 }"
+                ))
+              })
+          }
+        }
+      } else {
+        output$multi_typing_result_table <- NULL
+      }
+    } else {
+      output$multi_typing_result_table <- NULL
+    }
+  })
+  
+  observe({
+    if(!is.null(Typing$multi_result_status)) {
+      if(Typing$multi_result_status == "start" | Typing$multi_result_status == "finalized"){
+        
+        if(Typing$multi_help == TRUE) {
+          Typing$result_list <- readRDS(paste0(getwd(), "/execute/event_list.rds"))
+          Typing$multi_help <- FALSE
+        }
+      } 
+    }
+  })
+  
+  
+  observe({
+    #Render multi typing result feedback table
+    
+    if(!is.null(Typing$result_list)) {
+      if(length(Typing$result_list) > 0) {
+        output$multi_typing_results <- renderUI({
+          column(
+            width = 12,
+            fluidRow(
+              column(1),
+              column(
+                width = 9,
+                br(), br(),
+                br(), br(),
+                br(), 
+                div(
+                  class = "mult_res_sel",
+                  selectInput(
+                    "multi_results_picker",
+                    label = h5("Select Typing Results", style = "color:white"),
+                    choices = names(Typing$result_list),
+                    selected = names(Typing$result_list)[length(names(Typing$result_list))],
+                  )
+                ),
+                br(), br()
+              )
+            ),
+            rHandsontableOutput("multi_typing_result_table")
+          )
+        })
+      }
+    }
+  })
+  
+  observe({
+    
+    # Render log content
+    output$logText <- renderPrint({
+      cat(rev(paste0(tail(readLogFile(), 50), "\n")))
+    })
+    
+    output$logTextFull <- renderPrint({
+      cat(rev(paste0(readLines(paste0(getwd(), "/logs/script_log.txt")), "\n")))
+    })
+    
+    # Render Pending UI
+    if(!grepl("Multi Typing", tail(readLogFile(), n = 1)) & grepl("Start Multi Typing", head(readLogFile(), n = 1))) {
+      
+      Typing$multi_result_status <- "start"
+      
+      output$initiate_multi_typing_ui <- NULL
+      
+      output$pending_typing <- renderUI({
+        fluidRow(
+          fluidRow(
+            br(), br(),
+            column(width = 2),
+            column(
+              width = 4,
+              h3(p("Pending Typing ..."), style = "color:white"),
+              br(), br(),
+              fluidRow(
+                column(
+                  width = 5,
+                  HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:24px;color:white;margin-top:5px"></i>'))
+                ),
+                column(
+                  width = 6,
+                  align = "left",
+                  actionButton(
+                    "reset_multi",
+                    "Terminate",
+                    icon = icon("ban")
+                  )
+                )
+              ),
+            )
+          ),
+          br(), br(),
+          fluidRow(
+            column(width = 2),
+            column(
+              width = 10,
+              verbatimTextOutput("logText")
+            )  
+          )
+        )
+      })
+    } else if(grepl("Multi Typing finalized", tail(readLogFile(), n = 1))) {
+      
+      Typing$multi_result_status <- "finalized"
+      
+      Typing$last_scheme <- NULL
+      
+      output$initiate_multi_typing_ui <- NULL
+      
+      output$pending_typing <- renderUI({
+        
+        fluidRow(
+          fluidRow(
+            br(), br(),
+            column(width = 2),
+            column(
+              width = 4,
+              h3(p("Pending Multi Typing ..."), style = "color:white"),
+              br(), br(),
+              HTML(paste("<span style='color: white;'>", 
+                         paste("Typing of", sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "Processing")), "assemblies finalized."),
+                         paste(sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "Successful")), "successes."),
+                         paste(sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "failed")), "failures."),
+                         "Reset to start another typing process.", 
+                         sep = '<br/>')),
+              br(), br(),
+              fluidRow(
+                column(
+                  width = 5,
+                  actionButton(
+                    "reset_multi",
+                    "Reset",
+                    icon = icon("arrows-rotate")
+                  )
+                ),
+                column(
+                  width = 5,
+                  downloadButton(
+                    "print_log",
+                    "Logfile",
+                    icon = icon("floppy-disk")
+                  )
+                )
+              )
+            )
+          ),
+          br(), br(),
+          fluidRow(
+            column(width = 2),
+            column(
+              width = 10,
+              verbatimTextOutput("logTextFull"),
+            )
+          )
+        )
+      })
+    } else if (!grepl("Start Multi Typing", head(readLogFile(), n = 1))){
+      output$pending_typing <- NULL
+      Typing$multi_result_status <- "idle"
+    }
+  })
+  
+  observe({
+    # Get selected Genome in Multi Mode
+    shinyDirChoose(input,
+                   "hash_dir",
+                   roots = c(Home = path_home(), Root = "/"),
+                   defaultRoot = "Home",
+                   session = session,
+                   filetypes = c('', 'fasta', 'fna', 'fa'))
+  })
+  
+  observeEvent(input$hash_start, {
+    dir_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$hash_dir)
+    if (!is_empty(list.files(dir_path)) && all(endsWith(list.files(dir_path), ".fasta"))) {
+      log_print("Hashing directory using utilities")
+      shinyjs::hide("hash_start")
+      shinyjs::show("hash_loading")
+      show_toast(
+        title = "Hashing started!",
+        type = "success",
+        position = "bottom-end",
+        timer = 6000
+      )
+      hash_database(dir_path)
+      shinyjs::hide("hash_loading")
+      shinyjs::show("hash_start")
+      show_toast(
+        title = "Hashing completed!",
+        type = "success",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      show_toast(
+        title = "Incorrect folder selected!",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    }
+  })
+  
+} # end server
+
+# _______________________ ####
+
+# Shiny ----
+
+shinyApp(ui = ui, server = server)

From f32892da156f5605e789efb39ff68b060dde760e Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Tue, 20 Aug 2024 15:48:41 +0200
Subject: [PATCH 68/75] Added link to NCBI/AMRFinder

---
 App.R | 28 ++++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/App.R b/App.R
index 9f57ace..f19c5a1 100644
--- a/App.R
+++ b/App.R
@@ -23139,8 +23139,10 @@ server <- function(input, output, session) {
         HTML(
           paste(
             '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
+            '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
+            DB$scheme, 'available for gene screening with ',
+            '<a href="https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/" target="_blank" style="color:#008edb; text-decoration:none;">NCBI/AMRFinder</a>.',
+            '</span>'
           )
         )
       )
@@ -23148,9 +23150,11 @@ server <- function(input, output, session) {
       p(
         HTML(
           paste(
-            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
+            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000; position:relative; top:27px;margin-right: 10px;"></i>',
+            '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
+            DB$scheme, 'not available for gene screening with ',
+            '<a href="https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/" target="_blank" style="color:#008edb; text-decoration:none;">NCBI/AMRFinder</a>.',
+            '</span>'
           )
         )
       )
@@ -23163,8 +23167,10 @@ server <- function(input, output, session) {
         HTML(
           paste(
             '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
+            '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
+            DB$scheme, 'available for gene screening with ',
+            '<a href="https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/" target="_blank" style="color:#008edb; text-decoration:none;">NCBI/AMRFinder</a>.',
+            '</span>'
           )
         )
       )
@@ -23172,9 +23178,11 @@ server <- function(input, output, session) {
       p(
         HTML(
           paste(
-            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
+            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000; position:relative; top:27px;margin-right: 10px;"></i>',
+            '<span style="color: white; font-size: 15px; position:relative; top:25px;">',
+            DB$scheme, 'not available for gene screening with ',
+            '<a href="https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/" target="_blank" style="color:#008edb; text-decoration:none;">NCBI/AMRFinder</a>.',
+            '</span>'
           )
         )
       )

From 4ac6f0df74f4c7c8cf237f4b57081d426c509f3b Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Tue, 20 Aug 2024 17:38:06 +0200
Subject: [PATCH 69/75] Minor changes

---
 App.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/App.R b/App.R
index f19c5a1..2b69951 100644
--- a/App.R
+++ b/App.R
@@ -11184,11 +11184,11 @@ server <- function(input, output, session) {
       paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")
     },
     content = function(file) {
-      download_matrix <<- hot_to_r(input$db_entries)
+      download_matrix <- hot_to_r(input$db_entries)
       
-      if(input$download_table_hashes == TRUE) {
-        included_loci <<- colnames(select(download_matrix, -(1:(13 + nrow(DB$cust_var)))))
-        full_hashes <<- DB$allelic_profile[included_loci]
+      if(input$download_table_hashes == FALSE) {
+        included_loci <- colnames(select(download_matrix, -(1:(13 + nrow(DB$cust_var)))))
+        full_hashes <- DB$allelic_profile[included_loci]
         download_matrix[included_loci] <- full_hashes
       }
       

From 65d72b834d66627255b6b941b854c07d1f34ab5a Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Tue, 20 Aug 2024 17:43:01 +0200
Subject: [PATCH 70/75] Temporary removal of utilities tab allele database
 hashing feature

---
 App.R | 86 -----------------------------------------------------------
 1 file changed, 86 deletions(-)

diff --git a/App.R b/App.R
index 2b69951..dd5f675 100644
--- a/App.R
+++ b/App.R
@@ -5267,50 +5267,6 @@ ui <- dashboardPage(
         )
       ),
       
-      ## Tab Utilities -------------------------------------------------------
-      
-      tabItem(
-        tabName = "utilities",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Utilities"), style = "color:white")
-          )
-        ),
-        br(),
-        hr(),
-        column(
-          width = 5,
-          align = "left",
-          shinyDirButton(
-            "hash_dir",
-            "Choose folder with .fasta files",
-            title = "Locate folder with loci",
-            buttonType = "default",
-            style = "border-color: white; margin: 10px; min-width: 200px; text-align: center"
-          ),
-          actionButton("hash_start", "Start Hashing", icon = icon("circle-play")),
-          shinyjs::hidden(
-            div(id = "hash_loading",
-                HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
-          )
-        )
-          # br(),
-          # actionButton(
-          #   "backup_database",
-          #   "Create backup",
-          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
-          # ),
-          # br(),
-          # actionButton(
-          #   "import_db_backup",
-          #   "Restore backup",
-          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
-          # )
-      ),
-      
-      
       ## Tab Screening -------------------------------------------------------
       
       tabItem(
@@ -26036,48 +25992,6 @@ server <- function(input, output, session) {
       Typing$multi_result_status <- "idle"
     }
   })
-  
-  observe({
-    # Get selected Genome in Multi Mode
-    shinyDirChoose(input,
-                   "hash_dir",
-                   roots = c(Home = path_home(), Root = "/"),
-                   defaultRoot = "Home",
-                   session = session,
-                   filetypes = c('', 'fasta', 'fna', 'fa'))
-  })
-  
-  observeEvent(input$hash_start, {
-    dir_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$hash_dir)
-    if (!is_empty(list.files(dir_path)) && all(endsWith(list.files(dir_path), ".fasta"))) {
-      log_print("Hashing directory using utilities")
-      shinyjs::hide("hash_start")
-      shinyjs::show("hash_loading")
-      show_toast(
-        title = "Hashing started!",
-        type = "success",
-        position = "bottom-end",
-        timer = 6000
-      )
-      hash_database(dir_path)
-      shinyjs::hide("hash_loading")
-      shinyjs::show("hash_start")
-      show_toast(
-        title = "Hashing completed!",
-        type = "success",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      show_toast(
-        title = "Incorrect folder selected!",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    }
-  })
-  
 } # end server
 
 # _______________________ ####

From a711c43406bc2c8a60ba6ed101741f3629f619d4 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Tue, 20 Aug 2024 17:53:43 +0200
Subject: [PATCH 71/75] Removed Utilities tab UI

---
 App.R | 50 --------------------------------------------------
 1 file changed, 50 deletions(-)

diff --git a/App.R b/App.R
index dd5f675..d5f3753 100644
--- a/App.R
+++ b/App.R
@@ -6462,11 +6462,6 @@ server <- function(input, output, session) {
               text = "Visualization",
               tabName = "visualization",
               icon = icon("circle-nodes")
-            ),
-            menuItem(
-              text = "Utilities",
-              tabName = "utilities",
-              icon = icon("screwdriver-wrench")
             )
           )
         )
@@ -6642,11 +6637,6 @@ server <- function(input, output, session) {
                   text = "Visualization",
                   tabName = "visualization",
                   icon = icon("circle-nodes")
-                ),
-                menuItem(
-                  text = "Utilities",
-                  tabName = "utilities",
-                  icon = icon("screwdriver-wrench")
                 )
               )
             )
@@ -6732,11 +6722,6 @@ server <- function(input, output, session) {
                   text = "Visualization",
                   tabName = "visualization",
                   icon = icon("circle-nodes")
-                ),
-                menuItem(
-                  text = "Utilities",
-                  tabName = "utilities",
-                  icon = icon("screwdriver-wrench")
                 )
               )
             )
@@ -6824,11 +6809,6 @@ server <- function(input, output, session) {
                   text = "Visualization",
                   tabName = "visualization",
                   icon = icon("circle-nodes")
-                ),
-                menuItem(
-                  text = "Utilities",
-                  tabName = "utilities",
-                  icon = icon("screwdriver-wrench")
                 )
               )
             )
@@ -6945,11 +6925,6 @@ server <- function(input, output, session) {
                     text = "Visualization",
                     tabName = "visualization",
                     icon = icon("circle-nodes")
-                  ),
-                  menuItem(
-                    text = "Utilities",
-                    tabName = "utilities",
-                    icon = icon("screwdriver-wrench")
                   )
                 )
               )
@@ -7165,11 +7140,6 @@ server <- function(input, output, session) {
                         text = "Visualization",
                         tabName = "visualization",
                         icon = icon("circle-nodes")
-                      ),
-                      menuItem(
-                        text = "Utilities",
-                        tabName = "utilities",
-                        icon = icon("screwdriver-wrench")
                       )
                     )
                   )
@@ -7232,11 +7202,6 @@ server <- function(input, output, session) {
                         text = "Visualization",
                         tabName = "visualization",
                         icon = icon("circle-nodes")
-                      ),
-                      menuItem(
-                        text = "Utilities",
-                        tabName = "utilities",
-                        icon = icon("screwdriver-wrench")
                       )
                     )
                   )
@@ -9341,11 +9306,6 @@ server <- function(input, output, session) {
                       text = "Visualization",
                       tabName = "visualization",
                       icon = icon("circle-nodes")
-                    ),
-                    menuItem(
-                      text = "Utilities",
-                      tabName = "utilities",
-                      icon = icon("screwdriver-wrench")
                     )
                   )
                 )
@@ -9882,11 +9842,6 @@ server <- function(input, output, session) {
                 text = "Visualization",
                 tabName = "visualization",
                 icon = icon("circle-nodes")
-              ),
-              menuItem(
-                text = "Utilities",
-                tabName = "utilities",
-                icon = icon("screwdriver-wrench")
               )
             )
           )
@@ -9945,11 +9900,6 @@ server <- function(input, output, session) {
               text = "Visualization",
               tabName = "visualization",
               icon = icon("circle-nodes")
-            ),
-            menuItem(
-              text = "Utilities",
-              tabName = "utilities",
-              icon = icon("screwdriver-wrench")
             )
           )
         )

From 71ebf59aa4acd804c05545ed277f016ba2b49276 Mon Sep 17 00:00:00 2001
From: Marian Freisleben <marian@phylotrace.com>
Date: Tue, 20 Aug 2024 18:16:54 +0200
Subject: [PATCH 72/75] Added skeleton cluster width UI

---
 App.R | 51813 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 25917 insertions(+), 25896 deletions(-)

diff --git a/App.R b/App.R
index 0cd1d6b..5a25259 100644
--- a/App.R
+++ b/App.R
@@ -1,25896 +1,25917 @@
-######## PhyloTrace #########
-
-# _______________________ ####
-# CRAN Packages
-library(shiny)
-library(R.utils)
-library(igraph)
-library(shinyWidgets)
-library(shinydashboard)
-library(dashboardthemes)
-library(ggplot2)
-library(ggnewscale)
-library(ggplotify) 
-library(ape)
-library(tidyverse)
-library(rlang)
-library(tidytree)
-library(shinyFiles)
-library(dplyr)
-library(downloader)
-library(rvest)
-library(rmarkdown)
-library(knitr)
-library(kableExtra)
-library(fs)
-library(data.table)
-library(zoo)
-library(ggnetwork)
-library(rhandsontable)
-library(visNetwork)
-library(proxy)
-library(phangorn)
-library(cowplot)
-library(viridis)
-library(RColorBrewer)
-library(bslib)
-library(bsicons)
-library(DT)
-library(shinyBS)
-library(openssl)
-library(logr)
-# Bioconductor Packages
-library(treeio)
-library(ggtree)
-library(ggtreeExtra)
-
-source(paste0(getwd(), "/www/resources.R"))
-
-options(ignore.negative.edge=TRUE)
-
-# User Interface ----
-
-ui <- dashboardPage(
-  
-  title = "PhyloTrace 1.5.0",
-  
-  # Title
-  dashboardHeader(
-    
-    title = span(
-      div(
-        class = "img_logo",
-        img(
-          src = "PhyloTrace.jpg", width = 190
-        )
-      )
-    ),
-    uiOutput("loaded_scheme"),
-    uiOutput("databasetext"),
-    uiOutput("statustext"),
-    tags$li(class = "dropdown", 
-            tags$span(id = "currentTime", style = "color:white; font-weight:bold;")),
-    disable = FALSE
-  ),
-  
-  ## Sidebar ----
-  dashboardSidebar(
-    tags$head(includeCSS("www/head.css")),
-    tags$style(includeCSS("www/body.css")),
-    tags$style(HTML(
-      "@keyframes pulsate {
-          0% { transform: scale(1); }
-          50% { transform: scale(1.1); }
-          100% { transform: scale(1); }
-        }
-        .pulsating-button {
-          animation: pulsate 1s ease infinite;
-        }
-        .pulsating-button:hover {
-          animation: none;
-        }")),
-    br(), br(),
-    sidebarMenu(
-      id = "tabs",
-      sidebarMenuOutput("menu"),
-      uiOutput("menu_sep2"),
-      conditionalPanel(
-        "input.tabs==='db_browse_entries'",
-        uiOutput("entrytable_sidebar")
-      ),
-      conditionalPanel(
-        "input.tabs==='db_distmatrix'",
-        uiOutput("distmatrix_sidebar")
-      ),
-      conditionalPanel(
-        "input.tabs==='db_missing_values'",
-        uiOutput("missing_values_sidebar")
-      ),
-      conditionalPanel(
-        "input.tabs==='typing'",
-        uiOutput("typing_sidebar")
-      ),
-      conditionalPanel(
-        "input.tabs==='visualization'",
-        uiOutput("visualization_sidebar")
-      ),
-      conditionalPanel(
-        "input.tabs==='gs_profile'",
-        uiOutput("screening_sidebar")
-      )
-    )
-  ),
-  
-  dashboardBody(
-    tags$head(tags$link(rel = "shortcut icon", href = "favicon.ico")),
-    shinyjs::useShinyjs(),
-    
-    shinyDashboardThemeDIY(
-      ### general
-      appFontFamily = "Liberation Sans",
-      appFontColor = "#000000",
-      primaryFontColor = "#ffffff",
-      infoFontColor = "rgb(0,0,0)",
-      successFontColor = "rgb(0,0,0)",
-      warningFontColor = "rgb(0,0,0)",
-      dangerFontColor = "rgb(0,0,0)",
-      bodyBackColor = cssGradientThreeColors(
-        direction = "down",
-        colorStart = "#282f38",
-        colorMiddle = "#384454",
-        colorEnd = "#495d78",
-        colorStartPos = 0,
-        colorMiddlePos = 50,
-        colorEndPos = 100
-      ),
-      
-      ### header
-      logoBackColor = "#282f38",
-      headerButtonBackColor = "#282f38",
-      headerButtonIconColor = "#18ece1",
-      headerButtonBackColorHover = "#282f38",
-      headerButtonIconColorHover = "#ffffff",
-      headerBackColor = "#282f38",
-      headerBoxShadowColor = "#aaaaaa",
-      headerBoxShadowSize = "0px 0px 0px",
-      
-      ### sidebar
-      sidebarBackColor = cssGradientThreeColors(
-        direction = "down",
-        colorStart = "#282f38",
-        colorMiddle = "#384454",
-        colorEnd = "#495d78",
-        colorStartPos = 0,
-        colorMiddlePos = 50,
-        colorEndPos = 100),
-      
-      sidebarPadding = 0,
-      sidebarMenuBackColor = "transparent",
-      sidebarMenuPadding = 0,
-      sidebarMenuBorderRadius = 0,
-      sidebarShadowRadius = "5px 5px 5px",
-      sidebarShadowColor = "#282f38",
-      sidebarUserTextColor = "#ffffff",
-      sidebarSearchBackColor = "rgb(55,72,80)",
-      sidebarSearchIconColor = "rgb(153,153,153)",
-      sidebarSearchBorderColor = "rgb(55,72,80)",
-      sidebarTabTextColor = "rgb(255,255,255)",
-      sidebarTabTextSize = 15,
-      sidebarTabBorderStyle = "none none solid none",
-      sidebarTabBorderColor = "rgb(35,106,135)",
-      sidebarTabBorderWidth = 0,
-      sidebarTabBackColorSelected = cssGradientThreeColors(
-        direction = "right",
-        colorStart = "rgba(44,222,235,1)",
-        colorMiddle = "rgba(44,222,235,1)",
-        colorEnd = "rgba(0,255,213,1)",
-        colorStartPos = 0,
-        colorMiddlePos = 30,
-        colorEndPos = 100
-      ),
-      sidebarTabTextColorSelected = "rgb(0,0,0)",
-      sidebarTabRadiusSelected = "0px 0px 0px 0px",
-      sidebarTabBackColorHover = cssGradientThreeColors(
-        direction = "right",
-        colorStart = "rgba(44,222,235,1)",
-        colorMiddle = "rgba(44,222,235,1)",
-        colorEnd = "rgba(0,255,213,1)",
-        colorStartPos = 0,
-        colorMiddlePos = 30,
-        colorEndPos = 100
-      ),
-      sidebarTabTextColorHover = "rgb(50,50,50)",
-      sidebarTabBorderStyleHover = "none none solid none",
-      sidebarTabBorderColorHover = "rgb(75,126,151)",
-      sidebarTabBorderWidthHover = 0,
-      sidebarTabRadiusHover = "0px 0px 0px 0px",
-      
-      ### boxes
-      boxBackColor = "#ffffff",
-      boxBorderRadius = 7,
-      boxShadowSize = "0px 0px 0px",
-      boxShadowColor = "#ffffff",
-      boxTitleSize = 20,
-      boxDefaultColor = "#00a65a",
-      boxPrimaryColor = "#ffffff",
-      boxInfoColor = "#00a65a",
-      boxSuccessColor = "#00a65a",
-      boxWarningColor = "#ffffff",
-      boxDangerColor = "#ffffff",
-      tabBoxTabColor = "#ffffff",
-      tabBoxTabTextSize = 14,
-      tabBoxTabTextColor = "rgb(0,0,0)",
-      tabBoxTabTextColorSelected = "rgb(0,0,0)",
-      tabBoxBackColor = "#ffffff",
-      tabBoxHighlightColor = "#ffffff",
-      tabBoxBorderRadius = 5,
-      
-      ### inputs
-      buttonBackColor = "#282F38",
-      buttonTextColor = "#ffffff",
-      buttonBorderColor = "#282F38",
-      buttonBorderRadius = 5,
-      buttonBackColorHover = cssGradientThreeColors(
-        direction = "right",
-        colorStart = "rgba(44,222,235,1)",
-        colorMiddle = "rgba(44,222,235,1)",
-        colorEnd = "rgba(0,255,213,1)",
-        colorStartPos = 0,
-        colorMiddlePos = 30,
-        colorEndPos = 100
-      ),
-      buttonTextColorHover = "#000000",
-      buttonBorderColorHover = "transparent",
-      textboxBackColor = "#ffffff",
-      textboxBorderColor = "#ffffff",
-      textboxBorderRadius = 5,
-      textboxBackColorSelect = "#ffffff",
-      textboxBorderColorSelect = "#000000",
-      
-      ### tables
-      tableBackColor = "rgb(255,255,255)",
-      tableBorderColor = "rgb(240,240,240)",
-      tableBorderTopSize = 1,
-      tableBorderRowSize = 1
-    ),
-    
-    uiOutput("start_message"),
-    
-    tabItems(
-      
-      ## Tab Database ----
-      
-      ### Tab Browse Entries ----
-      
-      tabItem(
-        tabName = "db_browse_entries",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Browse Local Database"), style = "color:white")
-          )
-        ),
-        hr(), br(),
-        br(),
-        br(),
-        uiOutput("no_scheme_entries"),
-        uiOutput("db_no_entries"),
-        uiOutput("entry_table_controls"),
-        br(), br(),
-        fluidRow(
-          column(1),
-          column(
-            width = 8,
-            uiOutput("db_entries_table")
-          ),
-          column(
-            width = 3,
-            align = "left",
-            uiOutput("delete_box"),
-            uiOutput("compare_allele_box"),
-            uiOutput("download_entries"),
-            br(), br(), br(), br(), br(), br(), br(), br(),
-            br(), br(), br(), br(), br(), br(), br()
-          )
-        ),
-        br()
-      ),
-      
-      ### Tab Scheme Info  ----  
-      
-      tabItem(
-        tabName = "db_schemeinfo",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Scheme Info"), style = "color:white")
-          )
-        ),
-        hr(), br(), br(), br(),
-        uiOutput("no_scheme_info"),
-        fluidRow(
-          column(2),
-          column(
-            width = 7,
-            align = "center",
-            fluidRow(
-              column(
-                width = 7,
-                align = "right",
-                uiOutput("scheme_header")
-              ),
-              column(
-                width = 2,
-                align = "left",
-                uiOutput("download_scheme_info")
-              )
-            ),
-            br(),
-            br(),
-            uiOutput("scheme_info")
-          )
-        )
-      ),
-      
-      ### Tab Loci Info  ----  
-      
-      tabItem(
-        tabName = "db_loci_info",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Loci Info"), style = "color:white")
-          )
-        ),
-        hr(), br(), br(), br(),
-        fluidRow(
-          column(1),
-          column(
-            width = 10,
-            align = "center",
-            fluidRow(
-              column(
-                width = 6,
-                align = "right",
-                uiOutput("loci_header")
-              ),
-              column(
-                width = 2,
-                align = "left",
-                uiOutput("download_loci")
-              )
-            ),
-            br(),
-            div(class = "loci_table",
-                dataTableOutput("db_loci"))
-          )
-        ),
-        br(), br(),
-        fluidRow(
-          column(1),
-          uiOutput("sequence_selector"), 
-          column(1),
-          column(
-            width = 7,
-            br(),
-            uiOutput("loci_sequences")
-          )
-        )
-      ),
-      
-      ### Tab Distance Matrix  ----  
-      
-      tabItem(
-        tabName = "db_distmatrix",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Distance Matrix"), style = "color:white")
-          )
-        ),
-        hr(), br(), br(), br(),
-        uiOutput("no_scheme_distancematrix"),
-        uiOutput("distancematrix_no_entries"),
-        fluidRow(
-          column(1),
-          uiOutput("distmatrix_show")
-        ),
-        br(), br()
-      ),
-      
-      ### Tab Missing Values ----
-      
-      tabItem(
-        tabName = "db_missing_values",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Missing Values"), style = "color:white")
-          )
-        ),
-        hr(), br(), br(), br(),
-        fluidRow(
-          column(
-            width = 3,
-            uiOutput("missing_values"),
-            fluidRow(
-              column(
-                width = 2,
-                div(
-                  class = "rectangle-red-space" 
-                )
-              ),
-              column(
-                width = 10,
-                align = "left",
-                p(
-                  HTML(
-                    paste(
-                      tags$span(style="color: white; font-size: 15px; margin-left: 75px; position: relative; bottom: -12px", " =  ≥ 5% of loci missing")
-                    )
-                  )
-                )
-              )
-            )
-          ),
-          column(
-            width = 8,
-            rHandsontableOutput("table_missing_values")
-          )
-        )
-      ),
-      
-      ## Tab Manage Schemes  ----  
-      
-      tabItem(
-        tabName = "init",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Select cgMLST Scheme"), style = "color:white")
-          )
-        ),
-        hr(),
-        fluidRow(
-          column(1),
-          column(
-            width = 3,
-            br(),
-            br(),
-            br(),
-            pickerInput(
-              inputId = "select_cgmlst",
-              label = NULL,
-              choices = list(
-                "Acinetobacter baumanii",
-                "Bacillus anthracis",
-                "Bordetella pertussis",
-                "Brucella melitensis",
-                "Brucella spp.",
-                "Burkholderia mallei (FLI)",
-                "Burkholderia mallei (RKI)",
-                "Burkholderia pseudomallei",
-                "Campylobacter jejuni/coli",
-                "Clostridioides difficile",
-                "Clostridium perfringens",
-                "Corynebacterium diphtheriae",
-                "Cronobacter sakazakii/malonaticus",
-                "Enterococcus faecalis",
-                "Enterococcus faecium",
-                "Escherichia coli",
-                "Francisella tularensis",
-                "Klebsiella oxytoca sensu lato",
-                "Klebsiella pneumoniae sensu lato",
-                "Legionella pneumophila",
-                "Listeria monocytogenes",
-                "Mycobacterium tuberculosis complex",
-                "Mycobacteroides abscessus",
-                "Mycoplasma gallisepticum",
-                "Paenibacillus larvae",
-                "Pseudomonas aeruginosa",
-                "Salmonella enterica",
-                "Serratia marcescens",
-                "Staphylococcus aureus",
-                "Staphylococcus capitis",
-                "Streptococcus pyogenes"
-              ),
-              width = "300px",
-              options = list(
-                `live-search` = TRUE,
-                `actions-box` = TRUE,
-                size = 10,
-                style = "background-color: white; border-radius: 5px;"
-              ),
-              multiple = FALSE
-            )
-          ),
-          column(
-            width = 2,
-            br(),
-            br(),
-            br(),
-            h5(textOutput("scheme_update_info"), style = "color: white")
-          ),
-          column(
-            width = 2,
-            br(),
-            br(),
-            br(),
-            actionButton(
-              "download_cgMLST",
-              label = "Download",
-              icon = icon("download")
-            ),
-            shinyjs::hidden(
-              div(id = "loading",
-                  HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
-            )
-          )
-        ),
-        fluidRow(
-          column(1),
-          column(
-            width = 6,
-            align = "center",
-            br(),
-            br(),
-            br(),
-            addSpinner(
-              tableOutput("cgmlst_scheme"),
-              spin = "dots",
-              color = "#ffffff"
-            )
-          )
-        )
-      ),
-      
-      
-      
-      ## Tab Allelic Typing ----------------------------------------------
-      
-      
-      tabItem(
-        tabName = "typing",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Generate Allelic Profile"), style = "color:white")
-          )
-        ),
-        hr(),
-        uiOutput("typing_no_db"),
-        conditionalPanel(
-          "input.typing_mode == 'Single'",
-          fluidRow(
-            uiOutput("initiate_typing_ui"),
-            uiOutput("single_typing_progress"),
-            column(1),
-            uiOutput("metadata_single_box"),
-            column(1),
-            uiOutput("start_typing_ui")
-          )
-        ),
-        conditionalPanel(
-          "input.typing_mode == 'Multi'",
-          fluidRow(
-            uiOutput("initiate_multi_typing_ui"),
-            uiOutput("multi_stop"),
-            column(1),
-            uiOutput("metadata_multi_box"),
-            column(1),
-            uiOutput("start_multi_typing_ui")
-          ),
-          fluidRow(
-            column(
-              width = 6,
-              uiOutput("pending_typing")
-            ),
-            column(
-              width = 6,
-              uiOutput("multi_typing_results")
-            )
-          )
-        )
-      ),
-      
-      
-      ## Tab Visualization -------------------------------------------------------
-      
-      
-      tabItem(
-        tabName = "visualization",
-        fluidRow(
-          tags$script(src = "javascript_functions.js"),
-          column(
-            width = 12,
-            align = "center",
-            br(),
-            conditionalPanel(
-              "input.tree_algo=='Minimum-Spanning'",
-              uiOutput("mst_field")
-            ),
-            conditionalPanel(
-              "input.tree_algo=='Neighbour-Joining'",
-              uiOutput("nj_field")
-            ),
-            conditionalPanel(
-              "input.tree_algo=='UPGMA'",
-              uiOutput("upgma_field")
-            )
-          )
-        ),
-        br(),
-        hr(),
-        
-        ### Control panels MST ----
-        conditionalPanel(
-          "input.tree_algo=='Minimum-Spanning'",
-          fluidRow(
-            column(
-              width = 4,
-              box(
-                solidHeader = TRUE,
-                status = "primary",
-                width = "100%",
-                height = "500px",
-                h3(p("Layout"), style = "color:white; position:relative; right:-15px"),
-                hr(),
-                fluidRow(
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Title"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          textInput(
-                            "mst_title",
-                            label = "",
-                            width = "100%",
-                            placeholder = "Plot Title"
-                          ),
-                          fluidRow(
-                            column(
-                              width = 7,
-                              colorPickr(
-                                inputId = "mst_title_color",
-                                selected = "#000000",
-                                label = "",
-                                update = "changestop",
-                                interaction = list(clear = FALSE,
-                                                   save = FALSE),
-                                position = "right-start",
-                                width = "100%"
-                              )
-                            ),
-                            column(
-                              width = 5,
-                              dropMenu(
-                                actionBttn(
-                                  "mst_title_menu",
-                                  label = "",
-                                  color = "default",
-                                  size = "sm",
-                                  style = "material-flat",
-                                  icon = icon("sliders")
-                                ),
-                                placement = "top-start",
-                                theme = "translucent",
-                                numericInput(
-                                  "mst_title_size",
-                                  label = h5("Size", style = "color:white; margin-bottom: 0px;"),
-                                  value = 40,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Subtitle"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          textInput(
-                            "mst_subtitle",
-                            label = "",
-                            width = "100%",
-                            placeholder = "Plot Subtitle"
-                          ),
-                          fluidRow(
-                            column(
-                              width = 7,
-                              colorPickr(
-                                inputId = "mst_subtitle_color",
-                                selected = "#000000",
-                                label = "",
-                                update = "changestop",
-                                interaction = list(clear = FALSE,
-                                                   save = FALSE),
-                                position = "right-start",
-                                width = "100%"
-                              )
-                            ),
-                            column(
-                              width = 5,
-                              dropMenu(
-                                actionBttn(
-                                  "mst_subtitle_menu",
-                                  label = "",
-                                  color = "default",
-                                  size = "sm",
-                                  style = "material-flat",
-                                  icon = icon("sliders")
-                                ),
-                                placement = "top-start",
-                                theme = "translucent",
-                                numericInput(
-                                  "mst_subtitle_size",
-                                  label = h5("Size", style = "color:white; margin-bottom: 0px;"),
-                                  value = 20,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                ),
-                hr(),
-                fluidRow(
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Legend"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 7,
-                              colorPickr(
-                                inputId = "mst_legend_color",
-                                selected = "#000000",
-                                label = "",
-                                update = "changestop",
-                                interaction = list(clear = FALSE,
-                                                   save = FALSE),
-                                position = "right-start",
-                                width = "100%"
-                              )
-                            ),
-                            column(
-                              width = 5,
-                              dropMenu(
-                                actionBttn(
-                                  "mst_legend_menu",
-                                  label = "",
-                                  color = "default",
-                                  size = "sm",
-                                  style = "material-flat",
-                                  icon = icon("sliders")
-                                ),
-                                placement = "top-start",
-                                theme = "translucent",
-                                fluidRow(
-                                  column(
-                                    width = 11,
-                                    sliderInput(
-                                      "mst_font_size",
-                                      label = h5("Font Size", style = "color:white; margin-bottom: 0px;"),
-                                      value = 18,
-                                      min = 15,
-                                      max = 30,
-                                      step = 1,
-                                      ticks = FALSE,
-                                      width = "180px"
-                                    )
-                                  ),
-                                  column(1)
-                                ),
-                                br(),
-                                fluidRow(
-                                  column(
-                                    width = 11,
-                                    sliderInput(
-                                      "mst_symbol_size",
-                                      label = h5("Key Size", style = "color:white; margin-bottom: 0px;"),
-                                      value = 20,
-                                      min = 10,
-                                      max = 30,
-                                      step = 1,
-                                      ticks = FALSE,
-                                      width = "180px"
-                                    )
-                                  ),
-                                  column(1)
-                                )
-                              )
-                            )
-                          ),
-                          fluidRow(
-                            column(
-                              width = 7,
-                              selectInput(
-                                "mst_legend_ori",
-                                label = "",
-                                width = "100%",
-                                choices = c("Left" = "left", "Right" = "right")
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Background"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "left",
-                              div(
-                                class = "mat-switch-mst-nodes",
-                                materialSwitch(
-                                  "mst_background_transparent",
-                                  h5(p("Transparent"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            )
-                          ),
-                          fluidRow(
-                            column(
-                              width = 7,
-                              colorPickr(
-                                inputId = "mst_background_color",
-                                width = "100%",
-                                selected = "#ffffff",
-                                label = "",
-                                update = "changestop",
-                                interaction = list(clear = FALSE,
-                                                   save = FALSE),
-                                position = "right-start"
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            column(
-              width = 4,
-              box(
-                solidHeader = TRUE,
-                status = "primary",
-                width = "100%",
-                height = "500px",
-                h3(p("Nodes"), style = "color:white; position:relative; right:-15px"),
-                hr(),
-                fluidRow(
-                  column(
-                    width = 6,
-                    column(
-                      width = 12,
-                      align = "left",
-                      h4(p("Label"), style = "color:white;")
-                    ),
-                    column(
-                      width = 12,
-                      align = "center",
-                      div(
-                        class = "label_sel",
-                        uiOutput("mst_node_label")
-                      ),
-                      fluidRow(
-                        column(
-                          width = 7,
-                          colorPickr(
-                            inputId = "node_font_color",
-                            width = "100%",
-                            selected = "#000000",
-                            label = "",
-                            update = "changestop",
-                            interaction = list(clear = FALSE,
-                                               save = FALSE),
-                            position = "right-start"
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          dropMenu(
-                            actionBttn(
-                              "mst_label_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            numericInput(
-                              "node_label_fontsize",
-                              label = h5("Size", style = "color:white; margin-bottom: 0px;"),
-                              value = 14,
-                              min = 8,
-                              max = 30,
-                              step = 1,
-                              width = "80px"
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Color"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 10,
-                              align = "left",
-                              div(
-                                class = "mat-switch-mst-nodes",
-                                materialSwitch(
-                                  "mst_color_var",
-                                  h5(p("Add Variable"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            column(
-                              width = 2,
-                              bslib::tooltip(
-                                bsicons::bs_icon("info-circle", title = "Only categorical variables can \nbe mapped to the node color", color = "white", 
-                                                 height = "12px", width = "12px", position = "relative", top = "27px", right = "56px"),
-                                "Text shown in the tooltip.",
-                                show = FALSE,
-                                id = "mst_node_col_info"
-                              )
-                            )
-                          ),
-                          uiOutput("mst_color_mapping")
-                        )
-                      )
-                    ), br()
-                  )
-                ),
-                hr(),
-                fluidRow(
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Size"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "left",
-                              div(
-                                class = "mat-switch-mst-nodes",
-                                materialSwitch(
-                                  "scale_nodes",
-                                  h5(p("Scale by Duplicates"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                  value = TRUE,
-                                  right = TRUE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    column(
-                      width = 12,
-                      align = "left",
-                      fluidRow(
-                        column(
-                          width = 3,
-                          align = "left",
-                          conditionalPanel(
-                            "input.scale_nodes==true",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Range')
-                              )
-                            )
-                          ),
-                          conditionalPanel(
-                            "input.scale_nodes==false",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Size')
-                              )
-                            )
-                          )
-                        ),
-                        column(
-                          width = 9,
-                          align = "center",
-                          conditionalPanel(
-                            "input.scale_nodes==true",
-                            div(
-                              class = "mst_scale_slider",
-                              sliderInput(
-                                "mst_node_scale",
-                                label = "",
-                                min = 1,
-                                max = 80,
-                                value = c(20, 40),
-                                ticks = FALSE
-                              )
-                            )
-                          ),
-                          conditionalPanel(
-                            "input.scale_nodes==false",
-                            div(
-                              class = "mst_scale_slider",
-                              sliderInput(
-                                inputId = "mst_node_size",
-                                label = "",
-                                min = 1,
-                                max = 100,
-                                value = 30,
-                                ticks = FALSE
-                              ) 
-                            )
-                          )
-                        )
-                      ),
-                      br()
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Other Elements"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "left",
-                              div(
-                                class = "mat-switch-mst-nodes",
-                                materialSwitch(
-                                  "mst_shadow",
-                                  h5(p("Show Shadow"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                  value = TRUE,
-                                  right = TRUE
-                                )
-                              ),
-                              fluidRow(
-                                column(
-                                  width = 3,
-                                  align = "left",
-                                  HTML(
-                                    paste(
-                                      tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Shape')
-                                    )
-                                  )
-                                ),
-                                column(
-                                  width = 9,
-                                  align = "center",
-                                  div(
-                                    class = "mst_shape_sel",
-                                    selectInput(
-                                      "mst_node_shape",
-                                      "",
-                                      choices = list(`Label inside` = c("Circle" = "circle", "Box" = "box", "Text" = "text"),
-                                                     `Label outside` = c("Diamond" = "diamond", "Hexagon" = "hexagon","Dot" = "dot", "Square" = "square")),
-                                      selected = c("Dot" = "dot"),
-                                      width = "85%"
-                                    )
-                                  )
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            column(
-              width = 4,
-              box(
-                solidHeader = TRUE,
-                status = "primary",
-                width = "100%",
-                height = "500px",
-                h3(p("Edges"), style = "color:white; position:relative; right:-15px"),
-                hr(),
-                fluidRow(
-                  column(
-                    width = 6,
-                    column(
-                      width = 12,
-                      align = "left",
-                      h4(p("Label"), style = "color:white;")
-                    ),
-                    column(
-                      width = 12,
-                      align = "center",
-                      div(
-                        class = "label_sel",
-                        selectInput(
-                          "mst_edge_label",
-                          label = "",
-                          choices = c(
-                            `Allelic Distance` = "weight",
-                            Index = "index",
-                            `Assembly ID` = "assembly_id",
-                            `Assembly Name` = "assembly_name",
-                            `Isolation Date` = "isolation_date",
-                            Host = "host",
-                            Country = "country",
-                            City = "city"
-                          ),
-                          selected = c(`Allelic Distance` = "weight"),
-                          width = "100%"
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 7,
-                          colorPickr(
-                            inputId = "mst_edge_font_color",
-                            width = "100%",
-                            selected = "#000000",
-                            label = "",
-                            update = "changestop",
-                            interaction = list(clear = FALSE,
-                                               save = FALSE),
-                            position = "right-start"
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          dropMenu(
-                            actionBttn(
-                              "mst_edgelabel_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            width = 5,
-                            numericInput(
-                              "mst_edge_font_size",
-                              label = h5("Size", style = "color:white; margin-bottom: 0px;"),
-                              value = 18,
-                              step = 1,
-                              min = 8,
-                              max = 30,
-                              width = "80px"
-                            )
-                          )
-                        )
-                      ),
-                      br()
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Color"), style = "color:white; position: relative; right: -15px"),
-                        column(
-                          width = 12,
-                          align = "center",
-                          fluidRow(
-                            column(
-                              width = 7,
-                              div(
-                                class = "node_color",
-                                colorPickr(
-                                  inputId = "mst_color_edge",
-                                  width = "100%",
-                                  selected = "#000000",
-                                  label = "",
-                                  update = "changestop",
-                                  interaction = list(clear = FALSE,
-                                                     save = FALSE),
-                                  position = "right-start"
-                                )
-                              )
-                            ),
-                            column(
-                              width = 5,
-                              dropMenu(
-                                actionBttn(
-                                  "mst_edgecolor_menu",
-                                  label = "",
-                                  color = "default",
-                                  size = "sm",
-                                  style = "material-flat",
-                                  icon = icon("sliders")
-                                ),
-                                placement = "top-start",
-                                theme = "translucent",
-                                width = 5,
-                                sliderInput(
-                                  "mst_edge_opacity",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px;"),
-                                  value = 0.7,
-                                  step = 0.1,
-                                  min = 0,
-                                  max = 1,
-                                  ticks = FALSE,
-                                  width = "150px"
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                ),
-                hr(style = "margin-top: 3px !important"),
-                fluidRow(
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Length multiplier"), style = "color:white; position: relative; right: -15px; margin-bottom: -5px")
-                      )
-                    ),
-                    column(
-                      width = 12,
-                      align = "left",
-                      br(),
-                      div(
-                        class = "switch-mst-edges",
-                        materialSwitch(
-                          "mst_scale_edges",
-                          h5(p("Scale Allelic Distance"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                          value = FALSE,
-                          right = TRUE
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          align = "left",
-                          conditionalPanel(
-                            "input.mst_scale_edges==true",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Multiplier')
-                              )
-                            )
-                          ),
-                          conditionalPanel(
-                            "input.mst_scale_edges==false",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Length')
-                              )
-                            )
-                          )
-                        ),
-                        column(
-                          width = 9,
-                          align = "center",
-                          conditionalPanel(
-                            "input.mst_scale_edges==true",
-                            div(
-                              class = "slider_edge",
-                              sliderInput(
-                                inputId = "mst_edge_length_scale",
-                                label = NULL,
-                                min = 1,
-                                max = 40,
-                                value = 15,
-                                ticks = FALSE
-                              ) 
-                            )
-                          ),
-                          conditionalPanel(
-                            "input.mst_scale_edges==false",
-                            div(
-                              class = "slider_edge",
-                              sliderTextInput(
-                                inputId = "mst_edge_length",
-                                label = NULL,
-                                choices = append(seq(0.1, 1, 0.1), 2:100),
-                                selected = 35,
-                                hide_min_max = FALSE
-                              ) 
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 6,
-                    fluidRow(
-                      column(
-                        width = 6,
-                        align = "left",
-                        h4(p("Clustering"), style = "color:white; text-align: left; position: relative; right: -15px")
-                      ),
-                      column(
-                        width = 2,
-                        bslib::tooltip(
-                          bsicons::bs_icon("info-circle", 
-                                           title = "Cluster threshold according to species-specific\nComplex Type Distance (cgMLST.org)", 
-                                           color = "white", height = "14px", width = "14px", 
-                                           position = "relative", top = "9px", right = "28px"),
-                          "Text shown in the tooltip.",
-                          show = FALSE,
-                          id = "mst_cluster_info"
-                        )
-                      )
-                    ),
-                    br(),
-                    fluidRow(
-                      column(
-                        width = 9,
-                        div(
-                          class = "mst-cluster-switch",
-                          materialSwitch(
-                            "mst_show_clusters",
-                            h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        dropMenu(
-                          actionBttn(
-                            "mst_cluster_col_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          width = 5,
-                          selectInput(
-                            "mst_cluster_col_scale",
-                            label = h5("Color Scale", style = "color:white; margin-bottom: 0px;"),
-                            choices = c("Viridis", "Rainbow"),
-                            width = "150px"
-                          ),
-                          selectInput(
-                            "mst_cluster_type",
-                            label = h5("Cluster Type", style = "color:white; margin-bottom: 0px;"),
-                            choices = c("Type 1", "Type 2"),
-                            width = "150px"
-                          )
-                        )
-                      )
-                    ),
-                    br(),
-                    fluidRow(
-                      column(
-                        width = 4,
-                        HTML(
-                          paste(
-                            tags$span(style='color: white; text-align: left; font-size: 14px; margin-left: 15px', 'Threshold')
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        uiOutput("mst_cluster")
-                      ),
-                      column(
-                        width = 4,
-                        actionButton(
-                          "mst_cluster_reset",
-                          label = "",
-                          icon = icon("rotate")
-                        ),
-                        bsTooltip("mst_cluster_reset", 
-                                  HTML("Reset to default Complex Type Distance"), 
-                                  placement = "top", trigger = "hover")
-                      )
-                    )
-                  ),
-                  br(),
-                )
-              ), br(), br(), br(), br(), br(), br()
-            )
-          )
-        ),
-        
-        ### Control Panels NJ ----
-        
-        conditionalPanel(
-          "input.tree_algo=='Neighbour-Joining'",
-          fluidRow(
-            column(
-              width = 1,
-              radioGroupButtons(
-                inputId = "nj_controls",
-                label = "",
-                choices = c("Layout", "Label", "Elements", "Variables"),
-                direction = "vertical"
-              )
-            ),
-            conditionalPanel(
-              "input.nj_controls=='Layout'",
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Theme"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "center",
-                        selectInput(
-                          inputId = "nj_layout",
-                          label = "",
-                          choices = list(
-                            Linear = list(
-                              "Rectangular" = "rectangular",
-                              "Roundrect" = "roundrect",
-                              "Slanted" = "slanted",
-                              "Ellipse" = "ellipse"
-                            ),
-                            Circular = list("Circular" = "circular",
-                                            "Inward" = "inward")
-                          ),
-                          selected = "rectangular",
-                          width = "90%"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch-layout",
-                          materialSwitch(
-                            "nj_rootedge_show",
-                            h5(p("Rootedge"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "nj_rootedge_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("nj_rootedge_length"),
-                              br(),
-                              selectInput(
-                                "nj_rootedge_line",
-                                label = h5("Rootedge Line", style = "color:white"),
-                                choices = c(Solid = "solid", Dashed = "dashed", Dotted = "dotted"),
-                                selected = c(Dotted = "solid"),
-                                width = "100px"
-                              ),
-                              br(),
-                              conditionalPanel(
-                                "input.nj_layout=='circular'",
-                                sliderInput(
-                                  "nj_xlim",
-                                  label = h5("Adjust Circular", style = "color:white"),
-                                  min = -50,
-                                  max = 0,
-                                  value = -10,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.nj_layout=='inward'",
-                                sliderInput(
-                                  "nj_inward_xlim",
-                                  label = h5("Adjust Circular", style = "color:white"),
-                                  min = 30,
-                                  max = 120,
-                                  value = 50,
-                                  ticks = FALSE,
-                                  width = "150px",
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch-re",
-                          materialSwitch(
-                            "nj_ladder",
-                            h5(p("Ladderize"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                            value = TRUE,
-                            right = TRUE
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Color"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Lines/Text"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
-                      ),
-                      column(
-                        width = 7,
-                        colorPickr(
-                          inputId = "nj_color",
-                          width = "90%",
-                          selected = "#000000",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    br(),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Background"), style = "color:white; position: relative; right: -15px; margin-top: 7px; margin-bottom: 38px")
-                      ),
-                      column(
-                        width = 7,
-                        colorPickr(
-                          inputId = "nj_bg",
-                          width = "90%",
-                          selected = "#ffffff",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ), 
-                    br()
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Title"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      textInput(
-                        "nj_title",
-                        label = "",
-                        width = "100%",
-                        placeholder = "Plot Title"
-                      ),
-                      textInput(
-                        "nj_subtitle",
-                        label = "",
-                        width = "100%",
-                        placeholder = "Plot Subtitle"
-                      ),
-                      br(),
-                      fluidRow(
-                        column(
-                          width = 7,
-                          colorPickr(
-                            inputId = "nj_title_color",
-                            selected = "#000000",
-                            label = "",
-                            update = "changestop",
-                            interaction = list(clear = FALSE,
-                                               save = FALSE),
-                            position = "right-start",
-                            width = "100%"
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "nj_title_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                numericInput(
-                                  "nj_title_size",
-                                  label = h5("Title Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 30,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                ),
-                                br(),
-                                numericInput(
-                                  "nj_subtitle_size",
-                                  label = h5("Subtitle Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 20,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      br()
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Sizing"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      br(),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Ratio", style = "color: white; font-size: 14px;")
-                        ),
-                        column(
-                          width = 6,
-                          align = "left",
-                          div(
-                            class = "ratio-sel",
-                            selectInput(
-                              "nj_ratio",
-                              "",
-                              choices = c("16:10" = (16/10), "16:9" = (16/9), "4:3" = (4/3))
-                            )
-                          )
-                        ),
-                        column(
-                          width = 3,
-                          dropMenu(
-                            actionBttn(
-                              "nj_size_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                sliderInput(
-                                  "nj_v",
-                                  label = h5("Vertical Position", style = "color:white; margin-bottom: 0px"),
-                                  min = -0.5,
-                                  max = 0.5,
-                                  step = 0.01,
-                                  value = 0,
-                                  width = "150px",
-                                  ticks = FALSE
-                                ),
-                                br(),
-                                sliderInput(
-                                  "nj_h",
-                                  label = h5("Horizontal Position", style = "color:white; margin-bottom: 0px"),
-                                  min = -0.5,
-                                  max = 0.5,
-                                  step = 0.01,
-                                  value = 0,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Size", style = "color: white; font-size: 14px; margin-top: 30px")
-                        ),
-                        column(
-                          width = 9,
-                          sliderInput(
-                            "nj_scale",
-                            "",
-                            min = 500,
-                            max = 1200,
-                            value = 800,
-                            step = 5,
-                            width = "95%",
-                            ticks = FALSE
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Zoom", style = "color: white; font-size: 14px; margin-top: 30px")
-                        ),
-                        column(
-                          width = 9,
-                          div(
-                            class = "zoom-slider",
-                            sliderInput(
-                              "nj_zoom",
-                              label = NULL,
-                              min = 0.5,
-                              max = 1.5,
-                              step = 0.05,
-                              value = 0.95,
-                              ticks = FALSE
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Tree Scale"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      fluidRow(
-                        column(
-                          width = 8,
-                          align = "left",
-                          div(
-                            class = "mat-switch-layout",
-                            materialSwitch(
-                              "nj_treescale_show",
-                              h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                              value = TRUE,
-                              right = TRUE
-                            )
-                          ),
-                          br()
-                        ),
-                        column(
-                          width = 4,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "nj_treescale_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                uiOutput("nj_treescale_width"),
-                                br(),
-                                uiOutput("nj_treescale_x"),
-                                br(),
-                                uiOutput("nj_treescale_y")
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Legend"), style = "color:white; position: relative; right: -15px; margin-top: 10px; margin-bottom: -2px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      fluidRow(
-                        column(
-                          width = 7,
-                          align = "left",
-                          prettyRadioButtons(
-                            "nj_legend_orientation",
-                            "",
-                            choices = c(Horizontal = "horizontal",
-                                        Vertical = "vertical"),
-                            selected = c(Vertical = "vertical"),
-                            inline = FALSE
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "nj_legend_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                numericInput(
-                                  "nj_legend_size",
-                                  label = h5("Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 10,
-                                  min = 5,
-                                  max = 25,
-                                  step = 1,
-                                  width = "80px"
-                                ),
-                                br(),
-                                sliderInput(
-                                  "nj_legend_x",
-                                  label = h5("Horizontal Position", style = "color:white; margin-bottom: 0px"),
-                                  value = 0.9,
-                                  min = -0.9,
-                                  max = 1.9,
-                                  step = 0.2,
-                                  width = "150px",
-                                  ticks = FALSE
-                                ),
-                                br(),
-                                sliderInput(
-                                  "nj_legend_y",
-                                  label = h5("Vertical Position", style = "color:white; margin-bottom: 0px"),
-                                  value = 0.2,
-                                  min = -1.5,
-                                  max = 1.5,
-                                  step = 0.1,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.nj_controls=='Label'",
-              column(
-                width = 4,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Tips"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 4,
-                            align = "left",
-                            div(
-                              class = "mat-switch-lab",
-                              materialSwitch(
-                                "nj_tiplab_show",
-                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                                value = TRUE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 4,
-                            align = "center",
-                            uiOutput("nj_tiplab")
-                          ),
-                          column(
-                            width = 3,
-                            div(
-                              class = "mat-switch-align",
-                              materialSwitch(
-                                "nj_align",
-                                h5(p("Align"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 1,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "nj_labeltext_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-start",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  sliderInput(
-                                    "nj_tiplab_alpha",
-                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                    min = 0.1,
-                                    max = 1,
-                                    value = 1,
-                                    width = "150px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  conditionalPanel(
-                                    "!(input.nj_layout=='inward'|input.nj_layout=='circular')",
-                                    sliderInput(
-                                      inputId = "nj_tiplab_nudge_x",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = 0,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  conditionalPanel(
-                                    "input.nj_layout=='circular'",
-                                    sliderInput(
-                                      inputId = "nj_tiplab_position",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = -0.05,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  conditionalPanel(
-                                    "input.nj_layout=='inward'",
-                                    sliderInput(
-                                      inputId = "nj_tiplab_position_inw",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = 1.1,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "nj_tiplab_angle",
-                                    label = h5("Angle", style = "color:white; margin-bottom: 0px"),
-                                    min = -90,
-                                    max = 90,
-                                    value = 0,
-                                    ticks = FALSE,
-                                    width = "150px",
-                                  )      
-                                ),
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  uiOutput("nj_tiplab_size"),
-                                  br(),
-                                  selectInput(
-                                    "nj_tiplab_fontface",
-                                    label = h5("Fontface", style = "color:white; margin-bottom: 5px; margin-top: 16px"),
-                                    width = "250px",
-                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
-                                  )
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 4,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px")
-                      ),
-                      column(
-                        width = 4,
-                        align = "center",
-                        colorPickr(
-                          inputId = "nj_tiplab_color",
-                          width = "100%",
-                          selected = "#000000",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 4,
-                        align = "left",
-                        br(),
-                        div(
-                          class = "mat-switch-geom",
-                          materialSwitch(
-                            "nj_geom",
-                            h5(p("Panels"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        colorPickr(
-                          inputId = "nj_tiplab_fill",
-                          width = "100%",
-                          selected = "#84D9A0",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "left",
-                        dropMenu(
-                          actionBttn(
-                            "nj_labelformat_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("nj_tiplab_padding"),
-                              br(),
-                              sliderInput(
-                                inputId = "nj_tiplab_labelradius",
-                                label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
-                                min = 0,
-                                max = 0.5,
-                                value = 0.2,
-                                width = "150px",
-                                ticks = FALSE
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 3,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Branches"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 5,
-                            align = "left",
-                            div(
-                              class = "mat-switch-lab",
-                              materialSwitch(
-                                "nj_show_branch_label",
-                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 5,
-                            align = "center",
-                            uiOutput("nj_branch_label")
-                          ),
-                          column(
-                            width = 2,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "nj_branch_label_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-start",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  sliderInput(
-                                    "nj_branchlab_alpha",
-                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                    min = 0.1,
-                                    max = 1,
-                                    value = 0.65,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "nj_branch_x",
-                                    label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-                                    min = -3,
-                                    max = 3,
-                                    value = 0,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "nj_branch_y",
-                                    label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-                                    min = -3,
-                                    max = 3,
-                                    value = 0,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  )
-                                ),
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  uiOutput("nj_branch_size"),
-                                  selectInput(
-                                    "nj_branchlab_fontface",
-                                    label = h5("Fontface", style = "color:white; margin-bottom: 0px;"),
-                                    width = "250px",
-                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    "nj_branch_labelradius",
-                                    label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
-                                    min = 0,
-                                    max = 0.5,
-                                    value = 0.5,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  )
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px; margin-bottom: 109px")
-                      ),
-                      column(
-                        width = 5,
-                        colorPickr(
-                          inputId = "nj_branch_label_color",
-                          width = "100%",
-                          selected = "#FFB7B7",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 3,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Custom Labels"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 6,
-                            textInput(
-                              "nj_new_label_name",
-                              "",
-                              placeholder = "New Label"
-                            )
-                          ),
-                          column(
-                            width = 3,
-                            actionButton(
-                              "nj_add_new_label",
-                              "",
-                              icon = icon("plus")
-                            )
-                          ),
-                          column(
-                            width = 2,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "nj_custom_label_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-end",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 12,
-                                  align = "center",
-                                  uiOutput("nj_custom_labelsize"),
-                                  br(),
-                                  uiOutput("nj_sliderInput_y"),
-                                  br(),
-                                  uiOutput("nj_sliderInput_x")
-                                )
-                              )
-                            )
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 6,
-                            uiOutput("nj_custom_label_select")
-                          ),
-                          column(
-                            width = 4,
-                            uiOutput("nj_del_label"),
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 12,
-                            align = "center",
-                            uiOutput("nj_cust_label_save")
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.nj_controls=='Elements'",
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Tip Points"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "nj_tippoint_show",
-                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "nj_tippoint_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              sliderInput(
-                                "nj_tippoint_alpha",
-                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                value = 0.5,
-                                min = 0.1,
-                                max = 1,
-                                width = "150px",
-                                ticks = FALSE
-                              ), 
-                              br(),
-                              uiOutput("nj_tippoint_size")
-                            )
-                          )
-                        )  
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        colorPickr(
-                          inputId = "nj_tippoint_color",
-                          width = "100%",
-                          selected = "#3A4657",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        conditionalPanel(
-                          "input.nj_tipshape_mapping_show==false",
-                          selectInput(
-                            "nj_tippoint_shape",
-                            "",
-                            width = "100%",
-                            choices = c(
-                              Circle = "circle", 
-                              Square = "square", 
-                              Diamond = "diamond", 
-                              Triangle = "triangle",
-                              Cross = "cross", 
-                              Asterisk = "asterisk"
-                            )
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.nj_tipshape_mapping_show==true",
-                          h5(p("Variable assigned"), style = "color:white; position: relative; right: -15px; margin-top: 30px; font-style: italic")
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Node Points"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "nj_nodepoint_show",
-                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "nj_nodepoint_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              sliderInput(
-                                "nj_nodepoint_alpha",
-                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                value = 1,
-                                min = 0.1,
-                                max = 1,
-                                width = "150px",
-                                ticks = FALSE
-                              ), 
-                              br(),
-                              uiOutput("nj_nodepoint_size")
-                            )
-                          )
-                        )  
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        colorPickr(
-                          inputId = "nj_nodepoint_color",
-                          width = "100%",
-                          selected = "#3A4657",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        selectInput(
-                          "nj_nodepoint_shape",
-                          "",
-                          choices = c(
-                            Circle = "circle", 
-                            Square = "square", 
-                            Diamond = "diamond", 
-                            Triangle = "triangle",
-                            Cross = "cross", 
-                            Asterisk = "asterisk"
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 6,
-                        h4(p("Tiles"), style = "color:white; position: relative; right: -15px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        div(
-                          class = "sel-tile-number",
-                          selectInput(
-                            "nj_tile_number",
-                            "",
-                            choices = 1:5,
-                            width = "70px"
-                          )
-                        )
-                      ),
-                      column(
-                        width = 7,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "nj_tile_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              conditionalPanel(
-                                "input.nj_tile_num == 1",
-                                sliderInput(
-                                  "nj_fruit_alpha",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.nj_tile_num == 2",
-                                sliderInput(
-                                  "nj_fruit_alpha_2",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.nj_tile_num == 3",
-                                sliderInput(
-                                  "nj_fruit_alpha_3",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.nj_tile_num == 4",
-                                sliderInput(
-                                  "nj_fruit_alpha_4",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.nj_tile_num == 5",
-                                sliderInput(
-                                  "nj_fruit_alpha_5",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.nj_tile_num == 1",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_width"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 68px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_offset_circ"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.nj_tile_num == 2",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_width2"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_offset_circ_2"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.nj_tile_num == 3",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_width3"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_offset_circ_3"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.nj_tile_num == 4",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_width4"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_offset_circ_4"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.nj_tile_num == 5",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_width5"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("nj_fruit_offset_circ_5"),
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 6,
-                        h4(p("Heatmap"), style = "color:white; position: relative; right: -15px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        h5("Title", style = "color:white; margin-left: 15px; margin-top: 32px;")
-                      ),
-                      column(
-                        width = 6,
-                        align = "center",
-                        textInput(
-                          "nj_heatmap_title",
-                          label = "",
-                          value = "Heatmap",
-                          placeholder = "Heatmap" 
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "nj_heatmap_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("nj_colnames_angle"),
-                              br(),
-                              uiOutput("nj_colnames_y")
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5("Width", style = "color: white; margin-left: 15px; margin-top: 40px;")
-                      ),
-                      column(
-                        width = 7,
-                        uiOutput("nj_heatmap_width")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5("Position", style = "color:white; margin-left: 15px; margin-top: 36px;")
-                      ),
-                      column(
-                        width = 7,
-                        uiOutput("nj_heatmap_offset")
-                      )
-                    ),
-                    br(), br()
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Clade Highlight"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 12,
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "nj_nodelabel_show",
-                            h5(p("Toggle Node View"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        h5(p("Nodes"), style = "color:white; position: relative; right: -15px; margin-top: 20px")
-                      ),
-                      column(
-                        width = 9,
-                        uiOutput("nj_parentnode")
-                      )
-                    ),
-                    uiOutput("nj_clade_scale"),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Form"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
-                      ),
-                      column(
-                        width = 7,
-                        div(
-                          class = "sel-clade",
-                          selectInput(
-                            "nj_clade_type",
-                            "",
-                            choices = c("Rect" = "rect",
-                                        "Round" = "roundrect"),
-                            selected = c("Round" = "roundrect")
-                          ) 
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.nj_controls=='Variables'",
-              column(
-                width = 7,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 3,
-                        align = "center",
-                        h4(p("Element"), style = "color:white; margin-bottom: 20px")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        h4(p("Variable"), style = "color:white; margin-bottom: 20px; margin-right: 30px;")
-                      ),
-                      column(
-                        width = 6,
-                        align = "center",
-                        h4(p("Color Scale"), style = "color:white; margin-bottom: 20px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "nj_mapping_show",
-                            h5(p("Tip Label Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_color_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_tiplab_scale")
-                      ),
-                      uiOutput("nj_tiplab_mapping_info"),
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "nj_tipcolor_mapping_show",
-                            h5(p("Tip Point Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_tipcolor_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_tippoint_scale")
-                      ),
-                      uiOutput("nj_tipcolor_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "nj_tipshape_mapping_show",
-                            h5(p("Tip Point Shape"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_tipshape_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        HTML(
-                          paste(
-                            tags$span(style='color: white; font-size: 14px; font-style: italic; position: relative; bottom: -16px; right: -40px;', 'No scale for shapes')
-                          )
-                        )
-                      ),
-                      uiOutput("nj_tipshape_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        fluidRow(
-                          column(
-                            width = 8,
-                            conditionalPanel(
-                              "input.nj_tile_num == 1",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "nj_tiles_show_1",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px; margin-right: 10px"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.nj_tile_num == 2",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "nj_tiles_show_2",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.nj_tile_num == 3",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "nj_tiles_show_3",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.nj_tile_num == 4",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "nj_tiles_show_4",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.nj_tile_num == 5",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "nj_tiles_show_5",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            )
-                          ), 
-                          column(
-                            width = 4,
-                            align = "left",
-                            div(
-                              class = "tile-sel",
-                              selectInput(
-                                "nj_tile_num",
-                                "",
-                                choices = 1:5,
-                                width = "50px"
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        conditionalPanel(
-                          "input.nj_tile_num == 1",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_fruit_variable")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.nj_tile_num == 2",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_fruit_variable2")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.nj_tile_num == 3",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_fruit_variable3")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.nj_tile_num == 4",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_fruit_variable4")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.nj_tile_num == 5",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_fruit_variable5")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.nj_tile_num == 1",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_tiles_scale_1")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.nj_tile_num == 2",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_tiles_scale_2")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.nj_tile_num == 3",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_tiles_scale_3")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.nj_tile_num == 4",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_tiles_scale_4")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.nj_tile_num == 5",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("nj_tiles_scale_5")
-                          )
-                        )
-                      ),
-                      uiOutput("nj_fruit_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "nj_heatmap_show",
-                            h5(p("Heatmap"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("nj_heatmap_sel")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        div(
-                          class = "heatmap-scale",
-                          uiOutput("nj_heatmap_scale")
-                        )
-                      ),
-                      uiOutput("nj_heatmap_mapping_info")
-                    )
-                  )
-                )
-              )
-            )
-          ),
-          br(), br(), br(), br(), br(), br()
-        ),
-        
-        ### Control Panels UPGMA ----
-        
-        conditionalPanel(
-          "input.tree_algo=='UPGMA'",
-          fluidRow(
-            column(
-              width = 1,
-              radioGroupButtons(
-                inputId = "upgma_controls",
-                label = "",
-                choices = c("Layout", "Label", "Elements", "Variables"),
-                direction = "vertical"
-              )
-            ),
-            conditionalPanel(
-              "input.upgma_controls=='Layout'",
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Theme"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "center",
-                        selectInput(
-                          inputId = "upgma_layout",
-                          label = "",
-                          choices = list(
-                            Linear = list(
-                              "Rectangular" = "rectangular",
-                              "Roundrect" = "roundrect",
-                              "Slanted" = "slanted",
-                              "Ellipse" = "ellipse"
-                            ),
-                            Circular = list("Circular" = "circular",
-                                            "Inward" = "inward")
-                          ),
-                          selected = "rectangular",
-                          width = "90%"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch-layout",
-                          materialSwitch(
-                            "upgma_rootedge_show",
-                            h5(p("Rootedge"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_rootedge_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("upgma_rootedge_length"),
-                              br(),
-                              selectInput(
-                                "upgma_rootedge_line",
-                                label = h5("Rootedge Line", style = "color:white"),
-                                choices = c(Solid = "solid", Dashed = "dashed", Dotted = "dotted"),
-                                selected = c(Dotted = "solid"),
-                                width = "100px"
-                              ),
-                              br(),
-                              conditionalPanel(
-                                "input.upgma_layout=='circular'",
-                                sliderInput(
-                                  "upgma_xlim",
-                                  label = h5("Adjust Circular", style = "color:white"),
-                                  min = -50,
-                                  max = 0,
-                                  value = -10,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.upgma_layout=='inward'",
-                                sliderInput(
-                                  "upgma_inward_xlim",
-                                  label = h5("Adjust Circular", style = "color:white"),
-                                  min = 30,
-                                  max = 120,
-                                  value = 50,
-                                  ticks = FALSE,
-                                  width = "150px",
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch-re",
-                          materialSwitch(
-                            "upgma_ladder",
-                            h5(p("Ladderize"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                            value = TRUE,
-                            right = TRUE
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Color"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Lines/Text"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
-                      ),
-                      column(
-                        width = 7,
-                        colorPickr(
-                          inputId = "upgma_color",
-                          width = "90%",
-                          selected = "#000000",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    br(),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Background"), style = "color:white; position: relative; right: -15px; margin-top: 7px; margin-bottom: 38px")
-                      ),
-                      column(
-                        width = 7,
-                        colorPickr(
-                          inputId = "upgma_bg",
-                          width = "90%",
-                          selected = "#ffffff",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Title"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      textInput(
-                        "upgma_title",
-                        label = "",
-                        width = "100%",
-                        placeholder = "Plot Title"
-                      ),
-                      textInput(
-                        "upgma_subtitle",
-                        label = "",
-                        width = "100%",
-                        placeholder = "Plot Subtitle"
-                      ),
-                      br(),
-                      fluidRow(
-                        column(
-                          width = 7,
-                          colorPickr(
-                            inputId = "upgma_title_color",
-                            selected = "#000000",
-                            label = "",
-                            update = "changestop",
-                            interaction = list(clear = FALSE,
-                                               save = FALSE),
-                            position = "right-start",
-                            width = "100%"
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "upgma_title_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                numericInput(
-                                  "upgma_title_size",
-                                  label = h5("Title Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 30,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                ),
-                                br(),
-                                numericInput(
-                                  "upgma_subtitle_size",
-                                  label = h5("Subtitle Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 20,
-                                  min = 15,
-                                  max = 40,
-                                  step = 1,
-                                  width = "80px"
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Sizing"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      br(),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Ratio", style = "color: white; font-size: 14px;")
-                        ),
-                        column(
-                          width = 6,
-                          align = "left",
-                          div(
-                            class = "ratio-sel",
-                            selectInput(
-                              "upgma_ratio",
-                              "",
-                              choices = c("16:10" = (16/10), "16:9" = (16/9), "4:3" = (4/3))
-                            )
-                          )
-                        ),
-                        column(
-                          width = 3,
-                          dropMenu(
-                            actionBttn(
-                              "upgma_size_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                sliderInput(
-                                  "upgma_v",
-                                  label = "Vertical Position",
-                                  min = -0.5,
-                                  max = 0.5,
-                                  step = 0.01,
-                                  value = 0,
-                                  width = "150px",
-                                  ticks = FALSE
-                                ),
-                                br(),
-                                sliderInput(
-                                  "upgma_h",
-                                  label = "Horizontal Position",
-                                  min = -0.5,
-                                  max = 0.5,
-                                  step = 0.01,
-                                  value = 0,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Size", style = "color: white; font-size: 14px; margin-top: 30px")
-                        ),
-                        column(
-                          width = 9,
-                          sliderInput(
-                            "upgma_scale",
-                            "",
-                            min = 500,
-                            max = 1200,
-                            value = 800,
-                            step = 5,
-                            width = "95%",
-                            ticks = FALSE
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 3,
-                          h5("Zoom", style = "color: white; font-size: 14px; margin-top: 30px")
-                        ),
-                        column(
-                          width = 9,
-                          div(
-                            class = "zoom-slider",
-                            sliderInput(
-                              "upgma_zoom",
-                              label = NULL,
-                              min = 0.5,
-                              max = 1.5,
-                              step = 0.05,
-                              value = 0.95,
-                              ticks = FALSE
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "250px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Tree Scale"), style = "color:white; position: relative; right: -15px"),
-                    column(
-                      width = 12,
-                      fluidRow(
-                        column(
-                          width = 8,
-                          align = "left",
-                          div(
-                            class = "mat-switch-layout",
-                            materialSwitch(
-                              "upgma_treescale_show",
-                              h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                              value = TRUE,
-                              right = TRUE
-                            )
-                          ),
-                          br()
-                        ),
-                        column(
-                          width = 4,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "upgma_treescale_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                uiOutput("upgma_treescale_width"),
-                                br(),
-                                uiOutput("upgma_treescale_x"),
-                                br(),
-                                uiOutput("upgma_treescale_y")
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  ),
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Legend"), style = "color:white; position: relative; right: -15px; margin-top: 10px; margin-bottom: -2px"),
-                    column(
-                      width = 12,
-                      align = "center",
-                      fluidRow(
-                        column(
-                          width = 7,
-                          align = "left",
-                          prettyRadioButtons(
-                            "upgma_legend_orientation",
-                            "",
-                            choices = c(Horizontal = "horizontal",
-                                        Vertical = "vertical"),
-                            selected = c(Vertical = "vertical"),
-                            inline = FALSE
-                          )
-                        ),
-                        column(
-                          width = 5,
-                          align = "right",
-                          dropMenu(
-                            actionBttn(
-                              "upgma_legend_menu",
-                              label = "",
-                              color = "default",
-                              size = "sm",
-                              style = "material-flat",
-                              icon = icon("sliders")
-                            ),
-                            placement = "top-start",
-                            theme = "translucent",
-                            fluidRow(
-                              column(
-                                width = 12,
-                                align = "center",
-                                numericInput(
-                                  "upgma_legend_size",
-                                  label = h5("Size", style = "color:white; margin-bottom: 0px"),
-                                  value = 10,
-                                  min = 5,
-                                  max = 25,
-                                  step = 1,
-                                  width = "80px"
-                                ),
-                                br(),
-                                sliderInput(
-                                  "upgma_legend_x",
-                                  label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-                                  value = 0.9,
-                                  min = -0.9,
-                                  max = 1.9,
-                                  step = 0.2,
-                                  width = "150px",
-                                  ticks = FALSE
-                                ),
-                                br(),
-                                sliderInput(
-                                  "upgma_legend_y",
-                                  label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-                                  value = 0.2,
-                                  min = -1.5,
-                                  max = 1.5,
-                                  step = 0.1,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.upgma_controls=='Label'",
-              column(
-                width = 4,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Tips"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 4,
-                            align = "left",
-                            div(
-                              class = "mat-switch-lab",
-                              materialSwitch(
-                                "upgma_tiplab_show",
-                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                                value = TRUE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 4,
-                            align = "center",
-                            uiOutput("upgma_tiplab")
-                          ),
-                          column(
-                            width = 3,
-                            div(
-                              class = "mat-switch-align",
-                              materialSwitch(
-                                "upgma_align",
-                                h5(p("Align"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 1,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "upgma_labeltext_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-start",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  sliderInput(
-                                    "upgma_tiplab_alpha",
-                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                    min = 0.1,
-                                    max = 1,
-                                    value = 1,
-                                    width = "150px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  conditionalPanel(
-                                    "!(input.upgma_layout=='inward'|input.upgma_layout=='circular')",
-                                    sliderInput(
-                                      inputId = "upgma_tiplab_nudge_x",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = 0,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  conditionalPanel(
-                                    "input.upgma_layout=='circular'",
-                                    sliderInput(
-                                      inputId = "upgma_tiplab_position",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = -0.05,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  conditionalPanel(
-                                    "input.upgma_layout=='inward'",
-                                    sliderInput(
-                                      inputId = "upgma_tiplab_position_inw",
-                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
-                                      min = -3,
-                                      max = 3,
-                                      step = 0.05,
-                                      value = 1.1,
-                                      width = "150px",
-                                      ticks = FALSE
-                                    )
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "upgma_tiplab_angle",
-                                    label = h5("Angle", style = "color:white; margin-bottom: 0px"),
-                                    min = -90,
-                                    max = 90,
-                                    value = 0,
-                                    ticks = FALSE,
-                                    width = "150px",
-                                  )      
-                                ),
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  uiOutput("upgma_tiplab_size"),
-                                  br(),
-                                  selectInput(
-                                    "upgma_tiplab_fontface",
-                                    label = h5("Fontface", style = "color:white; margin-bottom: 5px; margin-top: 16px"),
-                                    width = "250px",
-                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
-                                  )
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 4,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px")
-                      ),
-                      column(
-                        width = 4,
-                        align = "center",
-                        colorPickr(
-                          inputId = "upgma_tiplab_color",
-                          width = "100%",
-                          selected = "#000000",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 4,
-                        align = "left",
-                        br(),
-                        div(
-                          class = "mat-switch-geom",
-                          materialSwitch(
-                            "upgma_geom",
-                            h5(p("Panels"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        colorPickr(
-                          inputId = "upgma_tiplab_fill",
-                          width = "100%",
-                          selected = "#84D9A0",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "left",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_labelformat_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("upgma_tiplab_padding"),
-                              br(),
-                              sliderInput(
-                                inputId = "upgma_tiplab_labelradius",
-                                label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
-                                min = 0,
-                                max = 0.5,
-                                value = 0.2,
-                                width = "150px",
-                                ticks = FALSE
-                              )
-                            )
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 3,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Branches"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 5,
-                            align = "left",
-                            div(
-                              class = "mat-switch-lab",
-                              materialSwitch(
-                                "upgma_show_branch_label",
-                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            )
-                          ),
-                          column(
-                            width = 5,
-                            align = "center",
-                            uiOutput("upgma_branch_label")
-                          ),
-                          column(
-                            width = 2,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "upgma_branch_label_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-start",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  sliderInput(
-                                    "upgma_branchlab_alpha",
-                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                    min = 0.1,
-                                    max = 1,
-                                    value = 0.65,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "upgma_branch_x",
-                                    label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-                                    min = -3,
-                                    max = 3,
-                                    value = 0,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    inputId = "upgma_branch_y",
-                                    label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-                                    min = -3,
-                                    max = 3,
-                                    value = 0,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  )
-                                ),
-                                column(
-                                  width = 6,
-                                  align = "center",
-                                  uiOutput("upgma_branch_size"),
-                                  selectInput(
-                                    "upgma_branchlab_fontface",
-                                    label = h5("Fontface", style = "color:white; margin-bottom: 0px;"),
-                                    width = "250px",
-                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
-                                  ),
-                                  br(),
-                                  sliderInput(
-                                    "upgma_branch_labelradius",
-                                    label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
-                                    min = 0,
-                                    max = 0.5,
-                                    value = 0.5,
-                                    width = "250px",
-                                    ticks = FALSE
-                                  )
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px; margin-bottom: 109px")
-                      ),
-                      column(
-                        width = 5,
-                        colorPickr(
-                          inputId = "upgma_branch_label_color",
-                          width = "100%",
-                          selected = "#FFB7B7",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        ),
-                        br(), br()
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 3,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "280px",
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "left",
-                        h4(p("Custom Labels"), style = "color:white; position: relative; right: -15px"),
-                        fluidRow(
-                          column(
-                            width = 6,
-                            textInput(
-                              "upgma_new_label_name",
-                              "",
-                              placeholder = "New Label"
-                            )
-                          ),
-                          column(
-                            width = 3,
-                            actionButton(
-                              "upgma_add_new_label",
-                              "",
-                              icon = icon("plus")
-                            )
-                          ),
-                          column(
-                            width = 2,
-                            align = "right",
-                            dropMenu(
-                              actionBttn(
-                                "upgma_custom_label_menu",
-                                label = "",
-                                color = "default",
-                                size = "sm",
-                                style = "material-flat",
-                                icon = icon("sliders")
-                              ),
-                              placement = "top-end",
-                              theme = "translucent",
-                              fluidRow(
-                                column(
-                                  width = 12,
-                                  align = "center",
-                                  uiOutput("upgma_custom_labelsize"),
-                                  br(),
-                                  uiOutput("upgma_sliderInput_y"),
-                                  br(),
-                                  uiOutput("upgma_sliderInput_x")
-                                )
-                              )
-                            )
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 6,
-                            uiOutput("upgma_custom_label_select")
-                          ),
-                          column(
-                            width = 4,
-                            uiOutput("upgma_del_label"),
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 12,
-                            align = "center",
-                            uiOutput("upgma_cust_label_save")
-                          )
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.upgma_controls=='Elements'",
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Tip Points"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "upgma_tippoint_show",
-                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_tippoint_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              sliderInput(
-                                "upgma_tippoint_alpha",
-                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                value = 0.5,
-                                min = 0.1,
-                                max = 1,
-                                width = "150px",
-                                ticks = FALSE
-                              ), 
-                              br(),
-                              uiOutput("upgma_tippoint_size")
-                            )
-                          )
-                        )  
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        colorPickr(
-                          inputId = "upgma_tippoint_color",
-                          width = "100%",
-                          selected = "#3A4657",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        align = "left",
-                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        conditionalPanel(
-                          "input.upgma_tipshape_mapping_show==false",
-                          selectInput(
-                            "upgma_tippoint_shape",
-                            "",
-                            width = "100%",
-                            choices = c(
-                              Circle = "circle", 
-                              Square = "square", 
-                              Diamond = "diamond", 
-                              Triangle = "triangle",
-                              Cross = "cross", 
-                              Asterisk = "asterisk"
-                            )
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.upgma_tipshape_mapping_show==true",
-                          h5(p("Variable assigned"), style = "color:white; position: relative; right: -15px; margin-top: 30px; font-style: italic")
-                        ),
-                        br()
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Node Points"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 8,
-                        align = "left",
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "upgma_nodepoint_show",
-                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_nodepoint_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              sliderInput(
-                                "upgma_nodepoint_alpha",
-                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                value = 1,
-                                min = 0.1,
-                                max = 1,
-                                width = "150px",
-                                ticks = FALSE
-                              ), 
-                              br(),
-                              uiOutput("upgma_nodepoint_size")
-                            )
-                          )
-                        )  
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        colorPickr(
-                          inputId = "upgma_nodepoint_color",
-                          width = "100%",
-                          selected = "#3A4657",
-                          label = "",
-                          update = "changestop",
-                          interaction = list(clear = FALSE,
-                                             save = FALSE),
-                          position = "right-start"
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
-                      ),
-                      column(
-                        width = 7,
-                        align = "center",
-                        selectInput(
-                          "upgma_nodepoint_shape",
-                          "",
-                          choices = c(
-                            Circle = "circle", 
-                            Square = "square", 
-                            Diamond = "diamond", 
-                            Triangle = "triangle",
-                            Cross = "cross", 
-                            Asterisk = "asterisk"
-                          )
-                        ),
-                        br()
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 6,
-                        h4(p("Tiles"), style = "color:white; position: relative; right: -15px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        div(
-                          class = "sel-tile-number",
-                          selectInput(
-                            "upgma_tile_number",
-                            "",
-                            choices = 1:5,
-                            width = "70px"
-                          )
-                        )
-                      ),
-                      column(
-                        width = 7,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_tile_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-start",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              conditionalPanel(
-                                "input.upgma_tile_num == 1",
-                                sliderInput(
-                                  "upgma_fruit_alpha",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.upgma_tile_num == 2",
-                                sliderInput(
-                                  "upgma_fruit_alpha_2",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.upgma_tile_num == 3",
-                                sliderInput(
-                                  "upgma_fruit_alpha_3",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.upgma_tile_num == 4",
-                                sliderInput(
-                                  "upgma_fruit_alpha_4",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.upgma_tile_num == 5",
-                                sliderInput(
-                                  "upgma_fruit_alpha_5",
-                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
-                                  min = 0.1,
-                                  max = 1,
-                                  value = 1,
-                                  step = 0.05,
-                                  width = "150px",
-                                  ticks = FALSE
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.upgma_tile_num == 1",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_width"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 68px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_offset_circ"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.upgma_tile_num == 2",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_width2"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_offset_circ_2"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.upgma_tile_num == 3",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_width3"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_offset_circ_3"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.upgma_tile_num == 4",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_width4"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_offset_circ_4"),
-                          br()
-                        )
-                      )
-                    ),
-                    conditionalPanel(
-                      "input.upgma_tile_num == 5",
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_width5"),
-                          br()
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 5,
-                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
-                        ),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("upgma_fruit_offset_circ_5"),
-                          br()
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 6,
-                        h4(p("Heatmap"), style = "color:white; position: relative; right: -15px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        h5("Title", style = "color:white; margin-left: 15px; margin-top: 32px;")
-                      ),
-                      column(
-                        width = 6,
-                        align = "center",
-                        textInput(
-                          "upgma_heatmap_title",
-                          label = "",
-                          value = "Heatmap",
-                          placeholder = "Heatmap" 
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "right",
-                        dropMenu(
-                          actionBttn(
-                            "upgma_heatmap_menu",
-                            label = "",
-                            color = "default",
-                            size = "sm",
-                            style = "material-flat",
-                            icon = icon("sliders")
-                          ),
-                          placement = "top-end",
-                          theme = "translucent",
-                          fluidRow(
-                            column(
-                              width = 12,
-                              align = "center",
-                              uiOutput("upgma_colnames_angle"),
-                              br(),
-                              uiOutput("upgma_colnames_y")
-                            )
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5("Width", style = "color: white; margin-left: 15px; margin-top: 40px;")
-                      ),
-                      column(
-                        width = 7,
-                        uiOutput("upgma_heatmap_width")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5("Position", style = "color:white; margin-left: 15px; margin-top: 36px;")
-                      ),
-                      column(
-                        width = 7,
-                        uiOutput("upgma_heatmap_offset")
-                      )
-                    ),
-                    br(), br()
-                  )
-                )
-              ),
-              column(
-                width = 2,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  height = "295px",
-                  column(
-                    width = 12,
-                    align = "left",
-                    h4(p("Clade Highlight"), style = "color:white; position: relative; right: -15px"),
-                    fluidRow(
-                      column(
-                        width = 12,
-                        div(
-                          class = "mat-switch",
-                          materialSwitch(
-                            "upgma_nodelabel_show",
-                            h5(p("Toggle Node View"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        h5(p("Nodes"), style = "color:white; position: relative; right: -15px; margin-top: 20px")
-                      ),
-                      column(
-                        width = 9,
-                        uiOutput("upgma_parentnode")
-                      )
-                    ),
-                    uiOutput("upgma_clade_scale"),
-                    fluidRow(
-                      column(
-                        width = 5,
-                        h5(p("Form"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
-                      ),
-                      column(
-                        width = 7,
-                        div(
-                          class = "sel-clade",
-                          selectInput(
-                            "upgma_clade_type",
-                            "",
-                            choices = c("Rect" = "rect",
-                                        "Round" = "roundrect"),
-                            selected = c("Round" = "roundrect")
-                          ) 
-                        )
-                      )
-                    )
-                  )
-                )
-              )
-            ),
-            conditionalPanel(
-              "input.upgma_controls=='Variables'",
-              column(
-                width = 7,
-                box(
-                  solidHeader = TRUE,
-                  status = "info",
-                  width = "100%",
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 3,
-                        align = "center",
-                        h4(p("Element"), style = "color:white; margin-bottom: 20px")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        h4(p("Variable"), style = "color:white; margin-bottom: 20px; margin-right: 30px;")
-                      ),
-                      column(
-                        width = 6,
-                        align = "center",
-                        h4(p("Color Scale"), style = "color:white; margin-bottom: 20px")
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "upgma_mapping_show",
-                            h5(p("Tip Label Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_color_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_tiplab_scale")
-                      ),
-                      uiOutput("upgma_tiplab_mapping_info"),
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "upgma_tipcolor_mapping_show",
-                            h5(p("Tip Point Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_tipcolor_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_tippoint_scale")
-                      ),
-                      uiOutput("upgma_tipcolor_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "upgma_tipshape_mapping_show",
-                            h5(p("Tip Point Shape"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_tipshape_mapping")
-                      ),
-                      column(
-                        width = 3,
-                        HTML(
-                          paste(
-                            tags$span(style='color: white; font-size: 14px; font-style: italic; position: relative; bottom: -16px; right: -40px;', 'No scale for shapes')
-                          )
-                        )
-                      ),
-                      uiOutput("upgma_tipshape_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        fluidRow(
-                          column(
-                            width = 8,
-                            conditionalPanel(
-                              "input.upgma_tile_num == 1",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "upgma_tiles_show_1",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px; margin-right: 10px"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.upgma_tile_num == 2",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "upgma_tiles_show_2",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.upgma_tile_num == 3",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "upgma_tiles_show_3",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.upgma_tile_num == 4",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "upgma_tiles_show_4",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            ),
-                            conditionalPanel(
-                              "input.upgma_tile_num == 5",
-                              div(
-                                class = "mat-switch-v",
-                                materialSwitch(
-                                  "upgma_tiles_show_5",
-                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                                  value = FALSE,
-                                  right = TRUE
-                                )
-                              )
-                            )
-                          ), 
-                          column(
-                            width = 4,
-                            align = "left",
-                            div(
-                              class = "tile-sel",
-                              selectInput(
-                                "upgma_tile_num",
-                                "",
-                                choices = 1:5,
-                                width = "50px"
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        conditionalPanel(
-                          "input.upgma_tile_num == 1",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_fruit_variable")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.upgma_tile_num == 2",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_fruit_variable2")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.upgma_tile_num == 3",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_fruit_variable3")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.upgma_tile_num == 4",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_fruit_variable4")
-                          )
-                        ),
-                        conditionalPanel(
-                          "input.upgma_tile_num == 5",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_fruit_variable5")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.upgma_tile_num == 1",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_tiles_scale_1")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.upgma_tile_num == 2",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_tiles_scale_2")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.upgma_tile_num == 3",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_tiles_scale_3")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.upgma_tile_num == 4",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_tiles_scale_4")
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.upgma_tile_num == 5",
-                        column(
-                          width = 3,
-                          align = "center",
-                          div(
-                            class = "heatmap-scale",
-                            uiOutput("upgma_tiles_scale_5")
-                          )
-                        )
-                      ),
-                      uiOutput("upgma_fruit_mapping_info")
-                    ),
-                    fluidRow(
-                      column(
-                        width = 3,
-                        div(
-                          class = "mat-switch-v",
-                          materialSwitch(
-                            "upgma_heatmap_show",
-                            h5(p("Heatmap"), style = "color:white; position: relative; top: -4px; right: -5px;"),
-                            value = FALSE,
-                            right = TRUE
-                          )
-                        )
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        uiOutput("upgma_heatmap_sel")
-                      ),
-                      column(
-                        width = 3,
-                        align = "center",
-                        div(
-                          class = "heatmap-scale",
-                          uiOutput("upgma_heatmap_scale")
-                        )
-                      ),
-                      uiOutput("upgma_heatmap_mapping_info")
-                    )
-                  )
-                )
-              )
-            )
-          ),
-          br(), br(), br(), br(), br(), br()
-        )
-      ),
-      
-      ## Tab Utilities -------------------------------------------------------
-      
-      tabItem(
-        tabName = "utilities",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Utilities"), style = "color:white")
-          )
-        ),
-        br(),
-        hr(),
-        column(
-          width = 5,
-          align = "left",
-          shinyDirButton(
-            "hash_dir",
-            "Choose folder with .fasta files",
-            title = "Locate folder with loci",
-            buttonType = "default",
-            style = "border-color: white; margin: 10px; min-width: 200px; text-align: center"
-          ),
-          actionButton("hash_start", "Start Hashing", icon = icon("circle-play")),
-          shinyjs::hidden(
-            div(id = "hash_loading",
-                HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
-          )
-        )
-          # br(),
-          # actionButton(
-          #   "backup_database",
-          #   "Create backup",
-          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
-          # ),
-          # br(),
-          # actionButton(
-          #   "import_db_backup",
-          #   "Restore backup",
-          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
-          # )
-      ),
-      
-      
-      ## Tab Screening -------------------------------------------------------
-      
-      tabItem(
-        tabName = "gs_screening",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Screening"), style = "color:white; margin-bottom: -20px;")
-          ),
-          column(
-            width = 7,
-            align = "left",
-            uiOutput("gene_screening_info")
-          )
-        ),
-        br(),
-        hr(),
-        fluidRow(
-          uiOutput("screening_interface")
-        )
-      ),
-      
-      ## Tab Resistance Profile -------------------------------------------------------
-      
-      tabItem(
-        tabName = "gs_profile",
-        fluidRow(
-          column(
-            width = 3,
-            align = "center",
-            h2(p("Browse Entries"), style = "color:white; margin-bottom: -20px")
-          ),
-          column(
-            width = 7,
-            align = "left",
-            uiOutput("gene_resistance_info")
-          )
-        ),
-        br(),
-        hr(),
-        br(), br(),
-        uiOutput("gs_table_selection"),
-        fluidRow(
-          column(1),
-          uiOutput("gs_profile_display")
-        )
-      )
-    ) # End tabItems
-  ) # End dashboardPage
-) # end UI
-
-# _______________________ ####
-
-# Server ----
-
-server <- function(input, output, session) {
-  
-  phylotraceVersion <- paste("1.5.0")
-  
-  #TODO Enable this, or leave disabled
-  # Kill server on session end
-  session$onSessionEnded( function() {
-    stopApp()
-  })
-  
-  # Disable various user inputs (visualization control)
-  shinyjs::disable('mst_edge_label') 
-  
-  ## Functions ----
-  
-  # Function to read and format FASTA sequences
-  format_fasta <- function(filepath) {
-    fasta <- readLines(filepath)
-    formatted_fasta <- list()
-    current_sequence <- ""
-    
-    for (line in fasta) {
-      if (startsWith(line, ">")) {
-        if (current_sequence != "") {
-          formatted_fasta <- append(formatted_fasta, list(current_sequence))
-          current_sequence <- ""
-        }
-        formatted_fasta <- append(formatted_fasta, list(line))
-      } else {
-        current_sequence <- paste0(current_sequence, line)
-      }
-    }
-    if (current_sequence != "") {
-      formatted_fasta <- append(formatted_fasta, list(current_sequence))
-    }
-    
-    formatted_fasta
-  }
-  
-  # Function to color-code the bases in a sequence
-  color_sequence <- function(sequence) {
-    sequence <- gsub("A", "<span class='base-a'>A</span>", sequence)
-    sequence <- gsub("T", "<span class='base-t'>T</span>", sequence)
-    sequence <- gsub("G", "<span class='base-g'>G</span>", sequence)
-    sequence <- gsub("C", "<span class='base-c'>C</span>", sequence)
-    sequence
-  }
-  
-  # Function to log messages to logfile
-  log_message <- function(log_file, message, append = TRUE) {
-    cat(format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "-", message, "\n", file = log_file, append = append)
-  }
-  
-  # Modified gheatmap function
-  gheatmap.mod <- function(p, data, offset=0, width=1, low="green", high="red", color="white",
-                           colnames=TRUE, colnames_position="bottom", colnames_angle=0, colnames_level=NULL,
-                           colnames_offset_x = 0, colnames_offset_y = 0, font.size=4, family="", hjust=0.5, legend_title = "value",
-                           colnames_color = "black") {
-    
-    colnames_position %<>% match.arg(c("bottom", "top"))
-    variable <- value <- lab <- y <- NULL
-    
-    ## if (is.null(width)) {
-    ##     width <- (p$data$x %>% range %>% diff)/30
-    ## }
-    
-    ## convert width to width of each cell
-    width <- width * (p$data$x %>% range(na.rm=TRUE) %>% diff) / ncol(data)
-    
-    isTip <- x <- y <- variable <- value <- from <- to <- NULL
-    
-    ## handle the display of heatmap on collapsed nodes
-    ## https://github.com/GuangchuangYu/ggtree/issues/242
-    ## extract data on leaves (& on collapsed internal nodes) 
-    ## (the latter is extracted only when the input data has data on collapsed
-    ## internal nodes)
-    df <- p$data
-    nodeCo <- intersect(df %>% filter(is.na(x)) %>% 
-                          select(.data$parent, .data$node) %>% unlist(), 
-                        df %>% filter(!is.na(x)) %>% 
-                          select(.data$parent, .data$node) %>% unlist())
-    labCo <- df %>% filter(.data$node %in% nodeCo) %>% 
-      select(.data$label) %>% unlist()
-    selCo <- intersect(labCo, rownames(data))
-    isSel <- df$label %in% selCo
-    
-    df <- df[df$isTip | isSel, ]
-    start <- max(df$x, na.rm=TRUE) + offset
-    
-    dd <- as.data.frame(data)
-    ## dd$lab <- rownames(dd)
-    i <- order(df$y)
-    
-    ## handle collapsed tree
-    ## https://github.com/GuangchuangYu/ggtree/issues/137
-    i <- i[!is.na(df$y[i])]
-    
-    lab <- df$label[i]
-    ## dd <- dd[lab, , drop=FALSE]
-    ## https://github.com/GuangchuangYu/ggtree/issues/182
-    dd <- dd[match(lab, rownames(dd)), , drop = FALSE]
-    
-    
-    dd$y <- sort(df$y)
-    dd$lab <- lab
-    ## dd <- melt(dd, id=c("lab", "y"))
-    dd <- gather(dd, variable, value, -c(lab, y))
-    
-    i <- which(dd$value == "")
-    if (length(i) > 0) {
-      dd$value[i] <- NA
-    }
-    if (is.null(colnames_level)) {
-      dd$variable <- factor(dd$variable, levels=colnames(data))
-    } else {
-      dd$variable <- factor(dd$variable, levels=colnames_level)
-    }
-    V2 <- start + as.numeric(dd$variable) * width
-    mapping <- data.frame(from=dd$variable, to=V2)
-    mapping <- unique(mapping)
-    
-    dd$x <- V2
-    dd$width <- width
-    dd[[".panel"]] <- factor("Tree")
-    if (is.null(color)) {
-      p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, inherit.aes=FALSE)
-    } else {
-      p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, color=color, inherit.aes=FALSE)
-    }
-    if (is(dd$value,"numeric")) {
-      p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value=NA, name = legend_title) # "white")
-    } else {
-      p2 <- p2 + scale_fill_discrete(na.value=NA, name = legend_title) #"white")
-    }
-    
-    if (colnames) {
-      if (colnames_position == "bottom") {
-        y <- 0
-      } else {
-        y <- max(p$data$y) + 1
-      }
-      mapping$y <- y
-      mapping[[".panel"]] <- factor("Tree")
-      p2 <- p2 + geom_text(data=mapping, aes(x=to, y = y, label=from), color = colnames_color, size=font.size, family=family, inherit.aes = FALSE,
-                           angle=colnames_angle, nudge_x=colnames_offset_x, nudge_y = colnames_offset_y, hjust=hjust)
-    }
-    
-    p2 <- p2 + theme(legend.position="right")
-    ## p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))
-    
-    if (!colnames) {
-      ## https://github.com/GuangchuangYu/ggtree/issues/204
-      p2 <- p2 + scale_y_continuous(expand = c(0,0))
-    }
-    
-    attr(p2, "mapping") <- mapping
-    return(p2)
-  }
-  
-  # Get rhandsontable
-  get.entry.table.meta <- reactive({
-    if(!is.null(hot_to_r(input$db_entries))){
-      table <- hot_to_r(input$db_entries)
-      select(select(table, -13), 1:(12 + nrow(DB$cust_var)))
-    }
-  })
-  
-  # Function to find columns with varying values
-  var_alleles <- function(dataframe) {
-    
-    varying_columns <- c()
-    
-    for (col in 1:ncol(dataframe)) {
-      unique_values <- unique(dataframe[, col])
-      
-      if (length(unique_values) > 1) {
-        varying_columns <- c(varying_columns, col)
-      }
-    }
-    
-    return(varying_columns)
-  }
-  
-  # Functions to compute hamming distances dependent on missing value handling
-  hamming.dist <- function(x, y) {
-    sum(x != y)
-  }
-  
-  hamming.distIgnore <- function(x, y) {
-    sum( (x != y) & !is.na(x) & !is.na(y) )
-  }
-  
-  hamming.distCategory <- function(x, y) {
-    sum((x != y | xor(is.na(x), is.na(y))) & !(is.na(x) & is.na(y)))
-  }
-  
-  compute.distMatrix <- function(profile, hamming.method) {
-    mat <- as.matrix(profile)
-    n <- nrow(mat)
-    dist_mat <- matrix(0, n, n)
-    for (i in 1:(n-1)) {
-      for (j in (i+1):n) {
-        dist_mat[i, j] <- hamming.method(x = mat[i, ], y = mat[j, ])
-        dist_mat[j, i] <- dist_mat[i, j]
-      }
-    }
-    return(dist_mat)
-  }
-  
-  # Function to determine entry table height
-  table_height <- reactive({
-    if (input$table_height == TRUE) {
-      NULL
-    } else {900}
-  })
-  
-  # Function to determine distance matrix height
-  distancematrix_height <- reactive({
-    if(DB$distancematrix_nrow > 33) {
-      800
-    } else {NULL}
-  })
-  
-  # Function to missing value table height
-  miss.val.height <- reactive({
-    if(input$miss_val_height == TRUE) {
-      NULL
-    } else {800}
-  })
-  
-  #Function to check custom variable classes
-  column_classes <- function(df) {
-    sapply(df, function(x) {
-      if (class(x) == "numeric") {
-        return("cont")
-      } else if (class(x) == "character") {
-        return("categ")
-      } else {
-        return(class(x))
-      }
-    })
-  }
-  
-  # Function to hash database
-  hash_database <- function(folder) {
-    loci_files <- list.files(folder)
-    loci_names <- sapply(strsplit(loci_files, "[.]"), function(x) x[1])
-    loci_paths <- file.path(folder, loci_files)
-    
-    hashes <- sapply(loci_paths, hash_locus)
-    names(hashes) <- loci_names
-    hashes
-  }
-  
-  # Function to hash a locus
-  hash_locus <- function(locus_path) {
-    locus_file <- readLines(locus_path)
-    seq_list <- locus_file[seq(2, length(locus_file), 3)]
-    seq_hash <- sha256(seq_list)
-    seq_idx <- paste0(">", seq_hash)
-    
-    locus_file[seq(1, length(locus_file), 3)] <- seq_idx
-    writeLines(locus_file, locus_path)
-    
-    seq_hash
-  }
-  
-  # Get locus hashes
-  get_locus_hashes <- function(locus_path) {
-    locus_file <- readLines(locus_path)
-    hash_list <- locus_file[seq(1, length(locus_file), 3)]
-    hash_list <- sapply(strsplit(hash_list, "[>]"), function(x) x[2])
-  }
-  
-  extract_seq <- function(locus_path, hashes) {
-    locus_file <- readLines(locus_path)
-    hash_list <- sapply(strsplit(locus_file[seq(1, length(locus_file), 3)], "[>]"), function(x) x[2])
-    seq_list <- locus_file[seq(2, length(locus_file), 3)]
-    seq_idx <- hash_list %in% hashes
-    
-    list(
-      idx = hash_list[seq_idx],
-      seq = seq_list[seq_idx]
-    )
-  }
-  
-  add_new_sequences <- function(locus_path, sequences) {
-    locus_file <- file(locus_path, open = "a+")
-    for (i in seq_along(sequences$idx)) {
-      writeLines(c("", paste0(">", sequences$idx[i]), sequences$seq[i]), locus_file)
-    }
-    close(locus_file)
-  }
-  
-  # Compute clusters to use in visNetwork
-  compute_clusters <- function(nodes, edges, threshold) {
-    groups <- rep(0, length(nodes$id))
-    edges_groups <- rep(0, length(edges$from))
-    
-    edges_table <- data.frame(
-      from = edges$from,
-      to = edges$to,
-      weight = edges$weight
-    )
-    
-    count <- 0
-    while (any(groups == 0)) {
-      group_na <- groups == 0
-      labels <- nodes$id[group_na]
-      
-      cluster <- nodes$id[group_na][1] # Initialize with 1 label
-      while (!is_empty(labels)) {
-        sub_tb <- edges_table[(edges_table$from %in% cluster | edges_table$to %in% cluster) & edges_table$weight <= threshold,]
-        
-        if (nrow(sub_tb) == 0 | length(unique(c(sub_tb$from, sub_tb$to))) == length(cluster)) {
-          count <- count + 1
-          groups[nodes$id %in% cluster] <- paste("Group", count)
-          edges_groups[edges$from %in% cluster & edges$to %in% cluster] <- paste("Group", count)
-          break
-        } else {
-          cluster <- unique(c(sub_tb$from, sub_tb$to))
-        }
-      }
-    }
-    list(groups = groups,
-         edges = edges_groups)
-  }
-  
-  # Check gene screening status
-  check_status <- function(isolate) {
-    iso_name <- gsub(".zip", "", basename(isolate))
-    if(file.exists(file.path(DB$database, gsub(" ", "_", DB$scheme),
-                             "Isolates", iso_name, "status.txt"))) {
-      if(str_detect(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
-                                        "Isolates", iso_name, "status.txt"))[1], 
-                    "successfully")) {
-        return("success")
-      } else {
-        return("fail")
-      }
-    } else {return("unfinished")}
-  }
-  
-  # Reset gene screening status
-  remove.screening.status <- function(isolate) {
-    if(file.exists(file.path(DB$database, 
-                             gsub(" ", "_", DB$scheme),
-                             "Isolates",
-                             isolate,
-                             "status.txt"))) {
-      file.remove(
-        file.path(DB$database, 
-                  gsub(" ", "_", DB$scheme),
-                  "Isolates",
-                  isolate,
-                  "status.txt")
-      )
-    }
-  }
-  
-  # Truncate hashes
-  truncHash <- function(hash) {
-    if(!is.na(hash)) {
-      paste0(str_sub(hash, 1, 4), "...", str_sub(hash, nchar(hash) - 3, nchar(hash))) 
-    } else {NA}
-  }
-  
-  # Function to check for duplicate isolate IDs for multi typing start
-  dupl_mult_id <- reactive({
-    req(Typing$multi_sel_table)
-    if(!is.null(DB$data)) {
-      selection <- Typing$multi_sel_table[which(unlist(Typing$multi_sel_table$Files) %in% unlist(DB$data["Assembly ID"])),]
-      selection$Files
-    } else {""}
-  })
-  
-  # Function to check single typing log file
-  check_new_entry <- reactive({
-    
-    invalidateLater(5000, session)
-    
-    if(!is.null(DB$database)) {
-      if(file_exists(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))) {
-        
-        Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
-        
-        if(is.null(DB$data)) {
-          if(nrow(Database[["Typing"]]) >= 1) {
-            TRUE
-          } else {FALSE}
-        } else {
-          if(nrow(DB$data) < nrow(Database[["Typing"]])) {
-            TRUE
-          } else {
-            FALSE
-          }
-        }
-      } else {FALSE}
-    }
-  })
-  
-  # Render Entry Table Highlights 
-  
-  diff_allele <- reactive({
-    if (!is.null(DB$data) & !is.null(input$compare_select) & !is.null(DB$cust_var)) {
-      var_alleles(select(DB$data, input$compare_select)) + (13 + nrow(DB$cust_var))
-    }
-  })
-  
-  err_thresh <- reactive({
-    if (!is.null(DB$data) & !is.null(DB$number_loci)) {
-      which(as.numeric(DB$data[["Errors"]]) >= (DB$number_loci * 0.05)) 
-    }
-  })
-  
-  err_thresh_na <- reactive({
-    if (!is.null(DB$na_table) & !is.null(DB$number_loci)) {
-      which(as.numeric(DB$na_table[["Errors"]]) >= (DB$number_loci * 0.05)) 
-    }
-  })
-  
-  true_rows <- reactive({
-    if (!is.null(DB$data)) {
-      which(DB$data$Include == TRUE)
-    }
-  })
-  
-  duplicated_names <- reactive({
-    if (!is.null(DB$meta)) {
-      which(duplicated(DB$meta$`Assembly Name`) | duplicated(DB$meta$`Assembly Name`, fromLast = TRUE))
-    }
-  })
-  
-  duplicated_ids <- reactive({
-    if (!is.null(DB$meta)) {
-      which(duplicated(DB$meta$`Assembly ID`) | duplicated(DB$meta$`Assembly ID`, fromLast = TRUE))
-    }
-  })
-  
-  # _______________________ ####
-  
-  ## Startup ----
-  shinyjs::addClass(selector = "body", class = "sidebar-collapse")
-  shinyjs::removeClass(selector = "body", class = "sidebar-toggle")
-  
-  output$messageMenu <- renderText({
-    HTML(format(Sys.time(), "%Y-%m-%d %H:%M:%S %Z"))
-  })
-  
-  # Initiate logging
-  if(!dir_exists(paste0(getwd(), "/logs"))) {
-    dir_create(paste0(getwd(), "/logs"))
-  }
-  
-  logfile <- file.path(paste0(getwd(), "/logs/phylotrace.log"))
-  
-  log <- log_open(logfile, logdir = FALSE)
-  
-  log_print("Session started")
-  
-  # Clear screening file
-  if(file.exists(paste0(getwd(), "/execute/screening/output_file.tsv"))) {
-    file.remove(paste0(getwd(), "/execute/screening/output_file.tsv"))
-  }
-  
-  if(file.exists(paste0(getwd(), "/execute/screening/error.txt"))) {
-    file.remove(paste0(getwd(), "/execute/screening/error.txt"))
-  }
-  
-  # Declare reactive variables
-  Startup <- reactiveValues(sidebar = TRUE, 
-                            header = TRUE) # reactive variables related to startup process
-  
-  DB <- reactiveValues(data = NULL, 
-                       block_db = FALSE, 
-                       load_selected = TRUE,
-                       no_na_switch = FALSE,
-                       first_look = FALSE) # reactive variables related to local database
-  
-  Typing <- reactiveValues(table = data.frame(), 
-                           single_path = data.frame(),
-                           progress = 0, 
-                           progress_format_start = 0, 
-                           progress_format_end = 0,
-                           result_list = NULL,
-                           status = "") # reactive variables related to typing process
-  
-  Screening <- reactiveValues(status = "idle",
-                              picker_status = TRUE,
-                              first_result = NULL) # reactive variables related to gene screening
-  
-  Vis <- reactiveValues(cluster = NULL, 
-                        metadata = list(),
-                        custom_label_nj = data.frame(),
-                        nj_label_pos_y = list(),
-                        nj_label_pos_x = list(),
-                        nj_label_size = list(),
-                        custom_label_upgma = data.frame(),
-                        upgma_label_pos_y = list(),
-                        upgma_label_pos_x = list(),
-                        upgma_label_size = list()) # reactive variables related to visualization
-  
-  Report <- reactiveValues() # reactive variables related to report functions
-  
-  Scheme <- reactiveValues() # reactive variables related to scheme  functions
-  
-  # Load last used database if possible
-  if(paste0(getwd(), "/execute/last_db.rds") %in% dir_ls(paste0(getwd(), "/execute"))) {
-    DB$last_db <- TRUE
-  }
-  
-  # Locate local Database
-  observe({
-    shinyDirChoose(input,
-                   "db_location",
-                   roots = c(Home = path_home(), Root = "/"),
-                   defaultRoot = "Home",
-                   session = session)
-    
-    if(!is.null(DB$select_new)) {
-      if(DB$select_new == FALSE) {
-        if(DB$block_db == FALSE) {
-          DB$database <- as.character(
-            parseDirPath(
-              roots = c(Home = path_home(), Root = "/"),
-              input$db_location
-            )
-          )
-          
-          DB$exist <- (length(dir_ls(DB$database)) == 0)  # Logical any local database present
-          
-          DB$available <- gsub("_", " ", basename(dir_ls(DB$database))) # List of local schemes available
-        }
-        
-      } else if (DB$select_new ==  TRUE) {
-        DB$database <- paste0(DB$new_database, "/Database")
-        
-      }
-    } else {
-      if(!is.null(DB$last_db) & file.exists(paste0(getwd(), "/execute/last_db.rds"))) {
-        
-        DB$database <- readRDS(paste0(getwd(), "/execute/last_db.rds"))
-        
-        if(dir_exists(DB$database)) {
-          DB$exist <- (length(dir_ls(DB$database)) == 0)  # Logical any local database present
-          
-          DB$available <- gsub("_", " ", basename(dir_ls(DB$database))) # List of local schemes available
-        }
-      }
-    }
-  })
-  
-  ### Set up typing environment ----
-  
-  # Null typing progress trackers
-  writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
-  writeLines("0\n", paste0(getwd(), "/logs/progress.txt"))
-  
-  if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
-    unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
-  }
-  
-  # Reset typing feedback values
-  Typing$pending <- FALSE
-  Typing$multi_started <- FALSE
-  Typing$multi_help <- FALSE
-  saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
-  Typing$last_success <- "0" # Null last multi typing success name
-  Typing$last_failure <- "0" # Null last multi typing failure name
-  
-  ### Landing page UI ----
-  observe({
-    if (Startup$sidebar == FALSE) {
-      shinyjs::removeClass(selector = "body", class = "sidebar-collapse")
-      shinyjs::addClass(selector = "body", class = "sidebar-toggle")
-    }
-  })
-  
-  output$start_message <- renderUI({
-    column(
-      width = 12, 
-      align = "center",
-      br(), br(), br(), br(), br(), br(),
-      div( 
-        class = "image",
-        imageOutput("imageOutput")
-      ),
-      br(), br(), br(),
-      p(
-        HTML(
-          paste(
-            tags$span(style='color: white; font-size: 16px;', 'Proceed by loading a compatible local database or create a new one.')
-          )
-        )
-      ),
-      br(), 
-      fluidRow(
-        column(
-          width = 6,
-          align = "right",
-          shinyDirButton(
-            "db_location",
-            "Browse",
-            icon = icon("folder-open"),
-            title = "Locate the database folder",
-            buttonType = "default",
-            root = path_home()
-          )
-        ),
-        column(
-          width = 6,
-          align = "left",
-          shinyDirButton(
-            "create_new_db",
-            "Create New",
-            icon = icon("plus"),
-            title = "Choose location for new PhyloTrace database",
-            buttonType = "default",
-            root = path_home()
-          )
-        )
-      ),
-      br(), br(),
-      fluidRow(
-        column(
-          width = 12,
-          align = "center",
-          uiOutput("load_db"),
-          br(), br(), br(), br(), br(), br(), br()
-        )
-      )
-    )
-  })
-  
-  # User selection new db or load db
-  observeEvent(input$create_new_db, {
-    log_print("Input create_new_db")
-    DB$select_new <- TRUE
-  })
-  
-  observeEvent(input$db_location, {
-    log_print("Input db_location")
-    DB$select_new <- FALSE
-  })
-  
-  # Load db & scheme selection UI
-  output$load_db <- renderUI({
-    if(!is.null(DB$select_new)) {
-      if(length(DB$new_database) > 0 & DB$select_new) {
-        column(
-          width = 12,
-          p(
-            tags$span(
-              style='color: white; font-size: 15px;',
-              HTML(
-                paste(
-                  'New database will be created in',
-                  DB$new_database
-                )
-              )
-            )
-          ),
-          br(),
-          actionButton(
-            "load",
-            "Create",
-            class = "load-start"
-          )
-        )
-      } else if(length(DB$available) > 0 & !(DB$select_new)) {
-        if(any(!(gsub(" ", "_", DB$available) %in% schemes))) {
-          column(
-            width = 12,
-            p(
-              tags$span(
-                style='color: white; font-size: 15px; font-style: italic;',
-                HTML(
-                  paste('Selected:', DB$database)
-                )
-              )
-            ),
-            uiOutput("scheme_db"),
-            br(), 
-            p(
-              HTML(
-                paste(
-                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
-                            'Warning: Folder contains invalid elements.')
-                )
-              )
-            ),
-            br(),
-            actionButton(
-              "load",
-              "Load",
-              class = "load-start"
-            )
-          )
-        } else {
-          column(
-            width = 12,
-            p(
-              tags$span(
-                style='color: white; font-size: 15px; font-style: italic;',
-                HTML(
-                  paste('Selected:', DB$database)
-                )
-              )
-            ),
-            uiOutput("scheme_db"),
-            br(), br(),
-            actionButton(
-              "load",
-              "Load",
-              class = "load-start"
-            )
-          )
-        }
-      } 
-    } else if((!is.null(DB$last_db)) & (!is.null(DB$available))) {
-      if (DB$last_db == TRUE & (length(DB$available) > 0)) {
-        if(any(!(gsub(" ", "_", DB$available) %in% schemes))) {
-          column(
-            width = 12,
-            p(
-              tags$span(
-                style='color: white; font-size: 15px; font-style: italic;',
-                HTML(
-                  paste('Last used:', DB$database)
-                )
-              )
-            ),
-            uiOutput("scheme_db"),
-            br(), 
-            p(
-              HTML(
-                paste(
-                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
-                            'Warning: Folder contains invalid elements.')
-                )
-              )
-            ),
-            br(),
-            actionButton(
-              "load",
-              "Load",
-              class = "load-start"
-            )
-          )
-        } else {
-          column(
-            width = 12,
-            p(
-              tags$span(
-                style='color: white; font-size: 15px; font-style: italic;',
-                HTML(
-                  paste('Last used:', DB$database)
-                )
-              )
-            ),
-            uiOutput("scheme_db"),
-            br(), br(),
-            actionButton(
-              "load",
-              "Load",
-              class = "load-start"
-            )
-          )
-        }
-      } else if (DB$last_db == TRUE & (length(DB$available) == 0)) {
-        column(
-          width = 12,
-          p(
-            tags$span(
-              style='color: white; font-size: 15px; font-style: italic;',
-              HTML(
-                paste('Last used:', DB$database)
-              )
-            )
-          ),
-          br(),
-          actionButton(
-            "load",
-            "Load",
-            class = "load-start"
-          )
-        )
-      }
-    }
-  })
-  
-  output$imageOutput <- renderImage({
-    # Path to your PNG image with a transparent background
-    image_path <- paste0(getwd(), "/www/PhyloTrace.png")
-    
-    # Use HTML to display the image with the <img> tag
-    list(src = image_path,
-         height = 180)
-  }, deleteFile = FALSE)
-  
-  ### Load app event ----
-  
-  observeEvent(input$load, {
-    
-    # Reset reactive screening variables 
-    output$screening_start <- NULL
-    output$screening_result_sel <- NULL
-    output$screening_result <- NULL
-    output$screening_fail <- NULL
-    Screening$status_df <- NULL
-    Screening$choices <- NULL
-    Screening$picker_status <- TRUE
-    Screening$status <- "idle"
-    Screening$first_result <- NULL
-    if(!is.null(input$screening_select)) {
-      if(!is.null(DB$data)) {
-        updatePickerInput(session, "screening_select", selected = character(0))
-      }
-    }
-    
-    log_print("Input load")
-    
-    # set typing start control variable
-    Typing$reload <- TRUE
-    
-    # reset typing status on start(
-    if(Typing$status == "Finalized") {Typing$status <- "Inactive"}
-    if(!is.null(Typing$single_path)) {Typing$single_path <- data.frame()}
-    
-    #### Render status bar ----
-    observe({
-      req(DB$scheme)
-      
-      if(is.null(input$scheme_position)) {
-        output$loaded_scheme <- renderUI({
-          fluidRow(
-            tags$li(
-              class = "dropdown", 
-              tags$span(HTML(
-                paste('<i class="fa-solid fa-layer-group"></i>', 
-                      "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
-                      DB$scheme,
-                      "</i>")), 
-                style = "color:white;")
-            )
-          )
-        })
-      } 
-      
-      if(!is.null(input$scheme_position)) {
-        output$loaded_scheme <- renderUI({
-          fluidRow(
-            tags$li(
-              class = "dropdown", 
-              tags$span(HTML(
-                paste('<i class="fa-solid fa-layer-group"></i>', 
-                      "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
-                      DB$scheme,
-                      "</i>")), 
-                style = "color:white;"),
-              div(
-                class = "reload-bttn",
-                style = paste0("margin-left:", 30 + input$scheme_position, "px; position: relative; top: -24px;"),
-                actionButton(
-                  "reload_db",
-                  label = "",
-                  icon = icon("rotate")
-                )
-              )
-            )
-          )
-        })
-      }
-    })
-    
-    observe({
-      if(!is.null(DB$database)){
-        if(nchar(DB$database) > 60) {
-          database <- paste0(substring(DB$database, first = 1, last = 60), "...")
-        } else {
-          database <- DB$database
-        }
-        output$databasetext <- renderUI({
-          fluidRow(
-            tags$li(
-              class = "dropdown", 
-              tags$span(HTML(
-                paste('<i class="fa-solid fa-folder-open"></i>', 
-                      "Database:&nbsp;&nbsp;&nbsp;<i>",
-                      database,
-                      "</i>")), 
-                style = "color:white;")
-            ),
-            if(nchar(database) > 60) {bsTooltip("databasetext", 
-                                                HTML(DB$database), 
-                                                placement = "bottom", 
-                                                trigger = "hover")}
-          )
-        })
-      }
-    })
-    
-    observe({
-      if(!is.null(DB$database)) {
-        if(Typing$status == "Finalized"){
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp; <i>typing finalized</i>")),
-                  style = "color:white;")
-              )
-            )
-          )
-        } else if(Typing$status == "Attaching"){
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp; <i>evaluating typing results</i>")),
-                  style = "color:white;")
-              )
-            )
-          )
-        } else if(Typing$status == "Processing") {
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp;<i> pending typing</i>")), 
-                  style = "color:white;")
-              )
-            )
-          )
-        } else if(Screening$status == "started") {
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp;<i> pending gene screening</i>")), 
-                  style = "color:white;")
-              )
-            )
-          )
-        } else if(Screening$status == "finished") {
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp;<i> gene screening finalized</i>")), 
-                  style = "color:white;")
-              )
-            )
-          )
-        } else {
-          output$statustext <- renderUI(
-            fluidRow(
-              tags$li(
-                class = "dropdown", 
-                tags$span(HTML(
-                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
-                        "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
-                  style = "color:white;")
-              )
-            )
-          )
-        }    
-      }
-    })
-    
-    # Null single typing status
-    if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
-      Typing$progress <- 0
-      
-      Typing$progress_format <- 900000
-      
-      output$single_typing_progress <- NULL
-      
-      output$typing_fin <- NULL
-      
-      output$single_typing_results <- NULL
-      
-      output$typing_formatting <- NULL
-      
-      Typing$single_path <- data.frame()
-      
-      # reset results file 
-      if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
-        unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
-        # Resetting single typing progress logfile bar 
-        con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
-        
-        cat("0\n", file = con)   
-        
-        close(con)
-      }
-    }
-    
-    shinyjs::runjs(
-      'if(document.querySelector("#loaded_scheme > div > li > span") !== null) {
-          // Select the span element
-          let spanElement = document.querySelector("#loaded_scheme > div > li > span");
-                    
-          // Get the bounding rectangle of the span element
-          let rect = spanElement.getBoundingClientRect();
-          
-          // Extract the width
-          let width = rect.width;
-          
-          Shiny.setInputValue("scheme_position", width);            
-        }'
-    )
-    
-    # Load app elements based on database availability and missing value presence
-    if(!is.null(DB$select_new)) {
-      if(DB$select_new & (paste0(DB$new_database, "/Database") %in% dir_ls(DB$new_database))) {
-        
-        log_print("Directory already contains a database")
-        
-        show_toast(
-          title = "Directory already contains a database",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-        DB$load_selected <- FALSE
-        
-      } else if(DB$select_new | (DB$select_new == FALSE & is.null(input$scheme_db))) {
-        
-        log_print(paste0("New database created in ", DB$new_database))
-        
-        DB$check_new_entries <- TRUE
-        DB$data <- NULL
-        DB$meta_gs <- NULL
-        DB$meta <- NULL
-        DB$meta_true <- NULL
-        DB$allelic_profile <- NULL
-        DB$allelic_profile_trunc <- NULL
-        DB$allelic_profile_true <- NULL
-        
-        # null Distance matrix, entry table and plots
-        output$db_distancematrix <- NULL 
-        output$db_entries_table <- NULL
-        output$tree_mst <- NULL
-        output$tree_nj <- NULL
-        output$tree_upgma <- NULL
-        
-        # null report values
-        Report$report_list_mst <- list()
-        Report$report_list_nj <- list()
-        Report$report_list_upgma <- list()
-        
-        # null plots
-        Vis$nj <- NULL
-        Vis$upgma <- NULL
-        Vis$ggraph_1 <- NULL
-        
-        removeModal()
-        
-        #### Render Menu Items ----
-        
-        Startup$sidebar <- FALSE
-        Startup$header <- FALSE
-        
-        output$menu_sep2 <- renderUI(hr())
-        
-        # Hide start message
-        output$start_message <- NULL
-        
-        DB$load_selected <- FALSE
-        
-        # Declare database path
-        DB$database <- file.path(DB$new_database, "Database")
-        
-        # Set database availability screening variables to present database
-        DB$block_db <- TRUE
-        DB$select_new <- FALSE
-        
-        # Render menu with Manage Schemes as start tab and no Missing values tab
-        output$menu <- renderMenu(
-          sidebarMenu(
-            menuItem(
-              text = "Database Browser",
-              tabName = "database",
-              icon = icon("hard-drive"),
-              startExpanded = TRUE,
-              menuSubItem(
-                text = "Browse Entries",
-                tabName = "db_browse_entries"
-              ),
-              menuSubItem(
-                text = "Scheme Info",
-                tabName = "db_schemeinfo"
-              ),
-              menuSubItem(
-                text = "Loci Info",
-                tabName = "db_loci_info"
-              ),
-              menuSubItem(
-                text = "Distance Matrix",
-                tabName = "db_distmatrix"
-              )
-            ),
-            menuItem(
-              text = "Manage Schemes",
-              tabName = "init",
-              icon = icon("layer-group"),
-              selected = TRUE
-            ),
-            menuItem(
-              text = "Allelic Typing",
-              tabName = "typing",
-              icon = icon("gears")
-            ),
-            menuItem(
-              text = "Resistance Profile",
-              tabName = "gene_screening",
-              icon = icon("dna"),
-              startExpanded = TRUE,
-              menuSubItem(
-                text = "Browse Entries",
-                tabName = "gs_profile"
-              ),
-              menuSubItem(
-                text = "Screening",
-                tabName = "gs_screening"
-              )
-            ),
-            menuItem(
-              text = "Visualization",
-              tabName = "visualization",
-              icon = icon("circle-nodes")
-            ),
-            menuItem(
-              text = "Utilities",
-              tabName = "utilities",
-              icon = icon("screwdriver-wrench")
-            )
-          )
-        )
-        
-        # Dont render these elements
-        output$db_no_entries <- NULL
-        output$distancematrix_no_entries <- NULL
-        output$db_entries <- NULL
-        output$edit_index <- NULL
-        output$edit_scheme_d <- NULL
-        output$edit_entries <- NULL
-        output$compare_select <- NULL
-        output$delete_select <- NULL
-        output$del_bttn <- NULL
-        output$compare_allele_box <- NULL
-        output$download_entries <- NULL
-        output$missing_values <- NULL
-        output$delete_box <- NULL
-        output$missing_values_sidebar <- NULL
-        output$distmatrix_sidebar <- NULL
-        output$download_scheme_info <- NULL
-        output$download_loci <- NULL
-        output$entry_table_controls <- NULL
-        output$multi_stop <- NULL
-        output$metadata_multi_box <- NULL
-        output$start_multi_typing_ui <- NULL
-        output$pending_typing <- NULL
-        output$multi_typing_results <- NULL
-        output$single_typing_progress <- NULL
-        output$metadata_single_box <- NULL
-        output$start_typing_ui <- NULL
-        
-      }
-    } else {
-      log_print(paste0("Loading existing ", input$scheme_db, " database from ", DB$database))
-    }
-    
-    if(DB$load_selected == TRUE) {
-      
-      if(gsub(" ", "_", input$scheme_db) %in% schemes) { #Check if selected scheme valid
-        
-        # Save database path for next start
-        saveRDS(DB$database, paste0(getwd(), "/execute/last_db.rds"))
-        
-        DB$check_new_entries <- TRUE
-        DB$data <- NULL
-        DB$meta_gs <- NULL
-        DB$meta <- NULL
-        DB$meta_true <- NULL
-        DB$allelic_profile <- NULL
-        DB$allelic_profile_trunc <- NULL
-        DB$allelic_profile_true <- NULL
-        DB$scheme <- input$scheme_db
-        
-        # null Distance matrix, entry table and plots
-        output$db_distancematrix <- NULL 
-        output$db_entries_table <- NULL
-        output$tree_mst <- NULL
-        output$tree_nj <- NULL
-        output$tree_upgma <- NULL
-        
-        # null typing initiation UI
-        output$multi_stop <- NULL
-        output$metadata_multi_box <- NULL
-        output$start_multi_typing_ui <- NULL
-        output$pending_typing <- NULL
-        output$multi_typing_results <- NULL
-        output$single_typing_progress <- NULL
-        output$metadata_single_box <- NULL
-        output$start_typing_ui <- NULL
-        
-        # null report values
-        Report$report_list_mst <- list()
-        Report$report_list_nj <- list()
-        Report$report_list_upgma <- list()
-        
-        # null plots
-        Vis$nj <- NULL
-        Vis$upgma <- NULL
-        Vis$ggraph_1 <- NULL
-        
-        removeModal()
-        
-        #### Render Menu Items ----
-        
-        Startup$sidebar <- FALSE
-        Startup$header <- FALSE
-        
-        output$menu_sep2 <- renderUI(hr())
-        
-        # Hide start message
-        output$start_message <- NULL
-        
-        if(any(grepl(gsub(" ", "_", DB$scheme), dir_ls(DB$database)))) {
-          
-          if(!any(grepl("alleles", dir_ls(paste0(
-            DB$database, "/", 
-            gsub(" ", "_", DB$scheme)))))) {
-            
-            log_print("Missing loci files")
-            
-            # Show message that loci files are missing
-            showModal(
-              modalDialog(
-                paste0("Whoops! No loci files are present in the local ", 
-                       DB$scheme, 
-                       " folder. Download the scheme again (no influence on already typed assemblies)."),
-                title = "Local Database Error",
-                fade = TRUE,
-                easyClose = TRUE,
-                footer = tagList(
-                  modalButton("Okay")
-                )
-              )
-            )
-            
-            # Render menu with Manage Schemes as start tab
-            output$menu <- renderMenu(
-              sidebarMenu(
-                menuItem(
-                  text = "Database Browser",
-                  tabName = "database",
-                  icon = icon("hard-drive"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "db_browse_entries"
-                  ),
-                  menuSubItem(
-                    text = "Scheme Info",
-                    tabName = "db_schemeinfo"
-                  ),
-                  menuSubItem(
-                    text = "Loci Info",
-                    tabName = "db_loci_info"
-                  ),
-                  menuSubItem(
-                    text = "Distance Matrix",
-                    tabName = "db_distmatrix"
-                  ),
-                  menuSubItem(
-                    text = "Missing Values",
-                    tabName = "db_missing_values",
-                    icon = icon("triangle-exclamation")
-                  )
-                ),
-                menuItem(
-                  text = "Manage Schemes",
-                  tabName = "init",
-                  icon = icon("layer-group"),
-                  selected = TRUE
-                ),
-                menuItem(
-                  text = "Allelic Typing",
-                  tabName = "typing",
-                  icon = icon("gears")
-                ),
-                menuItem(
-                  text = "Resistance Profile",
-                  tabName = "gene_screening",
-                  icon = icon("dna"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "gs_profile"
-                  ),
-                  menuSubItem(
-                    text = "Screening",
-                    tabName = "gs_screening"
-                  )
-                ),
-                menuItem(
-                  text = "Visualization",
-                  tabName = "visualization",
-                  icon = icon("circle-nodes")
-                ),
-                menuItem(
-                  text = "Utilities",
-                  tabName = "utilities",
-                  icon = icon("screwdriver-wrench")
-                )
-              )
-            )
-          } else if (!any(grepl("scheme_info.html", dir_ls(paste0(
-            DB$database, "/", 
-            gsub(" ", "_", DB$scheme)))))) {
-            
-            output$download_scheme_info <- NULL
-            
-            log_print("Scheme info file missing")
-            
-            # Show message that scheme info is missing
-            showModal(
-              modalDialog(
-                paste0("Whoops! Scheme info of the local ", 
-                       DB$scheme, 
-                       " database is missing. Download the scheme again (no influence on already typed assemblies)."),
-                title = "Local Database Error",
-                fade = TRUE,
-                easyClose = TRUE,
-                footer = tagList(
-                  modalButton("Okay")
-                )
-              )
-            )
-            
-            # Render menu with Manage Schemes as start tab
-            output$menu <- renderMenu(
-              sidebarMenu(
-                menuItem(
-                  text = "Database Browser",
-                  tabName = "database",
-                  icon = icon("hard-drive"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "db_browse_entries"
-                  ),
-                  menuSubItem(
-                    text = "Scheme Info",
-                    tabName = "db_schemeinfo"
-                  ),
-                  menuSubItem(
-                    text = "Loci Info",
-                    tabName = "db_loci_info"
-                  ),
-                  menuSubItem(
-                    text = "Distance Matrix",
-                    tabName = "db_distmatrix"
-                  ),
-                  menuSubItem(
-                    text = "Missing Values",
-                    tabName = "db_missing_values",
-                    icon = icon("triangle-exclamation")
-                  )
-                ),
-                menuItem(
-                  text = "Manage Schemes",
-                  tabName = "init",
-                  icon = icon("layer-group"),
-                  selected = TRUE
-                ),
-                menuItem(
-                  text = "Allelic Typing",
-                  tabName = "typing",
-                  icon = icon("gears")
-                ),
-                menuItem(
-                  text = "Resistance Profile",
-                  tabName = "gene_screening",
-                  icon = icon("dna"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "gs_profile"
-                  ),
-                  menuSubItem(
-                    text = "Screening",
-                    tabName = "gs_screening"
-                  )
-                ),
-                menuItem(
-                  text = "Visualization",
-                  tabName = "visualization",
-                  icon = icon("circle-nodes")
-                ),
-                menuItem(
-                  text = "Utilities",
-                  tabName = "utilities",
-                  icon = icon("screwdriver-wrench")
-                )
-              )
-            )
-            
-          } else if (!any(grepl("targets.csv", dir_ls(paste0(
-            DB$database, "/", 
-            gsub(" ", "_", DB$scheme)))))) {
-            
-            # Dont render target download button
-            output$download_loci <- NULL
-            
-            log_print("Missing loci info (targets.csv)")
-            
-            # Show message that scheme info is missing
-            showModal(
-              modalDialog(
-                paste0("Whoops! Loci info of the local ", 
-                       DB$scheme, 
-                       " database is missing. Download the scheme again (no influence on already typed assemblies)."),
-                title = "Local Database Error",
-                fade = TRUE,
-                easyClose = TRUE,
-                footer = tagList(
-                  modalButton("Okay")
-                )
-              )
-            )
-            
-            # Render menu with Manage Schemes as start tab
-            output$menu <- renderMenu(
-              sidebarMenu(
-                menuItem(
-                  text = "Database Browser",
-                  tabName = "database",
-                  icon = icon("hard-drive"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "db_browse_entries"
-                  ),
-                  menuSubItem(
-                    text = "Scheme Info",
-                    tabName = "db_schemeinfo"
-                  ),
-                  menuSubItem(
-                    text = "Loci Info",
-                    tabName = "db_loci_info"
-                  ),
-                  menuSubItem(
-                    text = "Distance Matrix",
-                    tabName = "db_distmatrix"
-                  ),
-                  menuSubItem(
-                    text = "Missing Values",
-                    tabName = "db_missing_values",
-                    icon = icon("triangle-exclamation")
-                  )
-                ),
-                menuItem(
-                  text = "Manage Schemes",
-                  tabName = "init",
-                  icon = icon("layer-group"),
-                  selected = TRUE
-                ),
-                menuItem(
-                  text = "Allelic Typing",
-                  tabName = "typing",
-                  icon = icon("gears")
-                ),
-                menuItem(
-                  text = "Resistance Profile",
-                  tabName = "gene_screening",
-                  icon = icon("dna"),
-                  startExpanded = TRUE,
-                  menuSubItem(
-                    text = "Browse Entries",
-                    tabName = "gs_profile"
-                  ),
-                  menuSubItem(
-                    text = "Screening",
-                    tabName = "gs_screening"
-                  )
-                ),
-                menuItem(
-                  text = "Visualization",
-                  tabName = "visualization",
-                  icon = icon("circle-nodes")
-                ),
-                menuItem(
-                  text = "Utilities",
-                  tabName = "utilities",
-                  icon = icon("screwdriver-wrench")
-                )
-              )
-            )
-            
-          } else {
-            # Produce Scheme Info Table
-            schemeinfo <-
-              read_html(paste0(
-                DB$database, "/",
-                gsub(" ", "_", DB$scheme),
-                "/scheme_info.html"
-              )) %>%
-              html_table(header = FALSE) %>%
-              as.data.frame(stringsAsFactors = FALSE)
-            names(schemeinfo) <- NULL
-            DB$schemeinfo <- schemeinfo
-            number_loci <- as.vector(DB$schemeinfo[6, 2])
-            DB$number_loci <- as.numeric(gsub(",", "", number_loci))
-            
-            # Produce Loci Info table
-            DB$loci_info <- read.csv(
-              file.path(DB$database, gsub(" ", "_", DB$scheme), "targets.csv"),
-              header = TRUE,
-              sep = "\t",
-              row.names = NULL,
-              colClasses = c(
-                "NULL",
-                "character",
-                "character",
-                "integer",
-                "integer",
-                "character",
-                "integer",
-                "NULL"
-              )
-            )
-            
-            # Check if number of loci/fastq-files of alleles is coherent with number of targets in scheme
-            if(DB$number_loci > length(dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")))) {
-              
-              log_print(paste0("Loci files are missing in the local ", DB$scheme, " folder"))
-              
-              # Show message that loci files are missing
-              showModal(
-                modalDialog(
-                  paste0("Whoops! Some loci files are missing in the local ", 
-                         DB$scheme, 
-                         " folder. Download the scheme again (no influence on already typed assemblies)."),
-                  title = "Local Database Error",
-                  fade = TRUE,
-                  easyClose = TRUE,
-                  footer = tagList(
-                    modalButton("Okay")
-                  )
-                )
-              )
-              
-              # Render menu with Manage Schemes as start tab
-              output$menu <- renderMenu(
-                sidebarMenu(
-                  menuItem(
-                    text = "Database Browser",
-                    tabName = "database",
-                    icon = icon("hard-drive"),
-                    startExpanded = TRUE,
-                    menuSubItem(
-                      text = "Browse Entries",
-                      tabName = "db_browse_entries"
-                    ),
-                    menuSubItem(
-                      text = "Scheme Info",
-                      tabName = "db_schemeinfo"
-                    ),
-                    menuSubItem(
-                      text = "Loci Info",
-                      tabName = "db_loci_info"
-                    ),
-                    menuSubItem(
-                      text = "Distance Matrix",
-                      tabName = "db_distmatrix"
-                    ),
-                    menuSubItem(
-                      text = "Missing Values",
-                      tabName = "db_missing_values",
-                      icon = icon("triangle-exclamation")
-                    )
-                  ),
-                  menuItem(
-                    text = "Manage Schemes",
-                    tabName = "init",
-                    icon = icon("layer-group"),
-                    selected = TRUE
-                  ),
-                  menuItem(
-                    text = "Allelic Typing",
-                    tabName = "typing",
-                    icon = icon("gears")
-                  ),
-                  menuItem(
-                    text = "Resistance Profile",
-                    tabName = "gene_screening",
-                    icon = icon("dna"),
-                    startExpanded = TRUE,
-                    menuSubItem(
-                      text = "Browse Entries",
-                      tabName = "gs_profile"
-                    ),
-                    menuSubItem(
-                      text = "Screening",
-                      tabName = "gs_screening"
-                    )
-                  ),
-                  menuItem(
-                    text = "Visualization",
-                    tabName = "visualization",
-                    icon = icon("circle-nodes")
-                  ),
-                  menuItem(
-                    text = "Utilities",
-                    tabName = "utilities",
-                    icon = icon("screwdriver-wrench")
-                  )
-                )
-              )
-              
-            } else {
-              ###### Alle checks bestanden -> Laden der DTB
-              # If typed entries present
-              if (any(grepl("Typing.rds", dir_ls(paste0(
-                DB$database, "/", gsub(" ", "_", DB$scheme)
-              ))))) {
-                
-                # Load database from files  
-                Database <- readRDS(file.path(DB$database, 
-                                              gsub(" ", "_", DB$scheme), 
-                                              "Typing.rds"))
-                
-                DB$data <- Database[["Typing"]]
-                
-                if(!is.null(DB$data)){
-                  if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-                    cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-                    DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
-                  } else {
-                    DB$cust_var <- data.frame()
-                  }
-                }
-                
-                DB$change <- FALSE
-                DB$meta_gs <- select(DB$data, c(1, 3:13))
-                DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-                DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-                DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-                DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
-                DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-                
-                # Null pipe 
-                con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
-                
-                cat("0\n", file = con)
-                
-                # Close the file connection
-                close(con)
-                
-                # Reset other reactive typing variables
-                Typing$progress_format_end <- 0 
-                Typing$progress_format_start <- 0
-                Typing$pending_format <- 0
-                Typing$entry_added <- 0
-                Typing$progress <- 0
-                Typing$progress_format <- 900000
-                output$single_typing_progress <- NULL
-                output$typing_fin <- NULL
-                output$single_typing_results <- NULL
-                output$typing_formatting <- NULL
-                Typing$single_path <- data.frame()
-                
-                # Null multi typing feedback variable
-                Typing$reset <- TRUE
-                
-                # Check need for new missing vlaue display
-                if(DB$first_look == TRUE) {
-                  if(sum(apply(DB$data, 1, anyNA)) >= 1) {
-                    DB$no_na_switch <- TRUE
-                  } else {
-                    DB$no_na_switch <- FALSE
-                  }
-                }
-                
-                DB$first_look <- TRUE
-                
-                output$initiate_typing_ui <- renderUI({
-                  column(
-                    width = 4,
-                    align = "center",
-                    br(),
-                    br(),
-                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-                    br(),
-                    br(),
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "center",
-                        shinyFilesButton(
-                          "genome_file",
-                          "Browse" ,
-                          icon = icon("file"),
-                          title = "Select the assembly in .fasta/.fna/.fa format:",
-                          multiple = FALSE,
-                          buttonType = "default",
-                          class = NULL,
-                          root = path_home()
-                        ),
-                        br(),
-                        br(),
-                        uiOutput("genome_path"),
-                        br()
-                      )
-                    )
-                  )
-                })
-                
-                output$initiate_multi_typing_ui <- renderUI({
-                  column(
-                    width = 4,
-                    align = "center",
-                    br(),
-                    br(),
-                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-                    br(), br(),
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "center",
-                        shinyDirButton(
-                          "genome_file_multi",
-                          "Browse",
-                          icon = icon("folder-open"),
-                          title = "Select the folder containing the genome assemblies (FASTA)",
-                          buttonType = "default",
-                          root = path_home()
-                        ),
-                        br(),
-                        br(),
-                        uiOutput("multi_select_info"),
-                        br()
-                      )
-                    ),
-                    uiOutput("multi_select_tab_ctrls"),
-                    br(),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "left",
-                        rHandsontableOutput("multi_select_table")
-                      )
-                    )
-                  )
-                })
-                
-                if(!anyNA(DB$allelic_profile)) {
-                  
-                  # no NA's -> dont render missing values sidebar elements
-                  output$missing_values_sidebar <- NULL
-                  
-                  # Render menu if no NA's present
-                  output$menu <- renderMenu(
-                    sidebarMenu(
-                      menuItem(
-                        text = "Database Browser",
-                        tabName = "database",
-                        icon = icon("hard-drive"),
-                        startExpanded = TRUE,
-                        menuSubItem(
-                          text = "Browse Entries",
-                          tabName = "db_browse_entries"
-                        ),
-                        menuSubItem(
-                          text = "Scheme Info",
-                          tabName = "db_schemeinfo"
-                        ),
-                        menuSubItem(
-                          text = "Loci Info",
-                          tabName = "db_loci_info"
-                        ),
-                        menuSubItem(
-                          text = "Distance Matrix",
-                          tabName = "db_distmatrix"
-                        )
-                      ),
-                      menuItem(
-                        text = "Manage Schemes",
-                        tabName = "init",
-                        icon = icon("layer-group")
-                      ),
-                      menuItem(
-                        text = "Allelic Typing",
-                        tabName = "typing",
-                        icon = icon("gears")
-                      ),
-                      menuItem(
-                        text = "Resistance Profile",
-                        tabName = "gene_screening",
-                        icon = icon("dna"),
-                        startExpanded = TRUE,
-                        menuSubItem(
-                          text = "Browse Entries",
-                          tabName = "gs_profile"
-                        ),
-                        menuSubItem(
-                          text = "Screening",
-                          tabName = "gs_screening"
-                        )
-                      ),
-                      menuItem(
-                        text = "Visualization",
-                        tabName = "visualization",
-                        icon = icon("circle-nodes")
-                      ),
-                      menuItem(
-                        text = "Utilities",
-                        tabName = "utilities",
-                        icon = icon("screwdriver-wrench")
-                      )
-                    )
-                  )
-                } else {
-                  output$menu <- renderMenu(
-                    sidebarMenu(
-                      menuItem(
-                        text = "Database Browser",
-                        tabName = "database",
-                        icon = icon("hard-drive"),
-                        startExpanded = TRUE,
-                        menuSubItem(
-                          text = "Browse Entries",
-                          tabName = "db_browse_entries",
-                          selected = TRUE
-                        ),
-                        menuSubItem(
-                          text = "Scheme Info",
-                          tabName = "db_schemeinfo"
-                        ),
-                        menuSubItem(
-                          text = "Loci Info",
-                          tabName = "db_loci_info"
-                        ),
-                        menuSubItem(
-                          text = "Distance Matrix",
-                          tabName = "db_distmatrix"
-                        ),
-                        menuSubItem(
-                          text = "Missing Values",
-                          tabName = "db_missing_values",
-                          icon = icon("triangle-exclamation")
-                        )
-                      ),
-                      menuItem(
-                        text = "Manage Schemes",
-                        tabName = "init",
-                        icon = icon("layer-group")
-                      ),
-                      menuItem(
-                        text = "Allelic Typing",
-                        tabName = "typing",
-                        icon = icon("gears")
-                      ),
-                      menuItem(
-                        text = "Resistance Profile",
-                        tabName = "gene_screening",
-                        icon = icon("dna"),
-                        startExpanded = TRUE,
-                        menuSubItem(
-                          text = "Browse Entries",
-                          tabName = "gs_profile"
-                        ),
-                        menuSubItem(
-                          text = "Screening",
-                          tabName = "gs_screening"
-                        )
-                      ),
-                      menuItem(
-                        text = "Visualization",
-                        tabName = "visualization",
-                        icon = icon("circle-nodes")
-                      ),
-                      menuItem(
-                        text = "Utilities",
-                        tabName = "utilities",
-                        icon = icon("screwdriver-wrench")
-                      )
-                    )
-                  )
-                }
-                
-                # Render custom variable display
-                output$show_cust_var <- renderTable(
-                  width = "100%", 
-                  {
-                    if((!is.null(DB$cust_var)) & (!is.null(input$cust_var_select))) {
-                      if(nrow(DB$cust_var) > 5) {
-                        low <- -4
-                        high <- 0
-                        for (i in 1:input$cust_var_select) {
-                          low <- low + 5
-                          if((nrow(DB$cust_var) %% 5) != 0) {
-                            if(i == ceiling(nrow(DB$cust_var) / 5 )) {
-                              high <- high + nrow(DB$cust_var) %% 5
-                            } else {
-                              high <- high + 5
-                            }
-                          } else {
-                            high <- high + 5
-                          }
-                        }
-                        DB$cust_var[low:high,]
-                      } else {
-                        DB$cust_var
-                      }
-                    } else if (!is.null(DB$cust_var)) {
-                      DB$cust_var
-                    }
-                  })
-                
-                # render visualization sidebar elements
-                observe({
-                  Vis$tree_algo <- input$tree_algo
-                })
-                
-                output$visualization_sidebar <- renderUI({
-                  if(!is.null(DB$data)) {
-                    column(
-                      width = 12,
-                      br(),
-                      fluidRow(
-                        column(1),
-                        column(
-                          width = 11,
-                          align = "left",
-                          prettyRadioButtons(
-                            "tree_algo",
-                            choices = c("Minimum-Spanning", "Neighbour-Joining", "UPGMA"),
-                            label = "",
-                            selected = if(!is.null(Vis$tree_algo)){Vis$tree_algo} else {"Minimum-Spanning"}
-                          ),
-                        )
-                      ),
-                      br(),
-                      fluidRow(
-                        column(
-                          width = 12,
-                          align = "center",
-                          tags$div(
-                            id = "button-wrapper",
-                            actionButton(
-                              "create_tree",
-                              h5("Create Tree", style = "position: relative; left: 15px; color: white; font-size: 15px;"),
-                              width = "100%"
-                            ),
-                            tags$img(
-                              src = "phylo.png",
-                              alt = "icon",
-                              class = "icon"
-                            )
-                          )
-                        )
-                      ), 
-                      br(),
-                      hr(),
-                      conditionalPanel(
-                        "input.tree_algo=='Minimum-Spanning'",
-                        fluidRow(
-                          column(
-                            width = 12,
-                            align = "left",
-                            br(),
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 16px; margin-left: 15px', "Sizing")
-                              )
-                            )
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 12,
-                            radioGroupButtons(
-                              "mst_ratio",
-                              "",
-                              choiceNames = c("16:10", "16:9", "4:3"),
-                              choiceValues = c((16/10), (16/9), (4/3)),
-                              width = "100%"
-                            ),
-                            br(),
-                            sliderInput(
-                              "mst_scale",
-                              "",
-                              min = 500,
-                              max = 1200,
-                              step = 5,
-                              value = 800,
-                              width = "95%",
-                              ticks = FALSE
-                            )
-                          )
-                        ),
-                        br(),
-                        hr(),
-                        fluidRow(
-                          column(
-                            width = 12,
-                            column(
-                              width = 5,
-                              align = "left",
-                              conditionalPanel(
-                                "input.mst_plot_format=='jpeg'",
-                                actionBttn(
-                                  "save_plot_jpeg",
-                                  style = "simple",
-                                  label = "Save Plot",
-                                  size = "sm",
-                                  icon = NULL,
-                                  color = "primary"
-                                )  
-                              ),
-                              conditionalPanel(
-                                "input.mst_plot_format=='png'",
-                                actionBttn(
-                                  "save_plot_png",
-                                  style = "simple",
-                                  label = "Save Plot",
-                                  size = "sm",
-                                  icon = NULL,
-                                  color = "primary"
-                                )
-                              ),
-                              conditionalPanel(
-                                "input.mst_plot_format=='bmp'",
-                                actionBttn(
-                                  "save_plot_bmp",
-                                  style = "simple",
-                                  label = "Save Plot",
-                                  size = "sm",
-                                  icon = NULL,
-                                  color = "primary"
-                                )  
-                              ),
-                              conditionalPanel(
-                                "input.mst_plot_format=='html'",
-                                downloadBttn(
-                                  "save_plot_html",
-                                  style = "simple",
-                                  label = "Save Plot",
-                                  size = "sm",
-                                  icon = NULL,
-                                  color = "primary"
-                                )
-                              )
-                            ),
-                            column(
-                              width = 7,
-                              div(
-                                style = "max-width: 150px",
-                                class = "format",
-                                selectInput(
-                                  inputId = "mst_plot_format",
-                                  label = "",
-                                  choices = c("html", "jpeg", "png", "bmp")
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.tree_algo=='Neighbour-Joining'",
-                        fluidRow(
-                          column(
-                            width = 12,
-                            column(
-                              width = 5,
-                              align = "left",
-                              downloadBttn(
-                                "download_nj",
-                                style = "simple",
-                                label = "Save Plot",
-                                size = "sm",
-                                icon = NULL,
-                                color = "primary"
-                              )
-                            ),
-                            column(
-                              width = 7,
-                              div(
-                                style = "max-width: 150px",
-                                class = "format",
-                                selectInput(
-                                  inputId = "filetype_nj",
-                                  label = "",
-                                  choices = c("png", "jpeg", "bmp", "svg")
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      conditionalPanel(
-                        "input.tree_algo=='UPGMA'",
-                        fluidRow(
-                          column(
-                            width = 12,
-                            column(
-                              width = 5,
-                              align = "left",
-                              downloadBttn(
-                                "download_upgma",
-                                style = "simple",
-                                label = "Save Plot",
-                                size = "sm",
-                                icon = NULL,
-                                color = "primary"
-                              )
-                            ),
-                            column(
-                              width = 7,
-                              div(
-                                style = "max-width: 150px",
-                                class = "format",
-                                selectInput(
-                                  inputId = "filetype_upgma",
-                                  label = "",
-                                  choices = c("png", "jpeg", "bmp", "svg")
-                                )
-                              )
-                            )
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 6,
-                          align = "left",
-                          br(),
-                          actionButton(
-                            "create_rep",
-                            "Print Report"
-                          )
-                        )
-                      )
-                    )
-                  }
-                })
-                
-                # Render entry table sidebar elements
-                output$entrytable_sidebar <- renderUI({
-                  if(!is.null(DB$data)) {
-                    column(
-                      width = 12,
-                      align = "center",
-                      br(), 
-                      fluidRow(
-                        column(1),
-                        column(
-                          width = 10,
-                          align = "left",
-                          if(nrow(DB$data) > 40) {
-                            div(
-                              class = "mat-switch-db-tab",
-                              materialSwitch(
-                                "table_height",
-                                h5(p("Show Full Table"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            )
-                          }
-                        )
-                      ),
-                      br(), br(), 
-                      fluidRow(
-                        column(
-                          width = 12,
-                          HTML(
-                            paste(
-                              tags$span(style='color: white; font-size: 18px; margin-bottom: 0px', 'Custom Variables')
-                            )
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 8,
-                          textInput(
-                            "new_var_name",
-                            label = "",
-                            placeholder = "New Variable"
-                          )
-                        ),
-                        column(
-                          width = 2,
-                          actionButton(
-                            "add_new_variable",
-                            "",
-                            icon = icon("plus")
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(
-                          width = 8,
-                          align = "left",
-                          div(
-                            class = "textinput_var",
-                            selectInput(
-                              "del_which_var",
-                              "",
-                              DB$cust_var$Variable
-                            )
-                          )
-                        ),
-                        column(
-                          width = 2,
-                          align = "left",
-                          actionButton(
-                            "delete_new_variable",
-                            "",
-                            icon = icon("minus")
-                          )
-                        )
-                      ),
-                      br(), 
-                      fluidRow(
-                        column(1),
-                        column(
-                          width = 4,
-                          uiOutput("cust_var_info")
-                        )
-                      ),
-                      fluidRow(
-                        column(1),
-                        column(
-                          width = 11,
-                          align = "center",
-                          tableOutput("show_cust_var")
-                        )
-                      ),
-                      fluidRow(
-                        column(4),
-                        column(
-                          width = 7,
-                          align = "center",
-                          uiOutput("cust_var_select")
-                        )
-                      )
-                    )
-                  } 
-                })
-                
-                # Render missing values sidebar elements
-                output$missing_values_sidebar <- renderUI({
-                  column(
-                    width = 12,
-                    fluidRow(
-                      column(
-                        width = 12,
-                        br(),
-                        materialSwitch(
-                          "miss_val_height",
-                          h5(p("Show Full Table"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                          value = FALSE,
-                          right = TRUE
-                        )
-                      ),
-                      br()
-                    ),
-                    fluidRow(
-                      column(
-                        width = 6,
-                        HTML(
-                          paste(
-                            tags$span(style='color: white; font-size: 14px; position: relative; bottom: -23px; right: -15px', 
-                                      'Download CSV')
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        downloadBttn(
-                          "download_na_matrix",
-                          style = "simple",
-                          label = "",
-                          size = "sm",
-                          icon = icon("download")
-                        )
-                      )
-                    )
-                  )
-                })
-                
-                # Render scheme info download button
-                output$download_loci <- renderUI({
-                  column(
-                    12,
-                    downloadBttn(
-                      "download_loci_info",
-                      style = "simple",
-                      label = "",
-                      size = "sm",
-                      icon = icon("download"),
-                      color = "primary"
-                    ),
-                    bsTooltip("download_loci_info_bttn", HTML("Save loci information <br> (without sequence)"), placement = "top", trigger = "hover")
-                  )
-                })
-                
-                # Render scheme info download button
-                output$download_scheme_info <- renderUI({
-                  downloadBttn(
-                    "download_schemeinfo",
-                    style = "simple",
-                    label = "",
-                    size = "sm",
-                    icon = icon("download"),
-                    color = "primary"
-                  )
-                })
-                
-                # Render distance matrix sidebar
-                output$distmatrix_sidebar <- renderUI({
-                  column(
-                    width = 12,
-                    align = "left",
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "center",
-                        selectInput(
-                          "distmatrix_label",
-                          label = "",
-                          choices = c("Index", "Assembly Name", "Assembly ID"),
-                          selected = c("Assembly Name"),
-                          width = "100%"
-                        ),
-                        br()
-                      )
-                    ),
-                    div(
-                      class = "mat-switch-dmatrix",
-                      materialSwitch(
-                        "distmatrix_true",
-                        h5(p("Only Included Entries"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                        value = FALSE,
-                        right = TRUE
-                      )
-                    ),
-                    div(
-                      class = "mat-switch-dmatrix",
-                      materialSwitch(
-                        "distmatrix_triangle",
-                        h5(p("Show Upper Triangle"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                        value = FALSE,
-                        right = TRUE
-                      )
-                    ),
-                    div(
-                      class = "mat-switch-dmatrix-last",
-                      materialSwitch(
-                        "distmatrix_diag",
-                        h5(p("Show Diagonal"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                        value = TRUE,
-                        right = TRUE
-                      )
-                    ),
-                    fluidRow(
-                      column(
-                        width = 6,
-                        HTML(
-                          paste(
-                            tags$span(style='color: white; font-size: 14px; position: relative; bottom: 37px; right: -15px', 
-                                      'Download CSV')
-                          )
-                        )
-                      ),
-                      column(
-                        width = 4,
-                        downloadBttn(
-                          "download_distmatrix",
-                          style = "simple",
-                          label = "",
-                          size = "sm",
-                          icon = icon("download")
-                        )
-                      )
-                    )
-                  )
-                })
-                
-                # Render select input to choose displayed loci
-                output$compare_select <- renderUI({
-                  
-                  if(nrow(DB$data) == 1) {
-                    HTML(
-                      paste(
-                        tags$span(style='color: white; font-size: 15px;', "Type at least two assemblies to compare")
-                      )
-                    )
-                  } else {
-                    if(!is.null(input$compare_difference)) {
-                      if (input$compare_difference == FALSE) {
-                        pickerInput(
-                          inputId = "compare_select",
-                          label = "",
-                          width = "85%",
-                          choices = names(DB$allelic_profile),
-                          selected = names(DB$allelic_profile)[1:20],
-                          options = list(
-                            `live-search` = TRUE,
-                            `actions-box` = TRUE,
-                            size = 10,
-                            style = "background-color: white; border-radius: 5px;"
-                          ),
-                          multiple = TRUE
-                        )
-                      } else {
-                        pickerInput(
-                          inputId = "compare_select",
-                          label = "",
-                          width = "85%",
-                          choices = names(DB$allelic_profile),
-                          selected = names(DB$allelic_profile)[var_alleles(DB$allelic_profile)],
-                          options = list(
-                            `live-search` = TRUE,
-                            `actions-box` = TRUE,
-                            size = 10,
-                            style = "background-color: white; border-radius: 5px;"
-                          ),
-                          multiple = TRUE
-                        )
-                      }
-                    }
-                  }
-                })
-                
-                #### Render Entry Data Table ----
-                output$db_entries_table <- renderUI({
-                  if(!is.null(DB$data)) {
-                    if(between(nrow(DB$data), 1, 30)) {
-                      rHandsontableOutput("db_entries")
-                    } else {
-                      addSpinner(
-                        rHandsontableOutput("db_entries"),
-                        spin = "dots",
-                        color = "#ffffff"
-                      )
-                    }
-                  }
-                })
-                
-                if (!is.null(DB$data)) {
-                  
-                  observe({
-                    
-                    if (!is.null(DB$data)) {
-                      if (nrow(DB$data) == 1) {
-                        if(!is.null(DB$data) & !is.null(DB$cust_var)) {
-                          output$db_entries <- renderRHandsontable({
-                            rhandsontable(
-                              select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                              error_highlight = err_thresh() - 1,                              
-                              rowHeaders = NULL,
-                              contextMenu = FALSE,
-                              highlightCol = TRUE, 
-                              highlightRow = TRUE
-                            ) %>%
-                              hot_col(1, 
-                                      valign = "htMiddle",
-                                      halign = "htCenter") %>%
-                              hot_col(3, readOnly = TRUE) %>%
-                              hot_col(c(1, 5, 10, 11, 12, 13),
-                                      readOnly = TRUE) %>%
-                              hot_col(3:(13 + nrow(DB$cust_var)), 
-                                      valign = "htMiddle",
-                                      halign = "htLeft") %>%
-                              hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                              hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                              hot_col(8, type = "dropdown", source = country_names) %>%
-                              hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                                      validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                              hot_cols(fixedColumnsLeft = 1) %>%
-                              hot_col(2, type = "checkbox", width = "auto",
-                                      valign = "htTop",
-                                      halign = "htCenter") %>%
-                              hot_rows(fixedRowsTop = 0) %>%
-                              hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-                          })
-                        }
-                      } else if (between(nrow(DB$data), 2, 40)) {
-                        if (length(input$compare_select) > 0) {
-                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
-                            output$db_entries <- renderRHandsontable({
-                              
-                              entry_data <- DB$data %>%
-                                select(1:(13 + nrow(DB$cust_var))) %>%
-                                add_column(select(DB$allelic_profile_trunc, input$compare_select))
-                              
-                              rhandsontable(
-                                entry_data,
-                                col_highlight = diff_allele() - 1,
-                                dup_names_high = duplicated_names() - 1,
-                                dup_ids_high = duplicated_ids() - 1,
-                                row_highlight = true_rows() - 1,
-                                error_highlight = err_thresh() - 1,
-                                rowHeaders = NULL,
-                                highlightCol = TRUE, 
-                                highlightRow = TRUE,
-                                contextMenu = FALSE
-                              )  %>%
-                                hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
-                                        valign = "htMiddle",
-                                        halign = "htCenter",
-                                        readOnly = TRUE) %>%
-                                hot_col(1, 
-                                        valign = "htMiddle",
-                                        halign = "htCenter") %>%
-                                hot_col(3, readOnly = TRUE) %>%
-                                hot_col(c(1, 5, 10, 11, 12, 13),
-                                        readOnly = TRUE) %>%
-                                hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(3:(13 + nrow(DB$cust_var)), 
-                                        valign = "htMiddle",
-                                        halign = "htLeft") %>%
-                                hot_col(8, type = "dropdown", source = country_names) %>%
-                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                                        validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                                hot_col(2, type = "checkbox", width = "auto",
-                                        valign = "htTop",
-                                        halign = "htCenter",
-                                        strict = TRUE,
-                                        allowInvalid = FALSE,
-                                        copyable = TRUE) %>%
-                                hot_cols(fixedColumnsLeft = 1) %>%
-                                hot_rows(fixedRowsTop = 0) %>%
-                                hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-  
-                       }
-              }") %>%
-                                hot_col(diff_allele(),
-                                        renderer = "
-                  function(instance, td, row, col, prop, value, cellProperties) {
-                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
-  
-                    if (instance.params) {
-                          hcols = instance.params.col_highlight;
-                          hcols = hcols instanceof Array ? hcols : [hcols];
-                        }
-  
-                    if (instance.params && hcols.includes(col)) {
-                      td.style.background = 'rgb(116, 188, 139)';
-                    }
-                }"
-                                ) %>%
-                                hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-                            })
-                          }
-                        } else {
-                          if(!is.null(DB$data) & !is.null(DB$cust_var)) {
-                            output$db_entries <- renderRHandsontable({
-                              rhandsontable(
-                                select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                                rowHeaders = NULL,
-                                row_highlight = true_rows() - 1,
-                                dup_names_high = duplicated_names()- 1,
-                                dup_ids_high = duplicated_ids() - 1,
-                                error_highlight = err_thresh() - 1,
-                                contextMenu = FALSE,
-                                highlightCol = TRUE, 
-                                highlightRow = TRUE
-                              ) %>%
-                                hot_cols(fixedColumnsLeft = 1) %>%
-                                hot_col(1, 
-                                        valign = "htMiddle",
-                                        halign = "htCenter") %>%
-                                hot_col(3, readOnly = TRUE) %>%
-                                hot_col(c(1, 5, 10, 11, 12, 13),
-                                        readOnly = TRUE) %>%
-                                hot_col(3:(13 + nrow(DB$cust_var)), 
-                                        valign = "htMiddle",
-                                        halign = "htLeft") %>%
-                                hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(8, type = "dropdown", source = country_names) %>%
-                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                                        validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                                hot_col(2, type = "checkbox", width = "auto",
-                                        valign = "htTop",
-                                        halign = "htCenter") %>%
-                                hot_rows(fixedRowsTop = 0) %>%
-                                hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-  
-                       }
-              }") %>%
-                                hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-                            })    
-                          }
-                        }
-                      } else {
-                        if (length(input$compare_select) > 0) {
-                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
-                            output$db_entries <- renderRHandsontable({
-                              
-                              entry_data <- DB$data %>%
-                                select(1:(13 + nrow(DB$cust_var))) %>%
-                                add_column(select(DB$allelic_profile_trunc, input$compare_select))
-                              
-                              rhandsontable(
-                                entry_data,
-                                col_highlight = diff_allele() - 1,
-                                rowHeaders = NULL,
-                                height = table_height(),
-                                row_highlight = true_rows() - 1,
-                                dup_names_high = duplicated_names() - 1,
-                                dup_ids_high = duplicated_ids() - 1,
-                                error_highlight = err_thresh() - 1,
-                                contextMenu = FALSE,
-                                highlightCol = TRUE, 
-                                highlightRow = TRUE
-                              ) %>%
-                                hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
-                                        readOnly = TRUE, 
-                                        valign = "htMiddle",
-                                        halign = "htCenter") %>%
-                                hot_col(3:(13 + nrow(DB$cust_var)), 
-                                        valign = "htMiddle",
-                                        halign = "htLeft") %>%
-                                hot_col(3, readOnly = TRUE) %>%
-                                hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(c(1, 5, 10, 11, 12, 13),
-                                        readOnly = TRUE) %>%
-                                hot_col(8, type = "dropdown", source = country_names) %>%
-                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                                        validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                                hot_col(1, 
-                                        valign = "htMiddle",
-                                        halign = "htCenter") %>%
-                                hot_col(2, type = "checkbox", width = "auto",
-                                        valign = "htTop",
-                                        halign = "htCenter",
-                                        allowInvalid = FALSE,
-                                        copyable = TRUE) %>%
-                                hot_cols(fixedColumnsLeft = 1) %>%
-                                hot_rows(fixedRowsTop = 0) %>%
-                                hot_col(1, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.row_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                                                             }
-                                                           }
-                                                       }") %>%
-                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") %>%
-                                hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(diff_allele(),
-                                        renderer = "
-                  function(instance, td, row, col, prop, value, cellProperties) {
-                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
-  
-                    if (instance.params) {
-                          hcols = instance.params.col_highlight;
-                          hcols = hcols instanceof Array ? hcols : [hcols];
-                        }
-  
-                    if (instance.params && hcols.includes(col)) {
-                      td.style.background = 'rgb(116, 188, 139)';
-                    }
-                }") 
-                            })    
-                          }
-                        } else {
-                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
-                            output$db_entries <- renderRHandsontable({
-                              rhandsontable(
-                                select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                                rowHeaders = NULL,
-                                height = table_height(),
-                                dup_names_high = duplicated_names() - 1,
-                                dup_ids_high = duplicated_ids() - 1,
-                                row_highlight = true_rows() - 1,
-                                error_highlight = err_thresh() - 1,
-                                contextMenu = FALSE,
-                                highlightCol = TRUE, 
-                                highlightRow = TRUE
-                              ) %>%
-                                hot_cols(fixedColumnsLeft = 1) %>%
-                                hot_col(1, 
-                                        valign = "htMiddle",
-                                        halign = "htCenter") %>%
-                                hot_col(3, readOnly = TRUE) %>%
-                                hot_col(c(1, 5, 10, 11, 12, 13),
-                                        readOnly = TRUE) %>%
-                                hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                                hot_col(8, type = "dropdown", source = country_names) %>%
-                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                                        validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                                hot_col(3:(13 + nrow(DB$cust_var)), 
-                                        valign = "htMiddle",
-                                        halign = "htLeft") %>%
-                                hot_rows(fixedRowsTop = 0) %>%
-                                hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(2, type = "checkbox", width = "auto",
-                                        valign = "htTop", halign = "htCenter") %>%
-                                hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-                            })
-                          }
-                        }
-                      }
-                    }
-                    
-                    # Dynamic save button when rhandsontable changes or new entries
-                    output$edit_entry_table <- renderUI({
-                      if(check_new_entry() & DB$check_new_entries) {
-                        Typing$reload <- FALSE
-                        fluidRow(
-                          column(
-                            width = 8,
-                            align = "left",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: absolute; bottom: -30px; right: -5px', 
-                                          'New entries - reload database')
-                              )
-                            )
-                          ),
-                          column(
-                            width = 4,
-                            actionButton(
-                              "load",
-                              "",
-                              icon = icon("rotate"),
-                              class = "pulsating-button"
-                            )
-                          )
-                        )
-                      } else if(Typing$status == "Attaching") {
-                        fluidRow(
-                          column(
-                            width = 11,
-                            align = "left",
-                            HTML(
-                              paste(
-                                tags$span(style='color: white; font-size: 14px; position: absolute; bottom: -30px; right: -5px', 'No database changes possible - pending entry addition')
-                              )
-                            )
-                          ),
-                          column(
-                            width = 1,
-                            HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px; color:white; margin-top: 10px"></i>'))
-                          )
-                        )
-                      } else if((DB$change == TRUE) | !identical(get.entry.table.meta(), select(DB$meta, -13))) {
-                        
-                        if(!is.null(input$db_entries)) {
-                          fluidRow(
-                            column(
-                              width = 5,
-                              HTML(
-                                paste(
-                                  tags$span(style='color: white; font-size: 16px; position: absolute; bottom: -30px; right: -5px', 'Confirm changes')
-                                )
-                              )
-                            ),
-                            column(
-                              width = 3,
-                              actionButton(
-                                "edit_button",
-                                "",
-                                icon = icon("bookmark"),
-                                class = "pulsating-button"
-                              )
-                            ),
-                            column(
-                              width = 4,
-                              actionButton(
-                                "undo_changes",
-                                "Undo",
-                                icon = icon("repeat")
-                              )
-                            )
-                          )
-                        }
-                      } else {NULL}
-                    })
-                    
-                  })
-                  
-                  # Hide no entry message
-                  output$db_no_entries <- NULL
-                  output$distancematrix_no_entries <- NULL
-                  
-                } else {
-                  
-                  # If database loading not successful dont show entry table
-                  output$db_entries_table <- NULL
-                  output$entry_table_controls <- NULL
-                }
-                
-                # Render Entry table controls
-                output$entry_table_controls <- renderUI({
-                  fluidRow(
-                    column(1),
-                    column(
-                      width = 3,
-                      align = "center",
-                      fluidRow(
-                        column(
-                          width = 4,
-                          align = "center",
-                          actionButton(
-                            "sel_all_entries",
-                            "Select All",
-                            icon = icon("check")
-                          )
-                        ),
-                        column(
-                          width = 4,
-                          align = "left",
-                          actionButton(
-                            "desel_all_entries",
-                            "Deselect All",
-                            icon = icon("xmark")
-                          )
-                        )
-                      )
-                    ),
-                    column(
-                      width = 3,
-                      uiOutput("edit_entry_table")
-                    )
-                  )
-                })
-                
-                #### Render Distance Matrix ----
-                observe({
-                  if(!is.null(DB$data)) {
-                    
-                    if(any(duplicated(DB$meta$`Assembly Name`)) | any(duplicated(DB$meta$`Assembly ID`))) {
-                      output$db_distancematrix <- NULL
-                      
-                      if( (sum(duplicated(DB$meta$`Assembly Name`)) > 0) & (sum(duplicated(DB$meta$`Assembly ID`)) == 0) ) {
-                        duplicated_txt <- paste0(
-                          paste(
-                            paste0("Name  # ", which(duplicated(DB$meta$`Assembly Name`)), " - "),
-                            DB$meta$`Assembly Name`[which(duplicated(DB$meta$`Assembly Name`))]
-                          ),
-                          "<br>"
-                        )
-                      } else if ( (sum(duplicated(DB$meta$`Assembly ID`)) > 0) & (sum(duplicated(DB$meta$`Assembly Name`)) == 0) ){
-                        duplicated_txt <- paste0(
-                          paste(
-                            paste0("ID  # ", which(duplicated(DB$meta$`Assembly ID`)), " - "),
-                            DB$meta$`Assembly ID`[which(duplicated(DB$meta$`Assembly ID`))]
-                          ),
-                          "<br>"
-                        )
-                      } else {
-                        duplicated_txt <- c(
-                          paste0(
-                            paste(
-                              paste0("Name  # ", which(duplicated(DB$meta$`Assembly Name`)), " - "),
-                              DB$meta$`Assembly Name`[which(duplicated(DB$meta$`Assembly Name`))]
-                            ),
-                            "<br>"
-                          ),
-                          paste0(
-                            paste(
-                              paste0("ID  # ", which(duplicated(DB$meta$`Assembly ID`)), " - "),
-                              DB$meta$`Assembly ID`[which(duplicated(DB$meta$`Assembly ID`))]
-                            ),
-                            "<br>"
-                          )
-                        )
-                      }
-                      
-                      output$distancematrix_duplicated <- renderUI({
-                        column(
-                          width = 12,
-                          tags$span(style = "font-size: 15; color: white",
-                                    "Change duplicated entry names to display distance matrix."),
-                          br(), br(), br(),
-                          actionButton("change_entries", "Go to Entry Table", class = "btn btn-default"),
-                          br(), br(), br(),
-                          tags$span(
-                            style = "font-size: 15; color: white",
-                            HTML(
-                              append(
-                                "Duplicated:",
-                                append(
-                                  "<br>",
-                                  duplicated_txt
-                                )
-                              )
-                            )
-                          )
-                        )
-                      })
-                    } else {
-                      output$distancematrix_duplicated <- NULL
-                      if(!is.null(DB$data) & !is.null(DB$allelic_profile) & !is.null(DB$allelic_profile_true) & !is.null(DB$cust_var) & !is.null(input$distmatrix_label) & !is.null(input$distmatrix_diag) & !is.null(input$distmatrix_triangle)) {
-                        output$db_distancematrix <- renderRHandsontable({
-                          rhandsontable(hamming_df(), 
-                                        digits = 1, 
-                                        readOnly = TRUE,
-                                        contextMenu = FALSE,
-                                        highlightCol = TRUE, 
-                                        highlightRow = TRUE,
-                                        height = distancematrix_height(), rowHeaders = NULL) %>%
-                            hot_heatmap(renderer = paste0("
-                            function (instance, td, row, col, prop, value, cellProperties) {
-                              Handsontable.renderers.TextRenderer.apply(this, arguments);
-                              heatmapScale  = chroma.scale(['#17F556', '#ED6D47']);
-                            
-                              if (instance.heatmap[col]) {
-                                mn = ", DB$matrix_min, ";
-                                mx = ", DB$matrix_max, ";
-                            
-                                pt = (parseInt(value, 10) - mn) / (mx - mn);    
-                            
-                                td.style.backgroundColor = heatmapScale(pt).hex();
-                              }
-                            }")) %>%
-                            hot_rows(fixedRowsTop = 0) %>%
-                            hot_cols(fixedColumnsLeft = 1) %>%
-                            hot_col(1:(dim(DB$ham_matrix)[1]+1),
-                                    halign = "htCenter",
-                                    valign = "htMiddle") %>%
-                            hot_col(1, renderer = "
-                            function(instance, td, row, col, prop, value, cellProperties) {
-                              Handsontable.renderers.NumericRenderer.apply(this, arguments);
-                              td.style.background = '#F0F0F0'
-                            }"
-                            )
-                        })  
-                      }
-                    }
-                    
-                    # Render Distance Matrix UI
-                    
-                    output$distmatrix_show <- renderUI({
-                      if(!is.null(DB$data)) {
-                        if(nrow(DB$data) > 1) {
-                          column(
-                            width = 10,
-                            uiOutput("distancematrix_duplicated"),
-                            div(
-                              class = "distmatrix",
-                              rHandsontableOutput("db_distancematrix")
-                            )
-                          )
-                        } else {
-                          column(
-                            width = 10,
-                            align = "left",
-                            p(
-                              HTML(
-                                paste(
-                                  tags$span(style='color: white; font-size: 15px;', "Type at least two assemblies to display a distance matrix.")
-                                )
-                              )
-                            ),
-                            br(),
-                            br()
-                          )
-                        }
-                      }
-                    })
-                    
-                  }
-                })
-                
-                
-                # Render delete entry box UI
-                output$delete_box <- renderUI({
-                  box(
-                    solidHeader = TRUE,
-                    status = "primary",
-                    width = "100%",
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "center",
-                        h3(p("Delete Entries"), style = "color:white")
-                      )
-                    ),
-                    hr(),
-                    fluidRow(
-                      column(
-                        width = 2,
-                        offset = 1,
-                        align = "right",
-                        br(),
-                        h5("Index", style = "color:white; margin-bottom: 0px;")
-                      ),
-                      column(
-                        width = 6,
-                        align = "center",
-                        uiOutput("delete_select")
-                      ),
-                      column(
-                        width = 2,
-                        align = "center",
-                        br(),
-                        uiOutput("del_bttn")
-                      )
-                    ),
-                    br()
-                  )
-                })
-                
-                # Render loci comparison box UI
-                output$compare_allele_box <- renderUI({
-                  box(
-                    solidHeader = TRUE,
-                    status = "primary",
-                    width = "100%",
-                    fluidRow(
-                      column(
-                        width = 12,
-                        align = "center",
-                        h3(p("Compare Loci"), style = "color:white")
-                      )
-                    ),
-                    hr(),
-                    column(
-                      width = 12,
-                      align = "center",
-                      br(),
-                      uiOutput("compare_select"),
-                      br(),
-                      column(2),
-                      column(
-                        width = 10,
-                        align = "left",
-                        uiOutput("compare_difference_box")
-                      )
-                    ),
-                    br()
-                  )
-                })
-                
-                # Render entry table download box UI
-                output$download_entries <- renderUI({
-                  fluidRow(
-                    column(
-                      width = 12,
-                      box(
-                        solidHeader = TRUE,
-                        status = "primary",
-                        width = "100%",
-                        fluidRow(
-                          column(
-                            width = 12,
-                            align = "center",
-                            h3(p("Download Table"), style = "color:white")
-                          )
-                        ),
-                        hr(),
-                        fluidRow(
-                          column(2),
-                          column(
-                            width = 10,
-                            align = "left",
-                            br(),
-                            div(
-                              class = "mat-switch-db",
-                              materialSwitch(
-                                "download_table_include",
-                                h5(p("Only Included Entries"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            ),
-                            div(
-                              class = "mat-switch-db",
-                              materialSwitch(
-                                "download_table_loci",
-                                h5(p("Include Displayed Loci"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-                                value = FALSE,
-                                right = TRUE
-                              )
-                            ),
-                            br(),
-                          )
-                        ),
-                        fluidRow(
-                          column(
-                            width = 12,
-                            align = "center",
-                            downloadBttn(
-                              "download_entry_table",
-                              style = "simple",
-                              label = "",
-                              size = "sm",
-                              icon = icon("download"),
-                              color = "primary"
-                            )
-                          )
-                        ),
-                        br()
-                      )
-                    ),
-                    column(
-                      width = 12,
-                      fluidRow(
-                        column(
-                          width = 2,
-                          div(
-                            class = "rectangle-blue" 
-                          ),
-                          div(
-                            class = "rectangle-orange" 
-                          ),
-                          div(
-                            class = "rectangle-red" 
-                          ),
-                          div(
-                            class = "rectangle-green" 
-                          )
-                        ),
-                        column(
-                          width = 10,
-                          align = "left",
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -12px", " = included for analyses")
-                              )
-                            )
-                          ),
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -13px", " =  duplicated name/ID")
-                              )
-                            )
-                          ),
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -14px", " =  ≥ 5% of loci missing")
-                              )
-                            )
-                          ),
-                          p(
-                            HTML(
-                              paste(
-                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -15px", " =  locus contains multiple variants")
-                              )
-                            )
-                          ),
-                        )
-                      )
-                    )
-                  )
-                })
-                
-                # Render entry deletion select input
-                output$delete_select <- renderUI({
-                  pickerInput("select_delete",
-                              label = "",
-                              choices = DB$data[, "Index"],
-                              options = list(
-                                `live-search` = TRUE,
-                                `actions-box` = TRUE,
-                                size = 10,
-                                style = "background-color: white; border-radius: 5px;"
-                              ),
-                              multiple = TRUE)
-                })
-                
-                # Render delete entry button
-                output$del_bttn <- renderUI({
-                  actionBttn(
-                    "del_button",
-                    label = "",
-                    color = "danger",
-                    size = "sm",
-                    style = "material-circle",
-                    icon = icon("xmark")
-                  )
-                })
-                
-                #### Missing Values UI ----
-                
-                # Missing values calculations and table 
-                observe({
-                  
-                  if (!is.null(DB$allelic_profile)) {
-                    NA_table <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) != 0]
-                    
-                    NA_table <- NA_table[rowSums(is.na(NA_table)) != 0,]
-                    
-                    NA_table[is.na(NA_table)] <- "NA"
-                    
-                    NA_table <- NA_table %>% 
-                      cbind("Assembly Name" = DB$meta[rownames(NA_table),]$`Assembly Name`) %>%
-                      cbind("Errors" = DB$meta[rownames(NA_table),]$Errors) %>%
-                      relocate("Assembly Name", "Errors")
-                    
-                    DB$na_table <- NA_table
-                    
-                    if(!is.null(input$miss_val_height)) {
-                      if(nrow(DB$na_table) < 31) {
-                        output$table_missing_values <- renderRHandsontable({
-                          rhandsontable(
-                            DB$na_table,
-                            readOnly = TRUE,
-                            rowHeaders = NULL,
-                            contextMenu = FALSE,
-                            highlightCol = TRUE, 
-                            highlightRow = TRUE,
-                            error_highlight = err_thresh_na() - 1
-                          ) %>%
-                            hot_cols(fixedColumnsLeft = 1) %>%
-                            hot_rows(fixedRowsTop = 0) %>%
-                            hot_col(1:ncol(DB$na_table), valign = "htMiddle", halign = "htLeft") %>%
-                            hot_col(2, renderer = "
-                            function (instance, td, row, col, prop, value, cellProperties) {
-                              Handsontable.renderers.TextRenderer.apply(this, arguments);
-                              if (instance.params) {
-                                hrows = instance.params.error_highlight
-                                hrows = hrows instanceof Array ? hrows : [hrows]
-                                if (hrows.includes(row)) { 
-                                  td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
-                                }
-                              }
-                            }") %>%
-                            hot_col(3:ncol(DB$na_table), renderer = htmlwidgets::JS(
-                              "function(instance, td, row, col, prop, value, cellProperties) {
-                                if (value.length > 8) {
-                                  value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                                }
-                                td.innerHTML = value;
-                                td.style.textAlign = 'center';
-                                return td;
-                               }"
-                            ))
-                        })
-                      } else {
-                        output$table_missing_values <- renderRHandsontable({
-                          rhandsontable(
-                            DB$na_table,
-                            readOnly = TRUE,
-                            rowHeaders = NULL,
-                            height = miss.val.height(),
-                            contextMenu = FALSE,
-                            highlightCol = TRUE, 
-                            highlightRow = TRUE,
-                            error_highlight = err_thresh() - 1
-                          ) %>%
-                            hot_cols(fixedColumnsLeft = 1) %>%
-                            hot_rows(fixedRowsTop = 0) %>%
-                            hot_col(1:ncol(DB$na_table), valign = "htMiddle", halign = "htLeft") %>%
-                            hot_col(2, renderer = "
-                            function (instance, td, row, col, prop, value, cellProperties) {
-                              Handsontable.renderers.TextRenderer.apply(this, arguments);
-                              if (instance.params) {
-                                hrows = instance.params.error_highlight
-                                hrows = hrows instanceof Array ? hrows : [hrows]
-                                if (hrows.includes(row)) { 
-                                  td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
-                                }
-                              }
-                            }") %>%
-                            hot_col(3:ncol(DB$na_table), renderer = htmlwidgets::JS(
-                              "function(instance, td, row, col, prop, value, cellProperties) {
-                                if (value.length > 8) {
-                                  value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                                }
-                                td.innerHTML = value;
-                                td.style.textAlign = 'center';
-                                return td;
-                               }"
-                            ))
-                        })
-                      }
-                    }
-                  }
-                  
-                })
-                
-                # Render missing value informatiojn box UI
-                output$missing_values <- renderUI({
-                  div(
-                    class = "miss_val_box",
-                    box(
-                      solidHeader = TRUE,
-                      status = "primary",
-                      width = "100%",
-                      fluidRow(
-                        div(
-                          class = "white",
-                          column(
-                            width = 12,
-                            align = "left",
-                            br(), 
-                            HTML(
-                              paste0("There are ", 
-                                     strong(as.character(sum(is.na(DB$data)))), 
-                                     " unsuccessful allele allocations (NA). ",
-                                     strong(sum(sapply(DB$allelic_profile, anyNA))),
-                                     " out of ",
-                                     strong(ncol(DB$allelic_profile)),
-                                     " total loci in this scheme contain NA's (",
-                                     strong(round((sum(sapply(DB$allelic_profile, anyNA)) / ncol(DB$allelic_profile) * 100), 1)),
-                                     " %). ",
-                                     "Decide how these missing values should be treated:")
-                              
-                            ),
-                            br()
-                          )
-                        )
-                      ),
-                      fluidRow(
-                        column(1),
-                        column(
-                          width = 11,
-                          align = "left",
-                          br(),
-                          prettyRadioButtons(
-                            "na_handling",
-                            "",
-                            choiceNames = c("Ignore missing values for pairwise comparison",
-                                            "Omit loci with missing values for all assemblies",
-                                            "Treat missing values as allele variant"),
-                            choiceValues = c("ignore_na", "omit", "category"),
-                            shape = "curve",
-                            selected = c("ignore_na")
-                          ),
-                          br()
-                        )
-                      )
-                    )
-                  )
-                })  
-                
-              } else { 
-                #if no typed assemblies present
-                
-                # null underlying database
-                
-                DB$data <- NULL
-                DB$meta <- NULL
-                DB$meta_gs <- NULL
-                DB$meta_true <- NULL
-                DB$allelic_profile <- NULL
-                DB$allelic_profile_trunc <- NULL
-                DB$allelic_profile_true <- NULL
-                
-                # Render menu without missing values tab
-                output$menu <- renderMenu(
-                  sidebarMenu(
-                    menuItem(
-                      text = "Database Browser",
-                      tabName = "database",
-                      icon = icon("hard-drive"),
-                      startExpanded = TRUE,
-                      selected = TRUE,
-                      menuSubItem(
-                        text = "Browse Entries",
-                        tabName = "db_browse_entries"
-                      ),
-                      menuSubItem(
-                        text = "Scheme Info",
-                        tabName = "db_schemeinfo"
-                      ),
-                      menuSubItem(
-                        text = "Loci Info",
-                        tabName = "db_loci_info"
-                      ),
-                      menuSubItem(
-                        text = "Distance Matrix",
-                        tabName = "db_distmatrix"
-                      )
-                    ),
-                    menuItem(
-                      text = "Manage Schemes",
-                      tabName = "init",
-                      icon = icon("layer-group")
-                    ),
-                    menuItem(
-                      text = "Allelic Typing",
-                      tabName = "typing",
-                      icon = icon("gears")
-                    ),
-                    menuItem(
-                      text = "Resistance Profile",
-                      tabName = "gene_screening",
-                      icon = icon("dna"),
-                      startExpanded = TRUE,
-                      menuSubItem(
-                        text = "Browse Entries",
-                        tabName = "gs_profile"
-                      ),
-                      menuSubItem(
-                        text = "Screening",
-                        tabName = "gs_screening"
-                      )
-                    ),
-                    menuItem(
-                      text = "Visualization",
-                      tabName = "visualization",
-                      icon = icon("circle-nodes")
-                    ),
-                    menuItem(
-                      text = "Utilities",
-                      tabName = "utilities",
-                      icon = icon("screwdriver-wrench")
-                    )
-                  )
-                )
-                
-                observe({
-                  if(is.null(DB$data)) {
-                    if(check_new_entry()) {
-                      output$db_no_entries <- renderUI(
-                        column(
-                          width = 12,
-                          fluidRow(
-                            column(1),
-                            column(
-                              width = 3,
-                              align = "left",
-                              HTML(
-                                paste(
-                                  tags$span(style='color: white; font-size: 15px; position: absolute; bottom: -30px; right: -5px', 'New entries - reload database')
-                                )
-                              )
-                            ),
-                            column(
-                              width = 4,
-                              actionButton(
-                                "load",
-                                "",
-                                icon = icon("rotate"),
-                                class = "pulsating-button"
-                              )
-                            )
-                          )
-                        )
-                      )
-                    } else {
-                      output$db_no_entries <- renderUI(
-                        column(
-                          width = 12,
-                          fluidRow(
-                            column(1),
-                            column(
-                              width = 11,
-                              align = "left",
-                              HTML(
-                                paste(
-                                  "<span style='color: white;'>",
-                                  "No Entries for this scheme available.\n",
-                                  "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
-                                  sep = '<br/>'
-                                )
-                              )
-                            )
-                          )
-                        )
-                      )
-                    }
-                  }
-                })
-                
-                output$distancematrix_no_entries <- renderUI(
-                  fluidRow(
-                    column(1),
-                    column(
-                      width = 11,
-                      align = "left",
-                      HTML(paste(
-                        "<span style='color: white;'>",
-                        "No Entries for this scheme available.",
-                        "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
-                        sep = '<br/>'
-                      ))
-                    )
-                  )
-                )
-                
-                output$db_entries <- NULL
-                output$edit_index <- NULL
-                output$edit_scheme_d <- NULL
-                output$edit_entries <- NULL
-                output$compare_select <- NULL
-                output$delete_select <- NULL
-                output$del_bttn <- NULL
-                output$compare_allele_box <- NULL
-                output$download_entries <- NULL
-                output$missing_values <- NULL
-                output$delete_box <- NULL
-                output$entry_table_controls <- NULL
-                output$multi_stop <- NULL
-                output$metadata_multi_box <- NULL
-                output$start_multi_typing_ui <- NULL
-                output$pending_typing <- NULL
-                output$multi_typing_results <- NULL
-                output$single_typing_progress <- NULL
-                output$metadata_single_box <- NULL
-                output$start_typing_ui <- NULL
-                
-                output$initiate_typing_ui <- renderUI({
-                  column(
-                    width = 4,
-                    align = "center",
-                    br(),
-                    br(),
-                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-                    br(),
-                    br(),
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "center",
-                        shinyFilesButton(
-                          "genome_file",
-                          "Browse" ,
-                          icon = icon("file"),
-                          title = "Select the assembly in .fasta/.fna/.fa format:",
-                          multiple = FALSE,
-                          buttonType = "default",
-                          class = NULL,
-                          root = path_home()
-                        ),
-                        br(),
-                        br(),
-                        uiOutput("genome_path"),
-                        br()
-                      )
-                    )
-                  )
-                })
-                
-                output$initiate_typing_ui <- renderUI({
-                  column(
-                    width = 4,
-                    align = "center",
-                    br(),
-                    br(),
-                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-                    br(),
-                    br(),
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "center",
-                        shinyFilesButton(
-                          "genome_file",
-                          "Browse" ,
-                          icon = icon("file"),
-                          title = "Select the assembly in .fasta/.fna/.fa format:",
-                          multiple = FALSE,
-                          buttonType = "default",
-                          class = NULL,
-                          root = path_home()
-                        ),
-                        br(),
-                        br(),
-                        uiOutput("genome_path"),
-                        br()
-                      )
-                    )
-                  )
-                })
-                
-                output$initiate_multi_typing_ui <- renderUI({
-                  column(
-                    width = 4,
-                    align = "center",
-                    br(),
-                    br(),
-                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-                    br(), br(),
-                    p(
-                      HTML(
-                        paste(
-                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
-                        )
-                      )
-                    ),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "center",
-                        shinyDirButton(
-                          "genome_file_multi",
-                          "Browse",
-                          icon = icon("folder-open"),
-                          title = "Select the folder containing the genome assemblies (FASTA)",
-                          buttonType = "default",
-                          root = path_home()
-                        ),
-                        br(),
-                        br(),
-                        uiOutput("multi_select_info"),
-                        br()
-                      )
-                    ),
-                    uiOutput("multi_select_tab_ctrls"),
-                    br(),
-                    fluidRow(
-                      column(1),
-                      column(
-                        width = 11,
-                        align = "left",
-                        rHandsontableOutput("multi_select_table")
-                      )
-                    )
-                  )
-                })
-              }
-            }
-          }
-        }
-      } else {
-        
-        log_print("Invalid scheme folder")
-        show_toast(
-          title = "Invalid scheme folder",
-          type = "warning",
-          position = "bottom-end",
-          timer = 4000
-        )
-      }
-    }
-    
-  })
-  
-  # _______________________ ####
-  
-  ## Database ----
-  
-  ### Conditional UI Elements rendering ----
-  
-  # Contro custom variables table
-  output$cust_var_select <- renderUI({
-    if(nrow(DB$cust_var) > 5) {
-      selectInput(
-        "cust_var_select",
-        "",
-        choices = 1:ceiling(nrow(DB$cust_var) / 5 )
-      )
-    }
-  })
-  
-  output$cust_var_info <- renderUI({
-    if((!is.null(DB$cust_var)) & (!is.null(input$cust_var_select))) {
-      if(nrow(DB$cust_var) > 5) {
-        low <- -4
-        high <- 0
-        for (i in 1:input$cust_var_select) {
-          low <- low + 5
-          if((nrow(DB$cust_var) %% 5) != 0) {
-            if(i == ceiling(nrow(DB$cust_var) / 5 )) {
-              high <- high + nrow(DB$cust_var) %% 5
-            } else {
-              high <- high + 5
-            }
-          } else {
-            high <- high + 5
-          }
-        }
-        h5(paste0("Showing ", low, " to ", high," of ", nrow(DB$cust_var), " variables"), style = "color: white; font-size: 10px;")
-      }
-    }
-  })
-  
-  # Message on Database tabs if no scheme available yet
-  observe({
-    if(!is.null(DB$exist)) {
-      if(DB$exist){
-        
-        # Message for tab Browse Entries
-        output$no_scheme_entries <- renderUI({
-          fluidRow(
-            column(1),
-            column(
-              width = 4,
-              align = "left",
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'No scheme available.')
-                  )
-                )
-              ),
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'Download a scheme first and type assemblies in the section Allelic Typing.')
-                  )
-                )
-              )
-            )
-          )
-        })
-        
-        # Message for Tab Scheme Info
-        output$no_scheme_info <- renderUI({
-          fluidRow(
-            column(1),
-            column(
-              width = 10,
-              align = "left",
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'No scheme available.')
-                  )
-                )
-              ),
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'Download a scheme first and type assemblies in the section Allelic Typing.')
-                  )
-                )
-              )
-            )
-          )
-        })
-        
-        # Message for Tab Distance Matrix
-        output$no_scheme_distancematrix <- renderUI({
-          fluidRow(
-            column(1),
-            column(
-              width = 10,
-              align = "left",
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'No scheme available.')
-                  )
-                )
-              ),
-              p(
-                HTML(
-                  paste(
-                    tags$span(style='color: white; font-size: 15px; ', 
-                              'Download a scheme first and type assemblies in the section Allelic Typing.')
-                  )
-                )
-              )
-            )
-          )
-        })
-        
-      } else {
-        output$no_scheme_entries <- NULL
-        output$no_scheme_info <- NULL
-        output$no_scheme_distancematrix <- NULL
-      }
-    }
-    
-  })
-  
-  observe({
-    # Conditional Missing Values Tab
-    if(!is.null(DB$allelic_profile)) {
-      if(anyNA(DB$allelic_profile)) {
-        if(DB$no_na_switch == FALSE) {
-          output$menu <- renderMenu(
-            sidebarMenu(
-              menuItem(
-                text = "Database Browser",
-                tabName = "database",
-                icon = icon("hard-drive"),
-                startExpanded = TRUE,
-                menuSubItem(
-                  text = "Browse Entries",
-                  tabName = "db_browse_entries"
-                ),
-                menuSubItem(
-                  text = "Scheme Info",
-                  tabName = "db_schemeinfo"
-                ),
-                menuSubItem(
-                  text = "Loci Info",
-                  tabName = "db_loci_info"
-                ),
-                menuSubItem(
-                  text = "Distance Matrix",
-                  tabName = "db_distmatrix"
-                ),
-                menuSubItem(
-                  text = "Missing Values",
-                  tabName = "db_missing_values",
-                  selected = TRUE,
-                  icon = icon("triangle-exclamation")
-                )
-              ),
-              menuItem(
-                text = "Manage Schemes",
-                tabName = "init",
-                icon = icon("layer-group")
-              ),
-              menuItem(
-                text = "Allelic Typing",
-                tabName = "typing",
-                icon = icon("gears")
-              ),
-              menuItem(
-                text = "Resistance Profile",
-                tabName = "gene_screening",
-                icon = icon("dna"),
-                startExpanded = TRUE,
-                menuSubItem(
-                  text = "Browse Entries",
-                  tabName = "gs_profile"
-                ),
-                menuSubItem(
-                  text = "Screening",
-                  tabName = "gs_screening"
-                )
-              ),
-              menuItem(
-                text = "Visualization",
-                tabName = "visualization",
-                icon = icon("circle-nodes")
-              ),
-              menuItem(
-                text = "Utilities",
-                tabName = "utilities",
-                icon = icon("screwdriver-wrench")
-              )
-            )
-          )
-        }
-        
-      } else {
-        output$menu <- renderMenu(
-          sidebarMenu(
-            menuItem(
-              text = "Database Browser",
-              tabName = "database",
-              icon = icon("hard-drive"),
-              startExpanded = TRUE,
-              menuSubItem(
-                text = "Browse Entries",
-                tabName = "db_browse_entries"
-              ),
-              menuSubItem(
-                text = "Scheme Info",
-                tabName = "db_schemeinfo"
-              ),
-              menuSubItem(
-                text = "Loci Info",
-                tabName = "db_loci_info"
-              ),
-              menuSubItem(
-                text = "Distance Matrix",
-                tabName = "db_distmatrix"
-              )
-            ),
-            menuItem(
-              text = "Manage Schemes",
-              tabName = "init",
-              icon = icon("layer-group")
-            ),
-            menuItem(
-              text = "Allelic Typing",
-              tabName = "typing",
-              icon = icon("gears")
-            ),
-            menuItem(
-              text = "Resistance Profile",
-              tabName = "gene_screening",
-              icon = icon("dna"),
-              startExpanded = TRUE,
-              menuSubItem(
-                text = "Browse Entries",
-                tabName = "gs_profile"
-              ),
-              menuSubItem(
-                text = "Screening",
-                tabName = "gs_screening"
-              )
-            ),
-            menuItem(
-              text = "Visualization",
-              tabName = "visualization",
-              icon = icon("circle-nodes")
-            ),
-            menuItem(
-              text = "Utilities",
-              tabName = "utilities",
-              icon = icon("screwdriver-wrench")
-            )
-          )
-        )
-      }
-    }
-    
-  })
-  
-  observe({
-    
-    if (!is.null(DB$available)) {
-      output$scheme_db <- renderUI({
-        if (length(DB$available) > 5) {
-          selectInput(
-            "scheme_db",
-            label = "",
-            choices = if(!is.null(Typing$last_scheme)) {
-              Typing$last_scheme
-            } else {DB$available},
-            selected = if(!is.null(Typing$last_scheme)) {
-              Typing$last_scheme
-            } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}
-          )
-        } else {
-          prettyRadioButtons(
-            "scheme_db",
-            label = "",
-            choices = if(!is.null(Typing$last_scheme)) {
-              Typing$last_scheme
-            } else {DB$available},
-            selected = if(!is.null(Typing$last_scheme)) {
-              Typing$last_scheme
-            } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}
-          )
-        }
-      })
-      
-      if (!is.null(DB$schemeinfo)) {
-        
-        output$scheme_info <- renderTable({
-          DB$schemeinfo
-        })
-        
-        output$scheme_header <- renderUI(h3(p("cgMLST Scheme"), style = "color:white"))
-        
-      } else {
-        
-        output$scheme_info <- NULL
-        output$scheme_header <- NULL
-        
-      }
-      
-      if (!is.null(DB$loci_info)) {
-        loci_info <- DB$loci_info
-        names(loci_info)[6] <- "Allele Count"
-        
-        output$db_loci <- renderDataTable(
-          loci_info,
-          selection = "single",
-          options = list(pageLength = 10,
-                         columnDefs = list(list(searchable = TRUE,
-                                                targets = "_all")),
-                         initComplete = DT::JS(
-                           "function(settings, json) {",
-                           "$('th:first-child').css({'border-top-left-radius': '5px'});",
-                           "$('th:last-child').css({'border-top-right-radius': '5px'});",
-                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                           "}"
-                         ),
-                         drawCallback = DT::JS(
-                           "function(settings) {",
-                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                           "}"
-                         ))
-        )
-        
-        output$loci_header <- renderUI(h3(p("Loci"), style = "color:white"))
-        
-      } else {
-        output$db_loci <- NULL
-        output$loci_header <- NULL
-      }
-    } 
-  })
-  
-  # If only one entry available disable varying loci checkbox
-  
-  output$compare_difference_box <- renderUI({
-    if(!is.null(DB$data)) {
-      if(nrow(DB$data) > 1) {
-        div(
-          class = "mat-switch-db",
-          materialSwitch(
-            "compare_difference",
-            h5(p("Only Varying Loci"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
-            value = FALSE,
-            right = TRUE
-          )
-        )
-      }
-    }
-  })
-  
-  ### Database Events ----
-  
-  # Invalid entries table input
-  observe({
-    req(DB$data, input$db_entries)
-    if (isTRUE(input$invalid_date)) {
-      show_toast(
-        title = "Invalid date",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-      DB$inhibit_change <- TRUE
-    } else if (isTRUE(input$empty_name)) {
-      show_toast(
-        title = "Empty name",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-      DB$inhibit_change <- TRUE
-    } else if (isTRUE(input$empty_id)) {
-      show_toast(
-        title = "Empty ID",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-      DB$inhibit_change <- TRUE
-    } else {
-      DB$inhibit_change <- FALSE
-    }
-  })
-  
-  # Change scheme
-  observeEvent(input$reload_db, {
-    log_print("Input reload_db")
-    
-    if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
-      show_toast(
-        title = "Pending Multi Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
-      show_toast(
-        title = "Pending Single Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if(Screening$status == "started") {
-      show_toast(
-        title = "Pending Screening",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      showModal(
-        modalDialog(
-          selectInput(
-            "scheme_db",
-            label = "",
-            choices = DB$available,
-            selected = DB$scheme),
-          title = "Select a local database to load.",
-          easyClose = TRUE,
-          footer = tagList(
-            modalButton("Cancel"),
-            actionButton("load", "Load", class = "btn btn-default")
-          )
-        )
-      )
-    }
-  })
-  
-  # Create new database
-  observe({
-    shinyDirChoose(input,
-                   "create_new_db",
-                   roots = c(Home = path_home(), Root = "/"),
-                   defaultRoot = "Home",
-                   session = session)
-    
-    if(!is.null(input$create_new_db)) {
-      DB$new_database <- as.character(
-        parseDirPath(
-          roots = c(Home = path_home(), Root = "/"),
-          input$create_new_db
-        )
-      )
-    }
-  })
-  
-  # Undo db changes
-  observeEvent(input$undo_changes, {
-    log_print("Input undo_changes")
-    
-    DB$inhibit_change <- FALSE
-    
-    Data <- readRDS(paste0(
-      DB$database, "/",
-      gsub(" ", "_", DB$scheme),
-      "/Typing.rds"
-    ))
-    
-    DB$data <- Data[["Typing"]]
-    
-    if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-      cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-      DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
-    } else {
-      DB$cust_var <- data.frame()
-    }
-    
-    DB$change <- FALSE
-    DB$count <- 0
-    DB$no_na_switch <- TRUE
-    DB$meta_gs <- select(DB$data, c(1, 3:13))
-    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
-    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-    DB$deleted_entries <- character(0)
-    
-    observe({
-      if (!is.null(DB$data)) {
-        if (nrow(DB$data) == 1) {
-          if(!is.null(DB$data) & !is.null(DB$cust_var)) {
-            output$db_entries <- renderRHandsontable({
-              rhandsontable(
-                select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                error_highlight = err_thresh() - 1,                              
-                rowHeaders = NULL,
-                contextMenu = FALSE,
-                highlightCol = TRUE, 
-                highlightRow = TRUE
-              ) %>%
-                hot_col(1, 
-                        valign = "htMiddle",
-                        halign = "htCenter") %>%
-                hot_col(3, readOnly = TRUE) %>%
-                hot_col(c(1, 5, 10, 11, 12, 13),
-                        readOnly = TRUE) %>%
-                hot_col(3:(13 + nrow(DB$cust_var)), 
-                        valign = "htMiddle",
-                        halign = "htLeft") %>%
-                hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                hot_col(8, type = "dropdown", source = country_names) %>%
-                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                        validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                hot_cols(fixedColumnsLeft = 1) %>%
-                hot_col(2, type = "checkbox", width = "auto",
-                        valign = "htTop",
-                        halign = "htCenter") %>%
-                hot_rows(fixedRowsTop = 0) %>%
-                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-            })
-          }
-        } else if (between(nrow(DB$data), 1, 40)) {
-          if (length(input$compare_select) > 0) {
-            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
-              output$db_entries <- renderRHandsontable({
-                
-                entry_data <- DB$data %>%
-                  select(1:(13 + nrow(DB$cust_var))) %>%
-                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
-                
-                rhandsontable(
-                  entry_data,
-                  col_highlight = diff_allele() - 1,
-                  dup_names_high = duplicated_names() - 1,
-                  dup_ids_high = duplicated_ids() - 1,
-                  row_highlight = true_rows() - 1,
-                  error_highlight = err_thresh() - 1,
-                  rowHeaders = NULL,
-                  highlightCol = TRUE, 
-                  highlightRow = TRUE,
-                  contextMenu = FALSE
-                )  %>%
-                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
-                          valign = "htMiddle",
-                          halign = "htCenter",
-                          readOnly = TRUE) %>%
-                  hot_col(1, 
-                          valign = "htMiddle",
-                          halign = "htCenter") %>%
-                  hot_col(3, readOnly = TRUE) %>%
-                  hot_col(c(1, 5, 10, 11, 12, 13),
-                          readOnly = TRUE) %>%
-                  hot_col(3:(13 + nrow(DB$cust_var)), 
-                          valign = "htMiddle",
-                          halign = "htLeft") %>%
-                  hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(8, type = "dropdown", source = country_names) %>%
-                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                          validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                  hot_col(2, type = "checkbox", width = "auto",
-                          valign = "htTop",
-                          halign = "htCenter",
-                          strict = TRUE,
-                          allowInvalid = FALSE,
-                          copyable = TRUE) %>%
-                  hot_cols(fixedColumnsLeft = 1) %>%
-                  hot_rows(fixedRowsTop = 0) %>%
-                  hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-  
-                       }
-              }") %>%
-                  hot_col(diff_allele(),
-                          renderer = "
-                  function(instance, td, row, col, prop, value, cellProperties) {
-                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
-  
-                    if (instance.params) {
-                          hcols = instance.params.col_highlight;
-                          hcols = hcols instanceof Array ? hcols : [hcols];
-                        }
-  
-                    if (instance.params && hcols.includes(col)) {
-                      td.style.background = 'rgb(116, 188, 139)';
-                    }
-                }"
-                  ) %>%
-                  hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-              })
-            }
-          } else {
-            if(!is.null(DB$data) & !is.null(DB$cust_var)) {
-              output$db_entries <- renderRHandsontable({
-                rhandsontable(
-                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                  rowHeaders = NULL,
-                  row_highlight = true_rows() - 1,
-                  dup_names_high = duplicated_names()- 1,
-                  dup_ids_high = duplicated_ids() - 1,
-                  error_highlight = err_thresh() - 1,
-                  contextMenu = FALSE,
-                  highlightCol = TRUE, 
-                  highlightRow = TRUE
-                ) %>%
-                  hot_cols(fixedColumnsLeft = 1) %>%
-                  hot_col(1, 
-                          valign = "htMiddle",
-                          halign = "htCenter") %>%
-                  hot_col(3, readOnly = TRUE) %>%
-                  hot_col(c(1, 5, 10, 11, 12, 13),
-                          readOnly = TRUE) %>%
-                  hot_col(3:(13 + nrow(DB$cust_var)), 
-                          valign = "htMiddle",
-                          halign = "htLeft") %>%
-                  hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(8, type = "dropdown", source = country_names) %>%
-                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                          validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                  hot_col(2, type = "checkbox", width = "auto",
-                          valign = "htTop",
-                          halign = "htCenter") %>%
-                  hot_rows(fixedRowsTop = 0) %>%
-                  hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-  
-                       }
-              }") %>%
-                  hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-              })    
-            }
-          }
-        } else {
-          if (length(input$compare_select) > 0) {
-            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
-              output$db_entries <- renderRHandsontable({
-                
-                entry_data <- DB$data %>%
-                  select(1:(13 + nrow(DB$cust_var))) %>%
-                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
-                
-                rhandsontable(
-                  entry_data,
-                  col_highlight = diff_allele() - 1,
-                  rowHeaders = NULL,
-                  height = table_height(),
-                  row_highlight = true_rows() - 1,
-                  dup_names_high = duplicated_names() - 1,
-                  dup_ids_high = duplicated_ids() - 1,
-                  error_highlight = err_thresh() - 1,
-                  contextMenu = FALSE,
-                  highlightCol = TRUE, 
-                  highlightRow = TRUE
-                ) %>%
-                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
-                          readOnly = TRUE, 
-                          valign = "htMiddle",
-                          halign = "htCenter") %>%
-                  hot_col(3:(13 + nrow(DB$cust_var)), 
-                          valign = "htMiddle",
-                          halign = "htLeft") %>%
-                  hot_col(3, readOnly = TRUE) %>%
-                  hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(c(1, 5, 10, 11, 12, 13),
-                          readOnly = TRUE) %>%
-                  hot_col(8, type = "dropdown", source = country_names) %>%
-                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                          validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                  hot_col(1, 
-                          valign = "htMiddle",
-                          halign = "htCenter") %>%
-                  hot_col(2, type = "checkbox", width = "auto",
-                          valign = "htTop",
-                          halign = "htCenter",
-                          allowInvalid = FALSE,
-                          copyable = TRUE) %>%
-                  hot_cols(fixedColumnsLeft = 1) %>%
-                  hot_rows(fixedRowsTop = 0) %>%
-                  hot_col(1, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.row_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                                                             }
-                                                           }
-                                                       }") %>%
-                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") %>%
-                  hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(diff_allele(),
-                          renderer = "
-                  function(instance, td, row, col, prop, value, cellProperties) {
-                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
-  
-                    if (instance.params) {
-                          hcols = instance.params.col_highlight;
-                          hcols = hcols instanceof Array ? hcols : [hcols];
-                        }
-  
-                    if (instance.params && hcols.includes(col)) {
-                      td.style.background = 'rgb(116, 188, 139)';
-                    }
-                }") 
-              })    
-            }
-          } else {
-            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
-              output$db_entries <- renderRHandsontable({
-                rhandsontable(
-                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
-                  rowHeaders = NULL,
-                  height = table_height(),
-                  dup_names_high = duplicated_names() - 1,
-                  dup_ids_high = duplicated_ids() - 1,
-                  row_highlight = true_rows() - 1,
-                  error_highlight = err_thresh() - 1,
-                  contextMenu = FALSE,
-                  highlightCol = TRUE, 
-                  highlightRow = TRUE
-                ) %>%
-                  hot_cols(fixedColumnsLeft = 1) %>%
-                  hot_col(1, 
-                          valign = "htMiddle",
-                          halign = "htCenter") %>%
-                  hot_col(c(1, 5, 10, 11, 12, 13),
-                          readOnly = TRUE) %>%
-                  hot_col(3, readOnly = TRUE) %>%
-                  hot_col(3, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(4, validator = "
-                                  function(value, callback) {
-                                    try {
-                                      if (value === null || value.trim() === '') {
-                                        callback(false); // Cell is empty
-                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                      } else {
-                                        callback(true); // Cell is not empty
-                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
-                                      }
-                                    } catch (err) {
-                                      console.log(err);
-                                      callback(false); // In case of error, consider it as invalid
-                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
-                                    }
-                                  }
-                                ") %>%
-                  hot_col(8, type = "dropdown", source = country_names) %>%
-                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
-                          validator = "
-                                function (value, callback) {
-                                  var today_date = new Date();
-                                  today_date.setHours(0, 0, 0, 0);
-                                  
-                                  var new_date = new Date(value);
-                                  new_date.setHours(0, 0, 0, 0);
-                                  
-                                  try {
-                                    if (new_date <= today_date) {
-                                      callback(true);
-                                      Shiny.setInputValue('invalid_date', false);
-                                    } else {
-                                      callback(false); 
-                                      Shiny.setInputValue('invalid_date', true);
-                                    }
-                                  } catch (err) {
-                                    console.log(err);
-                                    callback(false); 
-                                    Shiny.setInputValue('invalid_date', true);
-                                  }
-                                }") %>%
-                  hot_col(3:(13 + nrow(DB$cust_var)), 
-                          valign = "htMiddle",
-                          halign = "htLeft") %>%
-                  hot_rows(fixedRowsTop = 0) %>%
-                  hot_col(1, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.row_highlight
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(2, type = "checkbox", width = "auto",
-                          valign = "htTop", halign = "htCenter") %>%
-                  hot_col(4, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_names_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(3, renderer = "
-              function (instance, td, row, col, prop, value, cellProperties) {
-                       Handsontable.renderers.TextRenderer.apply(this, arguments);
-  
-                       if (instance.params) {
-                         hrows = instance.params.dup_ids_high
-                         hrows = hrows instanceof Array ? hrows : [hrows]
-  
-                         if (hrows.includes(row)) { 
-                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
-                         }
-                       }
-              }") %>%
-                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
-                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
-                                                           if (instance.params) {
-                                                             hrows = instance.params.error_highlight
-                                                             hrows = hrows instanceof Array ? hrows : [hrows]
-                                                             if (hrows.includes(row)) { 
-                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
-                                                             }
-                                                           }
-                                                       }") 
-              })
-            }
-          }
-        }
-      }
-    })
-  })
-  
-  observe({
-    if(!is.null(DB$data)){
-      if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-        cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-        DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
-        
-      } else {
-        DB$cust_var <- data.frame()
-      }
-    }
-  })
-  
-  DB$count <- 0
-  
-  observeEvent(input$add_new_variable, {
-    log_print("Input add_new_variable")
-    
-    if(nchar(input$new_var_name) > 12) {
-      log_print("Add variable; max. 10 character")
-      show_toast(
-        title = "Max. 10 characters",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      if (input$new_var_name == "") {
-        log_print("Add variable; min. 1 character")
-        show_toast(
-          title = "Min. 1 character",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-      } else {
-        if(trimws(input$new_var_name) %in% names(DB$meta)) {
-          log_print("Add variable; name already existing")
-          show_toast(
-            title = "Variable name already existing",
-            type = "warning",
-            position = "bottom-end",
-            timer = 6000
-          )
-        } else {
-          showModal(
-            modalDialog(
-              selectInput(
-                "new_var_type",
-                label = "",
-                choices = c("Categorical (character)",
-                            "Continous (numeric)")),
-              title = paste0("Select Data Type"),
-              easyClose = TRUE,
-              footer = tagList(
-                modalButton("Cancel"),
-                actionButton("conf_new_var", "Confirm", class = "btn btn-default")
-              )
-            )
-          )
-        }
-      }
-    }
-  })
-  
-  observeEvent(input$conf_new_var, {
-    log_print("Input conf_new_var")
-    
-    # User feedback variables
-    removeModal()
-    DB$count <- DB$count + 1
-    DB$change <- TRUE
-    
-    # Format variable name
-    name <- trimws(input$new_var_name)
-    
-    if(input$new_var_type == "Categorical (character)") {
-      DB$data <- DB$data %>%
-        mutate("{name}" := character(nrow(DB$data)), .after = 13)
-      
-      DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "categ"))
-    } else {
-      DB$data <- DB$data %>%
-        mutate("{name}" := numeric(nrow(DB$data)), .after = 13)
-      
-      DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "cont"))
-    }
-    
-    DB$meta_gs <- select(DB$data, c(1, 3:13))
-    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-    
-    log_print(paste0("New custom variable added: ", input$new_var_name))
-    
-    show_toast(
-      title = paste0("Variable ", trimws(input$new_var_name), " added"),
-      type = "success",
-      position = "bottom-end",
-      timer = 6000
-    )
-    
-  })
-  
-  observeEvent(input$delete_new_variable, {
-    log_print("Input delete_new_variable")
-    
-    if (input$del_which_var == "") {
-      log_print("Delete custom variables; no custom variable")
-      show_toast(
-        title = "No custom variables",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      showModal(
-        modalDialog(
-          paste0(
-            "Confirmation will lead to irreversible deletion of the custom ",
-            input$del_which_var,
-            " variable. Continue?"
-          ),
-          title = "Delete custom variables",
-          fade = TRUE,
-          easyClose = TRUE,
-          footer = tagList(
-            modalButton("Cancel"),
-            actionButton("conf_var_del", "Delete", class = "btn btn-danger")
-          )
-        )
-      )
-    }
-  })
-  
-  observeEvent(input$conf_var_del, {
-    log_print("Input conf_var_del")
-    
-    DB$change <- TRUE
-    
-    removeModal()
-    
-    if(DB$count >= 1) {
-      DB$count <- DB$count - 1
-    } 
-    
-    show_toast(
-      title = paste0("Variable ", input$del_which_var, " removed"),
-      type = "warning",
-      position = "bottom-end",
-      timer = 6000
-    )
-    
-    log_print(paste0("Variable ", input$del_which_var, " removed"))
-    
-    DB$cust_var <- DB$cust_var[-which(DB$cust_var$Variable == input$del_which_var),]
-    DB$data <- select(DB$data, -(input$del_which_var))
-    DB$meta_gs <- select(DB$data, c(1, 3:13))
-    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
-    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-  })
-  
-  # Select all button
-  
-  observeEvent(input$sel_all_entries, {
-    log_print("Input sel_all_entries")
-    
-    DB$data$Include <- TRUE
-  })
-  
-  observeEvent(input$desel_all_entries, {
-    log_print("Input desel_all_entries")
-    
-    DB$data$Include <- FALSE
-  })
-  
-  # Switch to entry table
-  
-  observeEvent(input$change_entries, {
-    log_print("Input change_entries")
-    
-    removeModal()
-    updateTabItems(session, "tabs", selected = "db_browse_entries")
-  })
-  
-  #### Save Missing Value as CSV ----
-  
-  output$download_na_matrix <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save missing values table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")))
-      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")
-    },
-    content = function(file) {
-      download_matrix <- hot_to_r(input$table_missing_values)
-      write.csv(download_matrix, file, sep = ",", row.names=FALSE, quote=FALSE) 
-    }
-  )
-  
-  #### Save scheme info table as CSV ----
-  
-  output$download_schemeinfo <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save scheme info table ", paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")))
-      
-      paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")
-    },
-    content = function(file) {
-      pub_index <- which(DB$schemeinfo[,1] == "Publications")
-      write.table(
-        DB$schemeinfo[1:(pub_index-1),],
-        file, 
-        sep = ";",
-        row.names = FALSE, 
-        quote = FALSE
-      ) 
-    }
-  )
-  
-  #### Save Loci info table as CSV ----
-  
-  output$download_loci_info <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save loci info table ", paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")))
-      
-      paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")
-    },
-    content = function(file) {
-      write.table(
-        DB$loci_info,
-        file, 
-        sep = ";",
-        row.names = FALSE, 
-        quote = FALSE
-      ) 
-    }
-  )
-  
-  #### Save entry table as CSV ----
-  
-  output$download_entry_table <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save entry table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")))
-      
-      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")
-    },
-    content = function(file) {
-      download_matrix <- hot_to_r(input$db_entries)
-      
-      if (input$download_table_include == TRUE) {
-        download_matrix <- download_matrix[which(download_matrix$Include == TRUE),]
-      }
-      
-      if (input$download_table_loci == FALSE) {
-        download_matrix <- select(download_matrix, 1:(13 + nrow(DB$cust_var)))
-      } 
-      
-      write.csv(download_matrix, file, row.names=FALSE, quote=FALSE) 
-    }
-  )
-  
-  # Save Edits Button
-  
-  observeEvent(input$edit_button, {
-    if(nrow(hot_to_r(input$db_entries)) > nrow(DB$data)) {
-      show_toast(
-        title = "Invalid rows entered. Saving not possible.",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      if(!isTRUE(DB$inhibit_change)) {
-        log_print("Input edit_button")
-        
-        showModal(
-          modalDialog(
-            if(length(DB$deleted_entries > 0)) {
-              paste0(
-                "Overwriting previous metadata of local ",
-                DB$scheme,
-                " database. Deleted entries will be irreversibly removed. Continue?"
-              )
-            } else {
-              paste0(
-                "Overwriting previous metadata of local ",
-                DB$scheme,
-                " database. Continue?"
-              )
-            },
-            title = "Save Database",
-            fade = TRUE,
-            easyClose = TRUE,
-            footer = tagList(
-              modalButton("Cancel"),
-              actionButton("conf_db_save", "Save", class = "btn btn-default")
-            )
-          )
-        )
-      } else {
-        log_print("Input edit_button, invalid values.")
-        show_toast(
-          title = "Invalid values entered. Saving not possible.",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-      }
-    }
-  })
-  
-  observeEvent(input$Cancel, {
-    log_print("Input Cancel")
-    removeModal()
-  })
-  
-  observeEvent(input$conf_db_save, {
-    log_print("Input conf_db_save")
-    
-    # Remove isolate assembly file if present
-    if(!is.null(DB$remove_iso)) {
-      if(length(DB$remove_iso) > 0) {
-        lapply(DB$remove_iso, unlink, recursive = TRUE, force = FALSE, expand = TRUE)
-      }
-    }
-    DB$remove_iso <- NULL
-    
-    Data <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
-    
-    if ((ncol(Data[["Typing"]]) - 13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-      cust_vars_pre <- select(Data[["Typing"]], 
-                              14:(ncol(Data[["Typing"]]) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-      cust_vars_pre <- names(cust_vars_pre)
-    } else {
-      cust_vars_pre <- character()
-    }
-    
-    Data[["Typing"]] <- select(Data[["Typing"]], -(1:(13 + length(cust_vars_pre))))
-    
-    meta_hot <- hot_to_r(input$db_entries)
-    
-    if(length(DB$deleted_entries > 0)) {
-      
-      meta_hot <- mutate(meta_hot, Index = as.character(1:nrow(DB$data)))
-      
-      Data[["Typing"]] <- mutate(Data[["Typing"]][-as.numeric(DB$deleted_entries),  ], 
-                                 meta_hot, .before = 1)
-      rownames(Data[["Typing"]]) <- Data[["Typing"]]$Index
-    } else {
-      Data[["Typing"]] <- mutate(Data[["Typing"]], meta_hot, .before = 1)
-    }
-    
-    # Ensure correct logical data type
-    Data[["Typing"]][["Include"]] <- as.logical(Data[["Typing"]][["Include"]])
-    saveRDS(Data, file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
-    
-    # Load database from files  
-    Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
-    
-    DB$data <- Database[["Typing"]]
-    
-    if(!is.null(DB$data)){
-      if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
-        cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
-        DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
-      } else {
-        DB$cust_var <- data.frame()
-      }
-    }
-    
-    DB$change <- FALSE
-    DB$count <- 0
-    DB$no_na_switch <- TRUE
-    DB$meta_gs <- select(DB$data, c(1, 3:13))
-    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
-    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-    DB$deleted_entries <- character(0)
-    
-    removeModal()
-    
-    show_toast(
-      title = "Database successfully saved",
-      type = "success",
-      position = "bottom-end",
-      timer = 4000
-    )
-  })
-  
-  observeEvent(input$del_button, {
-    log_print("Input del_button")
-    
-    if (length(input$select_delete) < 1) {
-      log_print("Delete entries; no entry selected")
-      show_toast(
-        title = "No entry selected",
-        type = "warning",
-        position = "bottom-end",
-        timer = 4000
-      )
-    } else if((readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") |
-              (tail(readLogFile(), 1) != "0")) {
-      log_print("Delete entries; pending typing")
-      
-      show_toast(
-        title = "Pending Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 4000
-      )
-    } else {
-      if( (length(input$select_delete) - nrow(DB$data) ) == 0) {
-        showModal(
-          modalDialog(
-            paste0("Deleting will lead to removal of all entries and assemblies from local ", DB$scheme, " database. The data can not be recovered afterwards. Continue?"),
-            easyClose = TRUE,
-            title = "Deleting Entries",
-            footer = tagList(
-              modalButton("Cancel"),
-              actionButton("conf_delete_all", "Delete", class = "btn btn-danger")
-            )
-          )
-        )
-      } else {
-        showModal(
-          modalDialog(
-            paste0(
-              "Confirmation will lead to irreversible removal of selected entries and the respectively saved assembly. Continue?"
-            ),
-            title = "Deleting Entries",
-            fade = TRUE,
-            easyClose = TRUE,
-            footer = tagList(
-              modalButton("Cancel"),
-              actionButton(
-                "conf_delete", 
-                "Delete", 
-                class = "btn btn-danger")
-            )
-          )
-        )
-      }
-    }
-  })
-  
-  observeEvent(input$conf_delete_all, {
-    log_print("Input conf_delete_all")
-    
-    # remove file with typing data
-    file.remove(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
-    unlink(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates"), recursive = TRUE, force = FALSE, expand =TRUE)
-    
-    showModal(
-      modalDialog(
-        selectInput(
-          "scheme_db",
-          label = "",
-          choices = if(!is.null(Typing$last_scheme)) {
-            Typing$last_scheme
-          } else {DB$available},
-          selected = if(!is.null(Typing$last_scheme)) {
-            Typing$last_scheme
-          } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}),
-        title = "All entries have been removed. Select a local database to load.",
-        footer = tagList(
-          actionButton("load", "Load", class = "btn btn-default")
-        )
-      )
-    )
-    
-  })
-  
-  DB$deleted_entries <- character(0)
-  
-  observeEvent(input$conf_delete, {
-    
-    log_print("Input conf_delete")
-    
-    # Get isolates selected for deletion
-    DB$deleted_entries <- append(DB$deleted_entries, DB$data$Index[as.numeric(input$select_delete)])
-    
-    # Set reactive status variables
-    DB$no_na_switch <- TRUE
-    DB$change <- TRUE
-    DB$check_new_entries <- FALSE
-    
-    # Set isolate directory deletion variables
-    isopath <- dir_ls(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates"))
-    DB$remove_iso <- isopath[which(basename(isopath) == DB$data$`Assembly ID`[as.numeric(input$select_delete)])]
-    
-    # Reload updated database reactive variables
-    DB$data <- DB$data[!(DB$data$Index %in% as.numeric(input$select_delete)),]
-    DB$meta_gs <- select(DB$data, c(1, 3:13))
-    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
-    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
-    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
-    
-    # User feedback
-    removeModal()
-    
-    if(length(input$select_delete) > 1) {
-      show_toast(
-        title = "Entries deleted",
-        type = "success",
-        position = "bottom-end",
-        timer = 4000
-      )
-    } else {
-      show_toast(
-        title = "Entry deleted",
-        type = "success",
-        position = "bottom-end",
-        timer = 4000
-      )
-    }
-  })
-  
-  
-  ### Distance Matrix ---- 
-  
-  hamming_df <- reactive({
-    if(input$distmatrix_true == TRUE) {
-      if(anyNA(DB$allelic_profile)) {
-        if(input$na_handling == "omit") {
-          allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
-          
-          allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
-          
-          hamming_mat <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
-          
-        } else if(input$na_handling == "ignore_na"){
-          hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
-          
-        } else {
-          hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
-          
-        } 
-      } else {
-        hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
-      }
-    } else {
-      if(anyNA(DB$allelic_profile)) {
-        if(input$na_handling == "omit") {
-          allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
-          hamming_mat <- compute.distMatrix(allelic_profile_noNA, hamming.dist)
-        } else if(input$na_handling == "ignore_na"){
-          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distIgnore)
-        } else {
-          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distCategory)
-        }  
-      } else {
-        hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.dist)
-      }
-    }
-    
-    # Extreme values for distance matrix heatmap display
-    DB$matrix_min <- min(hamming_mat, na.rm = TRUE)
-    DB$matrix_max <- max(hamming_mat, na.rm = TRUE)
-    
-    if(input$distmatrix_triangle == FALSE) {
-      hamming_mat[upper.tri(hamming_mat, diag = !input$distmatrix_diag)] <- NA
-    } 
-    
-    # Row- and colnames change
-    if(input$distmatrix_true == TRUE) {
-      rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label][which(DB$data$Include == TRUE),])
-    } else {
-      rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label])
-    }
-    colnames(hamming_mat) <- rownames(hamming_mat)
-    
-    mode(hamming_mat) <- "integer"
-    
-    DB$ham_matrix <- hamming_mat %>%
-      as.data.frame() %>%
-      mutate(Index = colnames(hamming_mat)) %>%
-      relocate(Index)
-    DB$distancematrix_nrow <- nrow(DB$ham_matrix)
-    
-    DB$ham_matrix
-  })
-  
-  output$download_distmatrix <- downloadHandler(
-    filename = function() {
-      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Distance_Matrix.csv")
-    },
-    content = function(file) {
-      download_matrix <- hot_to_r(input$db_distancematrix)
-      download_matrix[is.na(download_matrix)] <- ""
-      write.csv(download_matrix, file, row.names=FALSE, quote=FALSE) 
-    }
-  )
-  
-  # _______________________ ####
-  
-  ## Locus sequences ----
-  
-  observe({
-    if(!is.null(DB$database) & !is.null(DB$scheme)) {
-      DB$loci <- list.files(
-        path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
-        pattern = "\\.(fasta|fa|fna)$",
-        full.names = TRUE
-      )
-    }
-  })
-  
-  output$loci_sequences <- renderUI({
-    req(input$db_loci_rows_selected, DB$database, DB$scheme, input$seq_sel)
-    
-    DB$loci <- list.files(
-      path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
-      pattern = "\\.(fasta|fa|fna)$",
-      full.names = TRUE
-    )
-    
-    fasta <- format_fasta(DB$loci[input$db_loci_rows_selected])
-    
-    seq <- fasta[[which(fasta == paste0(">", gsub("Allele ", "", sub(" -.*", "", input$seq_sel)))) + 1]]
-    
-    DB$seq <- seq
-    
-    column(
-      width = 12,
-      HTML(
-        paste(
-          tags$span(style='color: white; font-size: 15px; position: relative; top: -15px; left: -50px', 
-                    sub(" -.*", "", input$seq_sel))
-        )
-      ),
-      tags$pre(HTML(color_sequence(seq)), class = "sequence")
-    )
-  })
-  
-  output$sequence_selector <- renderUI({
-    if(!is.null(input$db_loci_rows_selected)) {
-      
-      req(input$db_loci_rows_selected, DB$database, DB$scheme)
-      
-      DB$loci <- list.files(
-        path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
-        pattern = "\\.(fasta|fa|fna)$",
-        full.names = TRUE
-      )
-      
-      fasta <- format_fasta(DB$loci[input$db_loci_rows_selected])
-      
-      seq_names <- c()
-      for (i in seq_along(fasta)) {
-        if (startsWith(fasta[[i]], ">")) {
-          name <- sub(">", "", fasta[[i]])
-          seq_names <- c(seq_names, name)
-        }
-      }
-      
-      var_count <- table(DB$allelic_profile[gsub(".fasta", "", (basename(DB$loci[input$db_loci_rows_selected])))])
-      
-      vec <- prop.table(var_count)
-      
-      perc <- sapply(unname(vec), scales::percent, accuracy = 0.1)
-      
-      names(perc) <- names(vec)
-      
-      choices <- seq_names
-      
-      present <- which(choices %in% names(vec))
-      absent <- which(!(choices %in% names(vec)))
-      
-      choices[present] <- paste0("Allele ", choices[present], " - ", unname(var_count), " times in DB (", unname(perc), ")")
-      
-      choices[absent] <- paste0("Allele ", choices[absent], " - not present")
-      
-      choices <- c(choices[present], choices[absent])
-      
-      names(choices) <- sapply(choices, function(x) {
-        x <- strsplit(x, " ")[[1]]
-        x[2] <- paste0(substr(x[2], 1, 4), "...", substr(x[2], nchar(x[2])-3, nchar(x[2])))
-        paste(x, collapse = " ")
-      })
-      
-      column(
-        width = 3,
-        selectInput(
-          "seq_sel",
-          h5("Select Variant", style = "color:white;"),
-          choices = choices,
-          width = "80%"
-        ),
-        br(),
-        fluidRow(
-          column(
-            width = 8,
-            align = "left",
-            actionButton("copy_seq", "Copy Sequence",
-                         icon = icon("copy")),
-            bsTooltip("copy_seq", "Copy the variant sequence <br> to clipboard", placement = "top", trigger = "hover")
-          )
-        ),
-        br(),
-        fluidRow(
-          column(
-            width = 8,
-            align = "left",
-            downloadBttn(
-              "get_locus",
-              style = "simple",
-              label = "Save .fasta",
-              size = "sm",
-              icon = icon("download")
-            ),
-            bsTooltip("get_locus_bttn", "Save locus file with all variants", placement = "top", trigger = "hover")
-          )
-        ),
-        br(), br(), br(), br(), br(), br(), br()
-      )
-    }
-  })
-  
-  observeEvent(input$copy_seq, {
-    if(!is.null(DB$seq)) {
-      session$sendCustomMessage("txt", DB$seq)
-    }
-    show_toast(
-      title = "Copied sequence",
-      type = "success",
-      position = "bottom-end",
-      timer = 3000
-    )
-  })
-  
-  output$get_locus <- downloadHandler(
-    filename = function() {
-      fname <- basename(DB$loci[input$db_loci_rows_selected])
-      log_print(paste0("Get locus fasta ", fname))
-      fname
-    },
-    content = function(file) {
-      cont <- readLines(DB$loci[input$db_loci_rows_selected])
-      writeLines(cont, file)
-    }
-  )
-  
-  # _______________________ ####
-  
-  ## Download cgMLST ----
-  
-  observe({
-    if (input$select_cgmlst == "Acinetobacter baumanii") {
-      species <- "Abaumannii1907"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- Scheme$folder_name <- "Acinetobacter_baumanii"
-    } else if (input$select_cgmlst == "Bacillus anthracis") {
-      species <- "Banthracis1917"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Bacillus_anthracis"
-    } else if (input$select_cgmlst == "Bordetella pertussis") {
-      species <- "Bpertussis1917"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Bordetella_pertussis"
-    } else if (input$select_cgmlst == "Brucella melitensis") {
-      species <- "Bmelitensis1912"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Brucella_melitensis"
-    } else if (input$select_cgmlst == "Brucella spp.") {
-      species <- "Brucella1914"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Brucella_spp"
-    } else if (input$select_cgmlst == "Burkholderia mallei (FLI)") {
-      species <- "Bmallei_fli1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Burkholderia_mallei_FLI"
-    } else if (input$select_cgmlst == "Burkholderia mallei (RKI)") {
-      species <- "Bmallei_rki1909"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Burkholderia_mallei_RKI"
-    } else if (input$select_cgmlst == "Burkholderia pseudomallei") {
-      species <- "Bpseudomallei1906"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Burkholderia_pseudomallei"
-    } else if (input$select_cgmlst == "Campylobacter jejuni/coli") {
-      species <- "Cjejuni1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Campylobacter_jejuni_coli"
-    } else if (input$select_cgmlst == "Clostridioides difficile") {
-      species <- "Cdifficile1905"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Clostridioides_difficile"
-    } else if (input$select_cgmlst == "Clostridium perfringens") {
-      species <- "Cperfringens1907"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Clostridium_perfringens"
-    } else if (input$select_cgmlst == "Corynebacterium diphtheriae") {
-      species <- "Cdiphtheriae1907"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Corynebacterium_diphtheriae"
-    } else if (input$select_cgmlst == "Cronobacter sakazakii/malonaticus") {
-      species <- "Csakazakii1910"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Cronobacter_sakazakii_malonaticus"
-    } else if (input$select_cgmlst == "Enterococcus faecalis") {
-      species <- "Efaecalis1912"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Enterococcus_faecalis"
-    } else if (input$select_cgmlst == "Enterococcus faecium") {
-      species <- "Efaecium1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Enterococcus_faecium"
-    } else if (input$select_cgmlst == "Escherichia coli") {
-      species <- "Ecoli1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Escherichia_coli"
-    } else if (input$select_cgmlst == "Francisella tularensis") {
-      species <- "Ftularensis1913"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Francisella_tularensis"
-    } else if (input$select_cgmlst == "Klebsiella oxytoca sensu lato") {
-      species <- "Koxytoca717"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Klebsiella_oxytoca_sensu_lato"
-    } else if (input$select_cgmlst == "Klebsiella pneumoniae sensu lato") {
-      species <- "Kpneumoniae1909"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Klebsiella_pneumoniae_sensu_lato"
-    } else if (input$select_cgmlst == "Legionella pneumophila") {
-      species <- "Lpneumophila1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Legionella_pneumophila"
-    } else if (input$select_cgmlst == "Listeria monocytogenes") {
-      species <- "Lmonocytogenes1910"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Listeria_monocytogenes"
-    } else if (input$select_cgmlst == "Mycobacterium tuberculosis complex") {
-      species <- "Mtuberculosis1909"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Mycobacterium_tuberculosis_complex"
-    } else if (input$select_cgmlst == "Mycobacteroides abscessus") {
-      species <- "Mabscessus1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Mycobacteroides_abscessus"
-    } else if (input$select_cgmlst == "Mycoplasma gallisepticum") {
-      species <- "Mgallisepticum1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Mycoplasma_gallisepticum"
-    } else if (input$select_cgmlst == "Paenibacillus larvae") {
-      species <- "Plarvae1902"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Paenibacillus_larvae"
-    } else if (input$select_cgmlst == "Pseudomonas aeruginosa") {
-      species <- "Paeruginosa1911"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Pseudomonas_aeruginosa"
-    } else if (input$select_cgmlst == "Salmonella enterica") {
-      species <- "Senterica1913"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Salmonella_enterica"
-    } else if (input$select_cgmlst == "Serratia marcescens") {
-      species <- "Smarcescens1912"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Serratia_marcescens"
-    } else if (input$select_cgmlst == "Staphylococcus aureus") {
-      species <- "Saureus1908"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Staphylococcus_aureus"
-    } else if (input$select_cgmlst == "Staphylococcus capitis") {
-      species <- "Scapitis1905"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Staphylococcus_capitis"
-    } else if (input$select_cgmlst == "Streptococcus pyogenes") {
-      species <- "Spyogenes1904"
-      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
-      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
-      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
-      Scheme$folder_name <- "Streptococcus_pyogenes"
-    }
-  })
-  
-  observeEvent(input$download_cgMLST, {
-    log_print(paste0("Started download of scheme for ", Scheme$folder_name))
-    
-    shinyjs::hide("download_cgMLST")
-    shinyjs::show("loading")
-    
-    output$statustext <- renderUI(
-      fluidRow(
-        tags$li(
-          class = "dropdown", 
-          tags$span(HTML(
-            paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
-                  "Status:&nbsp;&nbsp;&nbsp; <i>Downloading scheme...</i>")),
-            style = "color:white;")
-        )
-      )
-    )
-    
-    show_toast(
-      title = "Download started",
-      type = "success",
-      position = "bottom-end",
-      timer = 5000
-    )
-    
-    if(length(DB$available) == 0) {
-      saveRDS(DB$new_database, paste0(getwd(), "/execute/new_db.rds"))
-      dir.create(file.path(readRDS(paste0(getwd(), "/execute/new_db.rds")), "Database"), recursive = TRUE)
-    }
-    
-    DB$load_selected <- TRUE
-    
-    # Check if .downloaded_schemes folder exists and if not create it
-    if (!dir.exists(file.path(DB$database, ".downloaded_schemes"))) {
-      dir.create(file.path(DB$database, ".downloaded_schemes"), recursive = TRUE)
-    }
-    
-    # Check if remains of old temporary folder exists and remove them
-    if (dir.exists(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")))) {
-      unlink(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")), recursive = TRUE)
-    }
-    
-    # Download Loci Fasta Files
-    options(timeout = 600)
-    
-    tryCatch({
-      download.file(Scheme$link_cgmlst, 
-                    file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")))
-      "Download successful!"
-    }, error = function(e) {
-      paste("Error: ", e$message)
-    })
-    
-    # Unzip the scheme in temporary folder
-    unzip(
-      zipfile = file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")),
-      exdir = file.path(DB$database, 
-                        Scheme$folder_name, 
-                        paste0(Scheme$folder_name, ".tmp")
-      )
-    )
-    
-    log_print("Hashing downloaded database")
-    # Hash temporary folder
-    hash_database(file.path(DB$database, 
-                            Scheme$folder_name, 
-                            paste0(Scheme$folder_name, ".tmp")))
-    
-    # Get list from local database
-    local_db_filelist <- list.files(file.path(DB$database, 
-                                              Scheme$folder_name, 
-                                              paste0(Scheme$folder_name, "_alleles")))
-    if (!is_empty(local_db_filelist)) {
-      # Get list from temporary database
-      tmp_db_filelist <- list.files(file.path(DB$database,
-                                              Scheme$folder_name,
-                                              paste0(Scheme$folder_name, ".tmp")))
-      
-      # Find the difference (extra files in local database)
-      local_db_extra <- setdiff(local_db_filelist, tmp_db_filelist)
-      
-      # Copy extra files to temporary folder
-      file.copy(file.path(DB$database,
-                          Scheme$folder_name, 
-                          paste0(Scheme$folder_name, "_alleles"), local_db_extra),
-                file.path(DB$database,
-                          Scheme$folder_name,
-                          paste0(Scheme$folder_name, ".tmp")))
-      
-      # Check differences in file pairs
-      local_db_hashes <- tools::md5sum(file.path(DB$database,
-                                                 Scheme$folder_name,
-                                                 paste0(Scheme$folder_name, "_alleles"),
-                                                 local_db_filelist))
-      tmp_db_hashes <- tools::md5sum(file.path(DB$database,
-                                               Scheme$folder_name,
-                                               paste0(Scheme$folder_name, ".tmp"),
-                                               local_db_filelist))
-      
-      diff_files <- local_db_hashes %in% tmp_db_hashes
-      diff_loci <- names(local_db_hashes)[diff_files == FALSE]
-      diff_loci <- sapply(strsplit(diff_loci, "/"), function(x) x[length(x)])
-      
-      # Check locus hashes
-      for (locus in diff_loci) {
-        local_db_hashes <- get_locus_hashes(file.path(DB$database,
-                                                      Scheme$folder_name,
-                                                      paste0(Scheme$folder_name, "_alleles"),
-                                                      locus))
-        tmp_db_hashes <- get_locus_hashes(file.path(DB$database,
-                                                    Scheme$folder_name,
-                                                    paste0(Scheme$folder_name, ".tmp"),
-                                                    locus))
-        diff_hashes <- setdiff(local_db_hashes, tmp_db_hashes)
-        
-        sequences <- extract_seq(file.path(DB$database,
-                                           Scheme$folder_name,
-                                           paste0(Scheme$folder_name, "_alleles"),
-                                           locus), diff_hashes)
-        if (!is_empty(sequences$idx) && !is_empty(sequences$seq) &&
-            length(sequences$idx) == length(sequences$seq)) {
-          add_new_sequences(file.path(DB$database,
-                                      Scheme$folder_name,
-                                      paste0(Scheme$folder_name, ".tmp"),
-                                      locus), sequences)
-        }
-      }
-    }
-    
-    unlink(file.path(DB$database, Scheme$folder_name, 
-                     paste0(Scheme$folder_name, "_alleles")), recursive = TRUE)
-    
-    file.rename(file.path(DB$database, Scheme$folder_name,
-                          paste0(Scheme$folder_name, ".tmp")),
-                file.path(DB$database, Scheme$folder_name,
-                          paste0(Scheme$folder_name, "_alleles")))
-    
-    # Download Scheme Info
-    download(
-      Scheme$link_scheme,
-      dest = file.path(DB$database, Scheme$folder_name, "scheme_info.html"),
-      mode = "wb"
-    )
-    
-    # Download Loci Info	
-    download(	
-      Scheme$link_targets,	
-      dest = file.path(DB$database, Scheme$folder_name, "targets.csv"),
-      mode = "wb"
-    )
-    
-    # Send downloaded scheme to database browser overview
-    DB$available <- gsub("_", " ", basename(dir_ls(DB$database)))
-    
-    Scheme$target_table <- read.csv(
-      file.path(DB$database, Scheme$folder_name, "targets.csv"),
-      header = TRUE,	
-      sep = "\t",	
-      row.names = NULL,	
-      colClasses = c(	
-        "NULL",	
-        "character",	
-        "character",	
-        "integer",	
-        "integer",	
-        "character",	
-        "integer",	
-        "NULL"	
-      )	
-    )
-    
-    DB$exist <- length(dir_ls(DB$database)) == 0
-    
-    shinyjs::show("download_cgMLST")
-    shinyjs::hide("loading")
-    
-    output$statustext <- renderUI(
-      fluidRow(
-        tags$li(
-          class = "dropdown", 
-          tags$span(HTML(
-            paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
-                  "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
-            style = "color:white;")
-        )
-      )
-    )
-    
-    show_toast(
-      title = "Download successful",
-      type = "success",
-      position = "bottom-end",
-      timer = 5000
-    )
-    
-    log_print("Download successful")
-    
-    showModal(
-      modalDialog(
-        selectInput(
-          "scheme_db",
-          label = "",
-          choices = if(!is.null(Typing$last_scheme)) {
-            Typing$last_scheme
-          } else {DB$available},
-          selected = if(!is.null(Typing$last_scheme)) {
-            Typing$last_scheme
-          } else {if(!is.null(DB$scheme)) {input$select_cgmlst} else {DB$available[1]}}),
-        title = "Select a local database to load.",
-        footer = tagList(
-          actionButton("load", "Load", class = "btn btn-default")
-        )
-      )
-    )
-  })
-  
-  # Download Target Info (CSV Table)
-  observe({
-    input$download_cgMLST
-    
-    scheme_overview <- read_html(Scheme$link_scheme) %>%
-      html_table(header = FALSE) %>%
-      as.data.frame(stringsAsFactors = FALSE)
-    
-    last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"],
-                                   format = "%B %d, %Y, %H:%M %p")
-    names(scheme_overview) <- NULL
-    
-    last_file_change <- format(
-      file.info(file.path(DB$database,
-                          ".downloaded_schemes",
-                          paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
-    
-    output$cgmlst_scheme <- renderTable({scheme_overview})
-    output$scheme_update_info <- renderText({
-      req(last_file_change)
-      if (last_file_change < last_scheme_change) {
-        "(Newer scheme available \u274c)"
-      } else {
-        "(Scheme is up-to-date \u2705)"
-      }
-    })
-  })
-  
-  # _______________________ ####
-  
-  ## Visualization ----
-  
-  # Render placeholder image
-  
-  output$placeholder <- renderImage({
-    # Path to your PNG image with a transparent background
-    image_path <- paste0(getwd(), "/www/PhyloTrace.png")
-    
-    # Use HTML to display the image with the <img> tag
-    list(src = image_path,
-         height = 180)
-  }, deleteFile = FALSE)
-  
-  # Render tree plot fields
-  
-  output$nj_field <- renderUI(
-    fluidRow(
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
-    )
-  )
-  
-  output$mst_field <- renderUI(
-    fluidRow(
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
-    )
-  )
-  
-  output$upgma_field <- renderUI(
-    fluidRow(
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
-      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
-    )
-  )
-  
-  ### Render Visualization Controls ----
-  
-  #### NJ and UPGMA controls ----
-  
-  # Control enable/disable of variable mapping inputs
-  observe({
-    shinyjs::toggleState(id = "nj_color_mapping", condition = isTRUE(input$nj_mapping_show))
-    shinyjs::toggleState(id = "nj_tiplab_scale", condition = isTRUE(input$nj_mapping_show))
-    shinyjs::toggleState(id = "upgma_color_mapping", condition = isTRUE(input$upgma_mapping_show))
-    shinyjs::toggleState(id = "upgma_tiplab_scale", condition = isTRUE(input$upgma_mapping_show))
-    
-    shinyjs::toggleState(id = "nj_tipcolor_mapping", condition = isTRUE(input$nj_tipcolor_mapping_show))
-    shinyjs::toggleState(id = "nj_tippoint_scale", condition = isTRUE(input$nj_tipcolor_mapping_show))
-    shinyjs::toggleState(id = "upgma_tipcolor_mapping", condition = isTRUE(input$upgma_tipcolor_mapping_show))
-    shinyjs::toggleState(id = "upgma_tippoint_scale", condition = isTRUE(input$upgma_tipcolor_mapping_show))
-    
-    shinyjs::toggleState(id = "nj_tipshape_mapping", condition = isTRUE(input$nj_tipshape_mapping_show))
-    shinyjs::toggleState(id = "upgma_tipshape_mapping", condition = isTRUE(input$upgma_tipshape_mapping_show))
-    
-    shinyjs::toggleState(id = "nj_fruit_variable", condition = isTRUE(input$nj_tiles_show_1))
-    shinyjs::toggleState(id = "upgma_fruit_variable", condition = isTRUE(input$upgma_tiles_show_1))
-    shinyjs::toggleState(id = "nj_fruit_variable_2", condition = isTRUE(input$nj_tiles_show_2))
-    shinyjs::toggleState(id = "upgma_fruit_variable_2", condition = isTRUE(input$upgma_tiles_show_2))
-    shinyjs::toggleState(id = "nj_fruit_variable_3", condition = isTRUE(input$nj_tiles_show_3))
-    shinyjs::toggleState(id = "upgma_fruit_variable_3", condition = isTRUE(input$upgma_tiles_show_3))
-    shinyjs::toggleState(id = "nj_fruit_variable_4", condition = isTRUE(input$nj_tiles_show_4))
-    shinyjs::toggleState(id = "upgma_fruit_variable_4", condition = isTRUE(input$upgma_tiles_show_4))
-    shinyjs::toggleState(id = "nj_fruit_variable_5", condition = isTRUE(input$nj_tiles_show_5))
-    shinyjs::toggleState(id = "upgma_fruit_variable_5", condition = isTRUE(input$upgma_tiles_show_5))
-    shinyjs::toggleState(id = "nj_tiles_scale_1", condition = isTRUE(input$nj_tiles_show_1))
-    shinyjs::toggleState(id = "upgma_tiles_scale_1", condition = isTRUE(input$upgma_tiles_show_1))
-    shinyjs::toggleState(id = "nj_tiles_scale_2", condition = isTRUE(input$nj_tiles_show_2))
-    shinyjs::toggleState(id = "upgma_tiles_scale_2", condition = isTRUE(input$upgma_tiles_show_2))
-    shinyjs::toggleState(id = "nj_tiles_scale_3", condition = isTRUE(input$nj_tiles_show_3))
-    shinyjs::toggleState(id = "upgma_tiles_scale_3", condition = isTRUE(input$upgma_tiles_show_3))
-    shinyjs::toggleState(id = "nj_tiles_scale_4", condition = isTRUE(input$nj_tiles_show_4))
-    shinyjs::toggleState(id = "upgma_tiles_scale_4", condition = isTRUE(input$upgma_tiles_show_4))
-    shinyjs::toggleState(id = "nj_tiles_scale_5", condition = isTRUE(input$nj_tiles_show_5))
-    shinyjs::toggleState(id = "upgma_tiles_scale_5", condition = isTRUE(input$upgma_tiles_show_5))
-    
-    shinyjs::toggleState(id = "nj_heatmap_sel", condition = isTRUE(input$nj_heatmap_show))
-    shinyjs::toggleState(id = "nj_heatmap_scale", condition = isTRUE(input$nj_heatmap_show))
-    shinyjs::toggleState(id = "upgma_heatmap_sel", condition = isTRUE(input$upgma_heatmap_show))
-    shinyjs::toggleState(id = "upgma_heatmap_scale", condition = isTRUE(input$upgma_heatmap_show))
-  })
-  
-  # Size scaling NJ
-  observe({
-    req(input$nj_ratio)
-    if(input$nj_ratio == "1.6") {
-      updateSliderInput(session, "nj_scale",
-                        step = 5, value = 800, min = 500, max = 1200)
-    } else if(input$nj_ratio == "1.77777777777778") {
-      updateSliderInput(session, "nj_scale",
-                        step = 9, value = 801, min = 504, max = 1197)
-    } else if(input$nj_ratio == "1.33333333333333"){
-      updateSliderInput(session, "nj_scale",
-                        step = 3, value = 801, min = 501, max = 1200)
-    }
-  })
-  
-  # Size scaling UPGMA
-  observe({
-    req(input$upgma_ratio)
-    if(input$upgma_ratio == "1.6") {
-      updateSliderInput(session, "upgma_scale",
-                        step = 5, value = 800, min = 500, max = 1200)
-    } else if(input$upgma_ratio == "1.77777777777778") {
-      updateSliderInput(session, "upgma_scale",
-                        step = 9, value = 801, min = 504, max = 1197)
-    } else if(input$upgma_ratio == "1.33333333333333"){
-      updateSliderInput(session, "upgma_scale",
-                        step = 3, value = 801, min = 501, max = 1200)
-    }
-  })
-  
-  # Size scaling MST
-  observe({
-    req(input$mst_ratio)
-    if(input$mst_ratio == "1.6") {
-      updateSliderInput(session, "mst_scale",
-                        step = 5, value = 800, min = 500, max = 1200)
-    } else if(input$mst_ratio == "1.77777777777778") {
-      updateSliderInput(session, "mst_scale",
-                        step = 9, value = 801, min = 504, max = 1197)
-    } else if(input$mst_ratio == "1.33333333333333"){
-      updateSliderInput(session, "mst_scale",
-                        step = 3, value = 801, min = 501, max = 1200)
-    }
-  })
-  
-  # Custom Labels
-  
-  # Add custom label
-  observeEvent(input$nj_add_new_label, {
-    
-    if(nchar(input$nj_new_label_name) > 0) {
-      if(!(input$nj_new_label_name %in% Vis$custom_label_nj)) {
-        Vis$custom_label_nj <- rbind(Vis$custom_label_nj, input$nj_new_label_name) 
-        if(!(nrow(Vis$custom_label_nj) == 1)) {
-          updateSelectInput(session, "nj_custom_label_sel", selected = input$nj_new_label_name)
-        }
-      } else {
-        show_toast(
-          title = "Label already exists",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-      }
-    } else {
-      show_toast(
-        title = "Min. 1 character",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    }
-  })
-  
-  observeEvent(input$upgma_add_new_label, {
-    
-    if(nchar(input$upgma_new_label_name) > 0) {
-      if(!(input$upgma_new_label_name %in% Vis$custom_label_upgma)) {
-        Vis$custom_label_upgma <- rbind(Vis$custom_label_upgma, input$upgma_new_label_name) 
-        if(!(nrow(Vis$custom_label_upgma) == 1)) {
-          updateSelectInput(session, "upgma_custom_label_sel", selected = input$upgma_new_label_name)
-        }
-      } else {
-        show_toast(
-          title = "Label already exists",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-      }
-    } else {
-      show_toast(
-        title = "Min. 1 character",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    }
-  })
-  
-  # Delete custom label
-  observeEvent(input$nj_del_label, {
-    
-    if(nrow(Vis$custom_label_nj) > 1) {
-      Vis$custom_label_nj <- Vis$custom_label_nj[-which(Vis$custom_label_nj[,1] == input$nj_custom_label_sel), , drop = FALSE]
-    } else if (nrow(Vis$custom_label_nj) == 1) {
-      Vis$nj_label_pos_x <- list()
-      Vis$nj_label_pos_y <- list()
-      Vis$nj_label_size <- list()
-      Vis$custom_label_nj <- data.frame()
-    }
-  })
-  
-  observeEvent(input$upgma_del_label, {
-    
-    if(nrow(Vis$custom_label_upgma) > 1) {
-      Vis$custom_label_upgma <- Vis$custom_label_upgma[-which(Vis$custom_label_upgma[,1] == input$upgma_custom_label_sel), , drop = FALSE]
-    } else if (nrow(Vis$custom_label_upgma) == 1) {
-      Vis$upgma_label_pos_x <- list()
-      Vis$upgma_label_pos_y <- list()
-      Vis$upgma_label_size <- list()
-      Vis$custom_label_upgma <- data.frame()
-    }
-  })
-  
-  # Select custom labels
-  output$nj_custom_label_select <- renderUI({
-    if(nrow(Vis$custom_label_nj) > 0) {
-      selectInput(
-        "nj_custom_label_sel",
-        "",
-        choices = Vis$custom_label_nj[,1]
-      )
-    }
-  })
-  
-  output$upgma_custom_label_select <- renderUI({
-    if(nrow(Vis$custom_label_upgma) > 0) {
-      selectInput(
-        "upgma_custom_label_sel",
-        "",
-        choices = Vis$custom_label_upgma[,1]
-      )
-    }
-  })
-  
-  # Select custom labels
-  output$nj_cust_label_save <- renderUI({
-    if(nrow(Vis$custom_label_nj) > 0) {
-      actionButton(
-        "nj_cust_label_save",
-        "Apply"
-      )
-    } else {
-      column(
-        width = 12,
-        br(), br(), br(), br(), br(), br(),
-        h5("test", style = "color: transparent; margin-bottom: 3px")
-      )
-    }
-  })
-  
-  output$upgma_cust_label_save <- renderUI({
-    if(nrow(Vis$custom_label_upgma) > 0) {
-      actionButton(
-        "upgma_cust_label_save",
-        "Apply"
-      )
-    } else {
-      column(
-        width = 12,
-        br(), br(), br(), br(), br(), br(),
-        h5("test", style = "color: transparent; margin-bottom: 3px")
-      )
-    }
-  })
-  
-  # Custom Label Size
-  output$nj_custom_labelsize <- renderUI({
-    if(length(Vis$custom_label_nj) > 0) {
-      if(!is.null(Vis$nj_label_size[[input$nj_custom_label_sel]])) {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_size"),
-                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
-                    min = 0, max = 10, step = 0.5, ticks = F,
-                    value = Vis$nj_label_size[[input$nj_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_size"),
-                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
-                    min = 0, max = 10, step = 0.5, ticks = F, value = 5,
-                    width = "150px")
-      }
-    } 
-  })
-  
-  output$upgma_custom_labelsize <- renderUI({
-    if(length(Vis$custom_label_upgma) > 0) {
-      if(!is.null(Vis$upgma_label_size[[input$upgma_custom_label_sel]])) {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_size"),
-                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
-                    min = 0, max = 10, step = 0.5, ticks = F,
-                    value = Vis$upgma_label_size[[input$upgma_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_size"),
-                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
-                    min = 0, max = 10, step = 0.5, ticks = F, value = 5,
-                    width = "150px")
-      }
-    } 
-  })
-  
-  # Render slider input based on selected label
-  output$nj_sliderInput_y <- renderUI({
-    if(length(Vis$custom_label_nj) > 0) {
-      if(!is.null(Vis$nj_label_pos_y[[input$nj_custom_label_sel]])) {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_y"),
-                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = 50, step = 1, ticks = F,
-                    value = Vis$nj_label_pos_y[[input$nj_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_y"),
-                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = sum(DB$data$Include), step = 1, ticks = F, 
-                    value = sum(DB$data$Include) / 2,
-                    width = "150px")
-      }
-    } 
-  })
-  
-  output$upgma_sliderInput_y <- renderUI({
-    if(length(Vis$custom_label_upgma) > 0) {
-      if(!is.null(Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]])) {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_y"),
-                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = 50, step = 1, ticks = F,
-                    value = Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_y"),
-                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = sum(DB$data$Include), step = 1, ticks = F, 
-                    value = sum(DB$data$Include) / 2,
-                    width = "150px")
-      }
-    } 
-  })
-  
-  output$nj_sliderInput_x <- renderUI({
-    if(length(Vis$custom_label_nj) > 0) {
-      if(!is.null(Vis$nj_label_pos_x[[input$nj_custom_label_sel]])) {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_x"),
-                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = 50, step = 1, ticks = F,
-                    value = Vis$nj_label_pos_x[[input$nj_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_x"),
-                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = round(Vis$nj_max_x, 0), step = 1, ticks = F, 
-                    value = round(Vis$nj_max_x / 2, 0),
-                    width = "150px")
-      }
-    }
-  })
-  
-  output$upgma_sliderInput_x <- renderUI({
-    if(length(Vis$custom_label_upgma) > 0) {
-      if(!is.null(Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]])) {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_x"),
-                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = 50, step = 1, ticks = F,
-                    value = Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]],
-                    width = "150px")
-      } else {
-        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_x"),
-                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
-                    min = 0, max = round(Vis$upgma_max_x, 0), step = 1, ticks = F, 
-                    value = round(Vis$upgma_max_x / 2, 0),
-                    width = "150px")
-      }
-    }
-  })
-  
-  # Apply custom label changes
-  observeEvent(input$nj_cust_label_save, {
-    
-    if(!is.null(Vis$nj_label_pos_y) &
-       !is.null(Vis$nj_label_pos_x) &
-       !is.null(Vis$nj_label_size) &
-       !is.null(input$nj_custom_label_sel)) {
-      Vis$nj_label_pos_y[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_y")]]
-      Vis$nj_label_pos_x[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_x")]]
-      Vis$nj_label_size[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_size")]]
-    }
-  })
-  
-  observeEvent(input$upgma_cust_label_save, {
-    
-    if(!is.null(Vis$upgma_label_pos_y) &
-       !is.null(Vis$upgma_label_pos_x) &
-       !is.null(Vis$upgma_label_size) &
-       !is.null(input$upgma_custom_label_sel)) {
-      Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_y")]]
-      Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_x")]]
-      Vis$upgma_label_size[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_size")]]
-    }
-  })
-  
-  # Show delete custom label button if custam label added
-  output$nj_del_label <- renderUI({
-    if(nrow(Vis$custom_label_nj) > 0) {
-      actionButton(
-        "nj_del_label",
-        "",
-        icon = icon("minus")
-      )
-    } else {NULL}
-  })
-  
-  output$upgma_del_label <- renderUI({
-    if(nrow(Vis$custom_label_upgma) > 0) {
-      actionButton(
-        "upgma_del_label",
-        "",
-        icon = icon("minus")
-      )
-    } else {NULL}
-  })
-  
-  # Mapping value number information
-  output$nj_tiplab_mapping_info <- renderUI({
-    if(!is.null(input$nj_color_mapping) & (!is.null(Vis$meta_nj))) {
-      if(is.numeric(unlist(Vis$meta_nj[input$nj_color_mapping]))) {
-        if(input$nj_tiplab_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-          column(
-            width = 3,
-            fluidRow(
-              column(
-                width = 4,
-                h5("Midpoint", style = "color: white; margin-top: 22px;")
-              ),
-              column(
-                width = 8,
-                div(
-                  class = "divmid-sel1",
-                  selectInput(
-                    "nj_color_mapping_div_mid",
-                    label = "",
-                    choices = c("Zero", "Mean", "Median"),
-                    selected = "Mean"
-                  )
-                )
-              )
-            )
-          )
-        } else {
-          column(
-            width = 3,
-            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
-          ) 
-        }
-      } else {
-        if(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))) > 7) {
-          column(
-            width = 3,
-            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$upgma_tiplab_mapping_info <- renderUI({
-    if(!is.null(input$upgma_color_mapping) & (!is.null(Vis$meta_upgma))) {
-      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) {
-        if(input$upgma_tiplab_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-          column(
-            width = 3,
-            fluidRow(
-              column(
-                width = 4,
-                h5("Midpoint", style = "color: white; margin-top: 22px;")
-              ),
-              column(
-                width = 8,
-                div(
-                  class = "divmid-sel1",
-                  selectInput(
-                    "upgma_color_mapping_div_mid",
-                    label = "",
-                    choices = c("Zero", "Mean", "Median"),
-                    selected = "Mean"
-                  )
-                )
-              )
-            )
-          )
-        } else {
-          column(
-            width = 3,
-            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
-          ) 
-        }
-      } else {
-        if(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) > 7) {
-          column(
-            width = 3,
-            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$nj_tipcolor_mapping_info <- renderUI({
-    if(!is.null(input$nj_tipcolor_mapping) & (!is.null(Vis$meta_nj))) {
-      if(is.numeric(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) {
-        if(input$nj_tippoint_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-          column(
-            width = 3,
-            fluidRow(
-              column(
-                width = 4,
-                h5("Midpoint", style = "color: white; margin-top: 22px;")
-              ),
-              column(
-                width = 8,
-                div(
-                  class = "divmid-sel1",
-                  selectInput(
-                    "nj_tipcolor_mapping_div_mid",
-                    label = "",
-                    choices = c("Zero", "Mean", "Median"),
-                    selected = "Mean"
-                  )
-                )
-              )
-            )
-          )
-        } else {
-          column(
-            width = 3,
-            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-          ) 
-        }
-      } else {
-        if(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) > 7) {
-          column(
-            width = 3,
-            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$upgma_tipcolor_mapping_info <- renderUI({
-    if(!is.null(input$upgma_tipcolor_mapping) & (!is.null(Vis$meta_upgma))) {
-      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) {
-        if(input$upgma_tippoint_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-          column(
-            width = 3,
-            fluidRow(
-              column(
-                width = 4,
-                h5("Midpoint", style = "color: white; margin-top: 22px;")
-              ),
-              column(
-                width = 8,
-                div(
-                  class = "divmid-sel1",
-                  selectInput(
-                    "upgma_tipcolor_mapping_div_mid",
-                    label = "",
-                    choices = c("Zero", "Mean", "Median"),
-                    selected = "Mean"
-                  )
-                )
-              )
-            )
-          )
-        } else {
-          column(
-            width = 3,
-            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-          ) 
-        }
-      } else {
-        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) > 7) {
-          column(
-            width = 3,
-            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$nj_tipshape_mapping_info <- renderUI({
-    if(!is.null(input$nj_tipshape_mapping) & (!is.null(Vis$meta_nj))) {
-      if(is.numeric(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))) {
-        column(
-          width = 3,
-          h5("Mapping continous variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
-        )
-      } else {
-        if(length(unique(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))) > 6) {
-          column(
-            width = 3,
-            h5("Mapping > 6 variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )    
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$upgma_tipshape_mapping_info <- renderUI({
-    if(!is.null(input$upgma_tipshape_mapping) & (!is.null(Vis$meta_upgma))) {
-      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))) {
-        column(
-          width = 3,
-          h5("Mapping continous variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
-        )
-      } else {
-        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))) > 6) {
-          column(
-            width = 3,
-            h5("Mapping > 6 variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
-          )
-        } else {
-          column(
-            width = 3,
-            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-          )    
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$nj_fruit_mapping_info <- renderUI({
-    if(input$nj_tile_num == 1) {
-      if(!is.null(input$nj_fruit_variable) & (!is.null(Vis$meta_nj))) {
-        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable]))) {
-          if(input$nj_tiles_scale_1 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_tiles_mapping_div_mid_1",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$nj_tile_num == 2) {
-      if(!is.null(input$nj_fruit_variable_2) & (!is.null(Vis$meta_nj))) {
-        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) {
-          if(input$nj_tiles_scale_2 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_tiles_mapping_div_mid_2",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$nj_tile_num == 3) {
-      if(!is.null(input$nj_fruit_variable_3) & (!is.null(Vis$meta_nj))) {
-        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) {
-          if(input$nj_tiles_scale_3 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_tiles_mapping_div_mid_3",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$nj_tile_num == 4) {
-      if(!is.null(input$nj_fruit_variable_4) & (!is.null(Vis$meta_nj))) {
-        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) {
-          if(input$nj_tiles_scale_4 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_tiles_mapping_div_mid_4",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$nj_tile_num == 5) {
-      if(!is.null(input$nj_fruit_variable_5) & (!is.null(Vis$meta_nj))) {
-        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) {
-          if(input$nj_tiles_scale_5 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_tiles_mapping_div_mid_5",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  output$upgma_fruit_mapping_info <- renderUI({
-    if(input$upgma_tile_num == 1) {
-      if(!is.null(input$upgma_fruit_variable) & (!is.null(Vis$meta_upgma))) {
-        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) {
-          if(input$upgma_tiles_scale_1 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_tiles_mapping_div_mid_1",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$upgma_tile_num == 2) {
-      if(!is.null(input$upgma_fruit_variable_2) & (!is.null(Vis$meta_upgma))) {
-        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) {
-          if(input$upgma_tiles_scale_2 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_tiles_mapping_div_mid_2",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$upgma_tile_num == 3) {
-      if(!is.null(input$upgma_fruit_variable_3) & (!is.null(Vis$meta_upgma))) {
-        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) {
-          if(input$upgma_tiles_scale_3 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_tiles_mapping_div_mid_3",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$upgma_tile_num == 4) {
-      if(!is.null(input$upgma_fruit_variable_4) & (!is.null(Vis$meta_upgma))) {
-        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) {
-          if(input$upgma_tiles_scale_4 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_tiles_mapping_div_mid_4",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    } else if (input$upgma_tile_num == 5) {
-      if(!is.null(input$upgma_fruit_variable_5) & (!is.null(Vis$meta_upgma))) {
-        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) {
-          if(input$upgma_tiles_scale_5 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_tiles_mapping_div_mid_5",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  output$nj_heatmap_mapping_info <- renderUI({
-    if(!is.null(input$nj_heatmap_select) & (!is.null(Vis$meta_nj))) {
-      if (any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)) & 
-          any(!sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric))) {
-        column(
-          width = 3,
-          h5("Heatmap with categorical and continous values not possible", 
-             style = "color: #E18B00; font-size: 12px; font-style: italic; margin-top: 15px;  margin-left: 40px")
-        ) 
-      } else {
-        if(any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric))) {
-          if(input$nj_heatmap_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "nj_heatmap_div_mid",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_nj[input$nj_heatmap_select]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Categorical values", style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      }
-    } else {NULL}
-  })
-  
-  output$upgma_heatmap_mapping_info <- renderUI({
-    if(!is.null(input$upgma_heatmap_select) & (!is.null(Vis$meta_upgma))) {
-      if (any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)) & 
-          any(!sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric))) {
-        column(
-          width = 3,
-          h5("Heatmap with categorical and continous values not possible", 
-             style = "color: #E18B00; font-size: 12px; font-style: italic; margin-top: 15px;  margin-left: 40px")
-        ) 
-      } else {
-        if(any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric))) {
-          if(input$upgma_heatmap_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
-            column(
-              width = 3,
-              fluidRow(
-                column(
-                  width = 4,
-                  h5("Midpoint", style = "color: white; margin-top: 22px;")
-                ),
-                column(
-                  width = 8,
-                  div(
-                    class = "divmid-sel1",
-                    selectInput(
-                      "upgma_heatmap_div_mid",
-                      label = "",
-                      choices = c("Zero", "Mean", "Median"),
-                      selected = "Mean"
-                    )
-                  )
-                )
-              )
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
-            ) 
-          }
-        } else {
-          if(length(unique(unlist(Vis$meta_upgma[input$upgma_heatmap_select]))) > 7) {
-            column(
-              width = 3,
-              h5(paste0("> 7 categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
-            )
-          } else {
-            column(
-              width = 3,
-              h5("Categorical values", style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
-            )
-          }
-        }
-      }
-    } else {NULL}
-  })
-  
-  # Tiles offset
-  output$nj_fruit_offset_circ <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "nj_fruit_offset_circ",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_fruit_offset_circ",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_fruit_offset_circ <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        offset <- 0.15
-        step <- 0.1
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.05
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "upgma_fruit_offset_circ",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_fruit_offset_circ",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.05,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$nj_fruit_offset_circ_2 <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "nj_fruit_offset_circ_2",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_fruit_offset_circ_2",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_fruit_offset_circ_2 <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "upgma_fruit_offset_circ_2",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_fruit_offset_circ_2",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$nj_fruit_offset_circ_3 <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "nj_fruit_offset_circ_3",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_fruit_offset_circ_3",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_fruit_offset_circ_3 <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "upgma_fruit_offset_circ_3",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_fruit_offset_circ_3",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$nj_fruit_offset_circ_4 <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "nj_fruit_offset_circ_4",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_fruit_offset_circ_4",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_fruit_offset_circ_4 <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "upgma_fruit_offset_circ_4",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_fruit_offset_circ_4",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$nj_fruit_offset_circ_5 <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "nj_fruit_offset_circ_5",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_fruit_offset_circ_5",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_fruit_offset_circ_5 <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        offset <- 0.15
-        step <- 0.03
-        min <- -0.6
-        max <- 0.6
-      } else {
-        offset <- 0.05
-        step <- 0.01
-        min <- -0.2
-        max <- 0.2
-      }
-      
-      sliderInput(
-        "upgma_fruit_offset_circ_5",
-        label = "",
-        min = min,
-        max = max,
-        step= step,
-        value = offset,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_fruit_offset_circ_5",
-        label = "",
-        min = -0.2,
-        max = 0.2,
-        step= 0.01,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  # For Layout change update tiles offset position
-  observeEvent(input$nj_layout, {
-    
-    if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-      offset <- 0.05
-      step <- 0.01
-      min <- -0.2
-      max <- 0.2
-    } else {
-      offset <- 0.15
-      step <- 0.03
-      min <- -0.6
-      max <- 0.6
-    }
-    
-    updateSliderInput(session, "nj_fruit_offset_circ", min = min, step = step, max = max)
-    updateSliderInput(session, "nj_fruit_offset_circ_2", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "nj_fruit_offset_circ_3", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "nj_fruit_offset_circ_4", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "nj_fruit_offset_circ_5", min = min, step = step, max = max, value = offset) 
-  })
-  
-  observeEvent(input$upgma_layout, {
-    
-    if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-      offset <- 0.05
-      step <- 0.01
-      min <- -0.2
-      max <- 0.2
-    } else {
-      offset <- 0.15
-      step <- 0.03
-      min <- -0.6
-      max <- 0.6
-    }
-    
-    updateSliderInput(session, "upgma_fruit_offset_circ", min = min, step = step, max = max)
-    updateSliderInput(session, "upgma_fruit_offset_circ_2", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "upgma_fruit_offset_circ_3", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "upgma_fruit_offset_circ_4", min = min, step = step, max = max, value = offset)
-    updateSliderInput(session, "upgma_fruit_offset_circ_5", min = min, step = step, max = max, value = offset) 
-  })
-  
-  # Heatmap width
-  output$nj_heatmap_width <- renderUI({
-    if(!is.null(input$nj_heatmap_select)) {
-      length_input <- length(input$nj_heatmap_select)
-      if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
-        if(length_input < 3) {
-          width <- 0.1
-        } else {
-          if (length_input >= 3 && length_input <= 50) {
-            width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-          } else {
-            width <- 1.5
-          }   
-        }
-      } else {
-        if(length_input < 3) {
-          width <- 0.3
-        } else if (length_input >= 3 && length_input <= 27) {
-          width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 3
-        }
-      }
-      
-      sliderInput(
-        "nj_heatmap_width",
-        label = "",
-        min = 0.05,
-        max = 1.5,
-        value = width,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_heatmap_width",
-        label = "",
-        min = 0.05,
-        max = 1.5,
-        value = 0.1,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_heatmap_width <- renderUI({
-    if(!is.null(input$upgma_heatmap_select)) {
-      length_input <- length(input$upgma_heatmap_select)
-      if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
-        if(length_input < 3) {
-          width <- 0.1
-        } else {
-          if (length_input >= 3 && length_input <= 50) {
-            width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-          } else {
-            width <- 1.5
-          }   
-        }
-      } else {
-        if(length_input < 3) {
-          width <- 0.3
-        } else if (length_input >= 3 && length_input <= 27) {
-          width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 3
-        }
-      }
-      
-      sliderInput(
-        "upgma_heatmap_width",
-        label = "",
-        min = 0.05,
-        max = 1.5,
-        value = width,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_heatmap_width",
-        label = "",
-        min = 0.05,
-        max = 1.5,
-        value = 0.1,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  # Update value if new variables added
-  observeEvent(input$nj_heatmap_select, {
-    
-    length_input <- length(input$nj_heatmap_select)
-    if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
-      if(length_input < 3) {
-        width <- 0.1
-      } else {
-        if (length_input >= 3 && length_input <= 50) {
-          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 1.5
-        }   
-      }
-    } else {
-      if(length_input < 3) {
-        width <- 0.3
-      } else if (length_input >= 3 && length_input <= 27) {
-        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-      } else {
-        width <- 3
-      }
-    }
-    updateSliderInput(session, "nj_heatmap_width", value = width)
-  })
-  
-  observeEvent(input$upgma_heatmap_select, {
-    
-    length_input <- length(input$upgma_heatmap_select)
-    if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
-      if(length_input < 3) {
-        width <- 0.1
-      } else {
-        if (length_input >= 3 && length_input <= 50) {
-          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 1.5
-        }   
-      }
-    } else {
-      if(length_input < 3) {
-        width <- 0.3
-      } else if (length_input >= 3 && length_input <= 27) {
-        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-      } else {
-        width <- 3
-      }
-    }
-    updateSliderInput(session, "upgma_heatmap_width", value = width)
-  })
-  
-  # Update value if layout changed
-  observeEvent(input$nj_layout, {
-    length_input <- length(input$nj_heatmap_select)
-    if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
-      if(length_input < 3) {
-        width <- 0.1
-      } else {
-        if (length_input >= 3 && length_input <= 50) {
-          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 1.5
-        }   
-      }
-    } else {
-      if(length_input < 3) {
-        width <- 0.3
-      } else if (length_input >= 3 && length_input <= 27) {
-        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-      } else {
-        width <- 3
-      }
-    }
-    updateSliderInput(session, "nj_heatmap_width", value = width)
-  })
-  
-  observeEvent(input$upgma_layout, {
-    length_input <- length(input$upgma_heatmap_select)
-    if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
-      if(length_input < 3) {
-        width <- 0.1
-      } else {
-        if (length_input >= 3 && length_input <= 50) {
-          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          width <- 1.5
-        }   
-      }
-    } else {
-      if(length_input < 3) {
-        width <- 0.3
-      } else if (length_input >= 3 && length_input <= 27) {
-        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-      } else {
-        width <- 3
-      }
-    }
-    updateSliderInput(session, "upgma_heatmap_width", value = width)
-  })
-  
-  # Heatmap column titles position
-  observeEvent(input$nj_layout, {
-    if(!(input$nj_layout == "inward" | input$nj_layout == "circular")) {
-      updateSliderInput(session, "nj_colnames_y", value = -1)
-    } else {
-      updateSliderInput(session, "nj_colnames_y", value = 0)
-    }
-  })
-  
-  observeEvent(input$upgma_layout, {
-    if(!(input$upgma_layout == "inward" | input$upgma_layout == "circular")) {
-      updateSliderInput(session, "upgma_colnames_y", value = -1)
-    } else {
-      updateSliderInput(session, "upgma_colnames_y", value = 0)
-    }
-  })
-  
-  output$nj_colnames_y <- renderUI({
-    if(!is.null(sum(DB$data$Include))) {
-      if(input$nj_layout == "inward" | input$nj_layout == "circular") {
-        min <- 0
-        val <- 0
-      } else {
-        val <- -1
-        if((sum(DB$data$Include) * -0.1) > -2) {
-          min <- -2
-        } else {
-          min <- round(sum(DB$data$Include) * -0.1, 0)
-        }
-      }
-      sliderInput(
-        "nj_colnames_y",
-        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
-        min = min,
-        max = sum(DB$data$Include),
-        value = val,
-        step = 1,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_colnames_y",
-        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
-        min = -10,
-        max = 10,
-        value = 0,
-        step = 1,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_colnames_y <- renderUI({
-    if(!is.null(sum(DB$data$Include))) {
-      if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
-        min <- 0
-        val <- 0
-      } else {
-        val <- -1
-        if((sum(DB$data$Include) * -0.1) > -2) {
-          min <- -2
-        } else {
-          min <- round(sum(DB$data$Include) * -0.1, 0)
-        }
-      }
-      sliderInput(
-        "upgma_colnames_y",
-        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
-        min = min,
-        max = sum(DB$data$Include),
-        value = val,
-        step = 1,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_colnames_y",
-        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
-        min = -10,
-        max = 10,
-        value = 0,
-        step = 1,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  # Heatmap column titles angle
-  output$nj_colnames_angle <- renderUI({
-    if(!is.null(input$nj_layout)) {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        angle <- 90
-      } else {angle <- -90}
-      sliderInput(
-        "nj_colnames_angle",
-        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
-        min = -90,
-        max = 90,
-        value = angle,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_colnames_angle",
-        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
-        min = -90,
-        max = 90,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_colnames_angle <- renderUI({
-    if(!is.null(input$upgma_layout)) {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        angle <- 90
-      } else {angle <- -90}
-      sliderInput(
-        "upgma_colnames_angle",
-        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
-        min = -90,
-        max = 90,
-        value = angle,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_colnames_angle",
-        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
-        min = -90,
-        max = 90,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  # Change heatmap column titles angle and label align when switching layout
-  observeEvent(input$nj_layout, {
-    if(input$nj_layout == "circular" | input$nj_layout == "inward"){
-      angle <- 90
-      val <- TRUE
-    } else {
-      angle <- -90
-      val <- FALSE
-    }
-    updateSwitchInput(session, "nj_align", value = val)
-    updateSliderInput(session, "nj_colnames_angle", value = angle)
-  })
-  
-  observeEvent(input$upgma_layout, {
-    if(input$upgma_layout == "circular" | input$upgma_layout == "inward"){
-      angle <- 90
-      val <- TRUE
-    } else {
-      angle <- -90
-      val <- FALSE
-    }
-    updateSwitchInput(session, "upgma_align", value = val)
-    updateSliderInput(session, "upgma_colnames_angle", value = angle)
-  })
-  
-  # Tile number selector update each other
-  observeEvent(input$nj_tile_num, {
-    updateSelectInput(session, "nj_tile_number", selected = input$nj_tile_num)
-  })
-  
-  observeEvent(input$nj_tile_number, {
-    updateSelectInput(session, "nj_tile_num", selected = input$nj_tile_number)
-  })
-  
-  observeEvent(input$upgma_tile_num, {
-    updateSelectInput(session, "upgma_tile_number", selected = input$upgma_tile_num)
-  })
-  
-  observeEvent(input$upgma_tile_number, {
-    updateSelectInput(session, "upgma_tile_num", selected = input$upgma_tile_number)
-  })
-  
-  # Clade coloring
-  output$nj_clade_scale <- renderUI({
-    if(length(input$nj_parentnode) <= 1) {
-      fluidRow(
-        column(
-          width = 5,
-          h5("Color", style = "color:white; position: relative; right: -15px; margin-top: 30px")
-        ),
-        column(
-          width = 7,
-          align = "center",
-          colorPickr(
-            inputId = "nj_clade_scale",
-            selected = "#D0F221",
-            label = "",
-            update = "changestop",
-            interaction = list(clear = FALSE,
-                               save = FALSE),
-            position = "right-start",
-            width = "100%"
-          )
-        )
-      )
-    } else {
-      fluidRow(
-        column(
-          width = 5,
-          h5("Scale", style = "color:white; position: relative; right: -15px; margin-top: 30px")
-        ),
-        column(
-          width = 7,
-          align = "center",
-          div(
-            class = "sel-clade-scale",
-            selectInput(
-              "nj_clade_scale",
-              "",
-              choices = list(
-                Qualitative = list(
-                  "Set1",
-                  "Set2",
-                  "Set3",
-                  "Pastel1",
-                  "Pastel2",
-                  "Paired",
-                  "Dark2",
-                  "Accent"
-                ),
-                Sequential = list(
-                  "YlOrRd",
-                  "YlOrBr",
-                  "YlGnBu",
-                  "YlGn",
-                  "Reds",
-                  "RdPu",
-                  "Purples",
-                  "PuRd",
-                  "PuBuGn",
-                  "PuBu",
-                  "OrRd",
-                  "Oranges",
-                  "Greys",
-                  "Greens",
-                  "GnBu",
-                  "BuPu",
-                  "BuGn",
-                  "Blues"
-                )
-              )
-            )
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_clade_scale <- renderUI({
-    if(length(input$upgma_parentnode) <= 1) {
-      fluidRow(
-        column(
-          width = 5,
-          h5("Color", style = "color:white; position: relative; right: -15px; margin-top: 30px")
-        ),
-        column(
-          width = 7,
-          align = "center",
-          colorPickr(
-            inputId = "upgma_clade_scale",
-            selected = "#D0F221",
-            label = "",
-            update = "changestop",
-            interaction = list(clear = FALSE,
-                               save = FALSE),
-            position = "right-start",
-            width = "100%"
-          )
-        )
-      )
-    } else {
-      fluidRow(
-        column(
-          width = 5,
-          h5("Scale", style = "color:white; position: relative; right: -15px; margin-top: 30px")
-        ),
-        column(
-          width = 7,
-          align = "center",
-          div(
-            class = "sel-clade-scale",
-            selectInput(
-              "upgma_clade_scale",
-              "",
-              choices = list(
-                Qualitative = list(
-                  "Set1",
-                  "Set2",
-                  "Set3",
-                  "Pastel1",
-                  "Pastel2",
-                  "Paired",
-                  "Dark2",
-                  "Accent"
-                ),
-                Sequential = list(
-                  "YlOrRd",
-                  "YlOrBr",
-                  "YlGnBu",
-                  "YlGn",
-                  "Reds",
-                  "RdPu",
-                  "Purples",
-                  "PuRd",
-                  "PuBuGn",
-                  "PuBu",
-                  "OrRd",
-                  "Oranges",
-                  "Greys",
-                  "Greens",
-                  "GnBu",
-                  "BuPu",
-                  "BuGn",
-                  "Blues"
-                )
-              )
-            )
-          )
-        )
-      )
-    }
-  })
-  
-  # Heatmap variable color scale
-  output$nj_heatmap_scale <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_heatmap_select])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_heatmap_scale",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_heatmap_select]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_heatmap_scale",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_heatmap_scale",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Paired"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_heatmap_scale <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_heatmap_select])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_heatmap_scale",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_heatmap_select]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_heatmap_scale",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_heatmap_scale",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Paired"
-          )
-        )
-      }
-    }
-  })
-  
-  # Tiles variable color scale
-  output$nj_tiles_scale_1 <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiles_scale_1",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_1",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_1",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiles_scale_1 <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiles_scale_1",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_1",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_1",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$nj_tiles_scale_2 <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_2])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiles_scale_2",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_2",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_2",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiles_scale_2 <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiles_scale_2",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_2",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_2",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$nj_tiles_scale_3 <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_3])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiles_scale_3",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_3",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_3",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiles_scale_3 <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiles_scale_3",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_3",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_3",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$nj_tiles_scale_4 <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_4])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiles_scale_4",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) > 7) {
-        shinyjs::disabled(selectInput(
-          "nj_tiles_scale_4",
-          "",
-          choices = list(
-            Gradient = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            )
-          ),
-          selected = "turbo"
-        ))
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_4",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiles_scale_4 <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiles_scale_4",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_4",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_4",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$nj_tiles_scale_5 <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_5])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiles_scale_5",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_5",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiles_scale_5",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiles_scale_5 <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiles_scale_5",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_5",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiles_scale_5",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            ),
-            selected = "Accent"
-          )
-        )
-      }
-    }
-  })
-  
-  # Tip Labels Variable Color Scale
-  output$nj_tiplab_scale <- renderUI({
-    if(class(unlist(Vis$meta_nj[input$nj_color_mapping])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tiplab_scale",
-          "",
-          selectize = FALSE,
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiplab_scale",
-            "",
-            selectize = FALSE,
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tiplab_scale",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            )
-          )
-        )
-      }
-    }
-  })
-  
-  output$upgma_tiplab_scale <- renderUI({
-    if(class(unlist(Vis$meta_upgma[input$upgma_color_mapping])) == "numeric") {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tiplab_scale",
-          "",
-          choices = list(
-            Continous = list(
-              "Magma" = "magma",
-              "Inferno" = "inferno",
-              "Plasma" = "plasma",
-              "Viridis" = "viridis",
-              "Cividis" = "cividis",
-              "Rocket" = "rocket",
-              "Mako" = "mako",
-              "Turbo" = "turbo"
-            ),
-            Diverging = list(
-              "Spectral",
-              "RdYlGn",
-              "RdYlBu",
-              "RdGy",
-              "RdBu",
-              "PuOr",
-              "PRGn",
-              "PiYG",
-              "BrBG"
-            )
-          )
-        )
-      )
-    } else {
-      if(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) > 7) {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiplab_scale",
-            "",
-            choices = list(
-              Gradient = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              )
-            ),
-            selected = "turbo"
-          )
-        )
-      } else {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tiplab_scale",
-            "",
-            choices = list(
-              Qualitative = list(
-                "Set1",
-                "Set2",
-                "Set3",
-                "Pastel1",
-                "Pastel2",
-                "Paired",
-                "Dark2",
-                "Accent"
-              ),
-              Sequential = list(
-                "YlOrRd",
-                "YlOrBr",
-                "YlGnBu",
-                "YlGn",
-                "Reds",
-                "RdPu",
-                "Purples",
-                "PuRd",
-                "PuBuGn",
-                "PuBu",
-                "OrRd",
-                "Oranges",
-                "Greys",
-                "Greens",
-                "GnBu",
-                "BuPu",
-                "BuGn",
-                "Blues"
-              )
-            )
-          )
-        )
-      }
-    }
-  })
-  
-  # Tippoint Scale
-  output$nj_tippoint_scale <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      if(class(unlist(Vis$meta_nj[input$nj_tipcolor_mapping])) == "numeric") {
-        shinyjs::disabled(
-          selectInput(
-            "nj_tippoint_scale",
-            "",
-            choices = list(
-              Continous = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              ),
-              Diverging = list(
-                "Spectral",
-                "RdYlGn",
-                "RdYlBu",
-                "RdGy",
-                "RdBu",
-                "PuOr",
-                "PRGn",
-                "PiYG",
-                "BrBG"
-              )
-            )
-          )
-        )
-      } else {
-        if(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) > 7) {
-          shinyjs::disabled(
-            selectInput(
-              "nj_tippoint_scale",
-              "",
-              choices = list(
-                Gradient = list(
-                  "Magma" = "magma",
-                  "Inferno" = "inferno",
-                  "Plasma" = "plasma",
-                  "Viridis" = "viridis",
-                  "Cividis" = "cividis",
-                  "Rocket" = "rocket",
-                  "Mako" = "mako",
-                  "Turbo" = "turbo"
-                )
-              ),
-              selected = "turbo"
-            )
-          )
-        } else {
-          shinyjs::disabled(
-            selectInput(
-              "nj_tippoint_scale",
-              "",
-              choices = list(
-                Qualitative = list(
-                  "Set1",
-                  "Set2",
-                  "Set3",
-                  "Pastel1",
-                  "Pastel2",
-                  "Paired",
-                  "Dark2",
-                  "Accent"
-                ),
-                Sequential = list(
-                  "YlOrRd",
-                  "YlOrBr",
-                  "YlGnBu",
-                  "YlGn",
-                  "Reds",
-                  "RdPu",
-                  "Purples",
-                  "PuRd",
-                  "PuBuGn",
-                  "PuBu",
-                  "OrRd",
-                  "Oranges",
-                  "Greys",
-                  "Greens",
-                  "GnBu",
-                  "BuPu",
-                  "BuGn",
-                  "Blues"
-                )
-              ),
-              selected = "Set2"
-            )
-          )
-        }
-      }
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tippoint_scale",
-          "",
-          choices = list(
-            Qualitative = list(
-              "Set1",
-              "Set2",
-              "Set3",
-              "Pastel1",
-              "Pastel2",
-              "Paired",
-              "Dark2",
-              "Accent"
-            ),
-            Sequential = list(
-              "YlOrRd",
-              "YlOrBr",
-              "YlGnBu",
-              "YlGn",
-              "Reds",
-              "RdPu",
-              "Purples",
-              "PuRd",
-              "PuBuGn",
-              "PuBu",
-              "OrRd",
-              "Oranges",
-              "Greys",
-              "Greens",
-              "GnBu",
-              "BuPu",
-              "BuGn",
-              "Blues"
-            )
-          ),
-          selected = "Set2"
-        )
-      )
-    }
-  })
-  
-  output$upgma_tippoint_scale <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      if(class(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping])) == "numeric") {
-        shinyjs::disabled(
-          selectInput(
-            "upgma_tippoint_scale",
-            "",
-            choices = list(
-              Continous = list(
-                "Magma" = "magma",
-                "Inferno" = "inferno",
-                "Plasma" = "plasma",
-                "Viridis" = "viridis",
-                "Cividis" = "cividis",
-                "Rocket" = "rocket",
-                "Mako" = "mako",
-                "Turbo" = "turbo"
-              ),
-              Diverging = list(
-                "Spectral",
-                "RdYlGn",
-                "RdYlBu",
-                "RdGy",
-                "RdBu",
-                "PuOr",
-                "PRGn",
-                "PiYG",
-                "BrBG"
-              )
-            ),
-            selected = c("Viridis" = "viridis")
-          )
-        )
-      } else {
-        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) > 7) {
-          shinyjs::disabled(
-            selectInput(
-              "upgma_tippoint_scale",
-              "",
-              choices = list(
-                Gradient = list(
-                  "Magma" = "magma",
-                  "Inferno" = "inferno",
-                  "Plasma" = "plasma",
-                  "Viridis" = "viridis",
-                  "Cividis" = "cividis",
-                  "Rocket" = "rocket",
-                  "Mako" = "mako",
-                  "Turbo" = "turbo"
-                )
-              ),
-              selected = "turbo"
-            )
-          )
-        } else {
-          shinyjs::disabled(
-            selectInput(
-              "upgma_tippoint_scale",
-              "",
-              choices = list(
-                Qualitative = list(
-                  "Set1",
-                  "Set2",
-                  "Set3",
-                  "Pastel1",
-                  "Pastel2",
-                  "Paired",
-                  "Dark2",
-                  "Accent"
-                ),
-                Sequential = list(
-                  "YlOrRd",
-                  "YlOrBr",
-                  "YlGnBu",
-                  "YlGn",
-                  "Reds",
-                  "RdPu",
-                  "Purples",
-                  "PuRd",
-                  "PuBuGn",
-                  "PuBu",
-                  "OrRd",
-                  "Oranges",
-                  "Greys",
-                  "Greens",
-                  "GnBu",
-                  "BuPu",
-                  "BuGn",
-                  "Blues"
-                )
-              ),
-              selected = "Set2"
-            )
-          )
-        }
-      }
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tippoint_scale",
-          "",
-          choices = list(
-            Qualitative = list(
-              "Set1",
-              "Set2",
-              "Set3",
-              "Pastel1",
-              "Pastel2",
-              "Paired",
-              "Dark2",
-              "Accent"
-            ),
-            Sequential = list(
-              "YlOrRd",
-              "YlOrBr",
-              "YlGnBu",
-              "YlGn",
-              "Reds",
-              "RdPu",
-              "Purples",
-              "PuRd",
-              "PuBuGn",
-              "PuBu",
-              "OrRd",
-              "Oranges",
-              "Greys",
-              "Greens",
-              "GnBu",
-              "BuPu",
-              "BuGn",
-              "Blues"
-            )
-          ),
-          selected = "Set2"
-        )
-      )
-    }
-  })
-  
-  # Clade Highlights
-  output$nj_parentnode <- renderUI({
-    if(!is.null(Vis$nj_parentnodes)) {
-      pickerInput(
-        "nj_parentnode",
-        label = "",
-        choices = sort(unique(as.numeric(Vis$nj_parentnodes))),
-        multiple = TRUE,
-        options = list(
-          `live-search` = TRUE,
-          size = 10,
-          style = "background-color: white; border-radius: 5px;"
-        ),
-        width = "99%"
-      )
-    } else {
-      pickerInput(
-        "nj_parentnode",
-        label = "",
-        choices = c(),
-        multiple = TRUE,
-        options = list(
-          `live-search` = TRUE,
-          size = 10,
-          style = "background-color: white; border-radius: 5px;"
-        ),
-        width = "99%"
-      )
-    }
-  })
-  
-  output$upgma_parentnode <- renderUI({
-    if(!is.null(Vis$upgma_parentnodes)) {
-      pickerInput(
-        "upgma_parentnode",
-        label = "",
-        choices = sort(unique(as.numeric(Vis$upgma_parentnodes))),
-        multiple = TRUE,
-        options = list(
-          `live-search` = TRUE,
-          size = 10,
-          style = "background-color: white; border-radius: 5px;"
-        ),
-        width = "99%"
-      )
-    } else {
-      pickerInput(
-        "upgma_parentnode",
-        label = "",
-        choices = c(),
-        multiple = TRUE,
-        options = list(
-          `live-search` = TRUE,
-          size = 10,
-          style = "background-color: white; border-radius: 5px;"
-        ),
-        width = "99%"
-      )
-    }
-  })
-  
-  # Branch label size
-  output$nj_branch_size <- renderUI(
-    numericInput(
-      "nj_branch_size",
-      label = h5("Size", style = "color:white; margin-bottom: 0px"),
-      min = 2,
-      max = 10,
-      step = 0.5,
-      value = Vis$branch_size_nj,
-      width = "80px"
-    )
-  )
-  
-  output$upgma_branch_size <- renderUI(
-    numericInput(
-      "upgma_branch_size",
-      label = h5("Size", style = "color:white; margin-bottom: 0px"),
-      min = 2,
-      max = 10,
-      step = 0.5,
-      value = Vis$branch_size_upgma,
-      width = "80px"
-    )
-  )
-  
-  # Tippanel size
-  output$nj_tiplab_padding <- renderUI(
-    if(!is.null(Vis$tiplab_padding_nj)) {
-      sliderInput(
-        inputId = "nj_tiplab_padding",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 0.05,
-        max = 1,
-        value = Vis$tiplab_padding_nj,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "nj_tiplab_padding",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 0.05,
-        max = 1,
-        value = 0.2,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  output$upgma_tiplab_padding <- renderUI(
-    if(!is.null(Vis$tiplab_padding_upgma)) {
-      sliderInput(
-        inputId = "upgma_tiplab_padding",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 0.05,
-        max = 1,
-        value = Vis$tiplab_padding_upgma,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "upgma_tiplab_padding",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 0.05,
-        max = 1,
-        value = 0.2,
-        step = 0.05,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  # Nodepoint size
-  output$nj_nodepoint_size <- renderUI(
-    if(!is.null(Vis$nodepointsize_nj)) {
-      sliderInput(
-        inputId = "nj_nodepoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        value = Vis$nodepointsize_nj,
-        step = 0.5,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "nj_nodepoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        value = 2.5,
-        step = 0.5,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  output$upgma_nodepoint_size <- renderUI(
-    if(!is.null(Vis$nodepointsize_upgma)) {
-      sliderInput(
-        inputId = "upgma_nodepoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        value = Vis$nodepointsize_upgma,
-        step = 0.5,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "upgma_nodepoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        value = 2.5,
-        step = 0.5,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  # Tippoint size 
-  output$nj_tippoint_size <- renderUI(
-    if(!is.null(Vis$tippointsize_nj)) {
-      sliderInput(
-        inputId = "nj_tippoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        step = 0.5,
-        value = Vis$tippointsize_nj,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "nj_tippoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        step = 0.5,
-        value = 4,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  output$upgma_tippoint_size <- renderUI(
-    if(!is.null(Vis$tippointsize_upgma)) {
-      sliderInput(
-        inputId = "upgma_tippoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        step = 0.5,
-        value = Vis$tippointsize_upgma,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        inputId = "upgma_tippoint_size",
-        label = h5("Size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 20,
-        step = 0.5,
-        value = 4,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  )
-  
-  # Tiplabel size
-  output$nj_tiplab_size <- renderUI(
-    if(!is.null(Vis$labelsize_nj)) {
-      numericInput(
-        "nj_tiplab_size",
-        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        step = 0.5,
-        value = Vis$labelsize_nj,
-        width = "80px"
-      )
-    } else {
-      numericInput(
-        "nj_tiplab_size",
-        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        step = 0.5,
-        value = 4,
-        width = "80px"
-      )
-    }
-  )
-  
-  output$upgma_tiplab_size <- renderUI(
-    if(!is.null(Vis$labelsize_upgma)) {
-      numericInput(
-        "upgma_tiplab_size",
-        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        step = 0.5,
-        value = Vis$labelsize_upgma,
-        width = "80px"
-      )
-    } else {
-      numericInput(
-        "upgma_tiplab_size",
-        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        step = 0.5,
-        value = 4,
-        width = "80px"
-      )
-    }
-  )
-  
-  # Rootedge length 
-  output$nj_rootedge_length <- renderUI({
-    if(!is.null(Vis$nj_max_x)) {
-      if(round(ceiling(Vis$nj_max_x) * 0.02, 0) < 1) {
-        min <- 1
-      } else {
-        min <- round(ceiling(Vis$nj_max_x) * 0.02, 0)  
-      }
-      max <- round(ceiling(Vis$nj_max_x) * 0.2, 0)
-      sliderInput(
-        "nj_rootedge_length",
-        label = h5("Rootedge Length", style = "color:white; margin-bottom: 0px"),
-        min = min,
-        max = max,
-        value = round(ceiling(Vis$nj_max_x) * 0.05, 0),
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_rootedge_length",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        value = 2,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_rootedge_length <- renderUI({
-    if(!is.null(Vis$upgma_max_x)) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.02, 0) < 1) {
-        min <- 1
-      } else {
-        min <- round(ceiling(Vis$upgma_max_x) * 0.02, 0)  
-      }
-      max <- round(ceiling(Vis$upgma_max_x) * 0.2, 0)
-      sliderInput(
-        "upgma_rootedge_length",
-        label = h5("Rootedge Length", style = "color:white; margin-bottom: 0px"),
-        min = min,
-        max = max,
-        value = round(ceiling(Vis$upgma_max_x) * 0.05, 0),
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_rootedge_length",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        value = 2,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  # Treescale 
-  output$nj_treescale_width <- renderUI({
-    if(!is.null(Vis$nj_max_x)) {
-      numericInput(
-        "nj_treescale_width",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        value = round(ceiling(Vis$nj_max_x) * 0.1, 0),
-        min = 1,
-        max = round(floor(Vis$nj_max_x) * 0.5, 0),
-        step = 1,
-        width = "80px"
-      )
-    } else {
-      numericInput(
-        "nj_treescale_width",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        value = 2,
-        min = 1,
-        max = 10,
-        step = 1,
-        width = "80px"
-      )
-    }
-  })
-  
-  output$upgma_treescale_width <- renderUI({
-    if(!is.null(Vis$upgma_max_x)) {
-      numericInput(
-        "upgma_treescale_width",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        value = round(ceiling(Vis$upgma_max_x) * 0.1, 0),
-        min = 1,
-        max = round(floor(Vis$upgma_max_x) * 0.5, 0),
-        step = 1,
-        width = "80px"
-      )
-    } else {
-      numericInput(
-        "upgma_treescale_width",
-        label = h5("Length", style = "color:white; margin-bottom: 0px"),
-        value = 2,
-        min = 1,
-        max = 10,
-        step = 1,
-        width = "80px"
-      )
-    }
-  })
-  
-  output$nj_treescale_x <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(ceiling(Vis$nj_min_x) < 1) {
-        floor <- 1
-      } else {
-        floor <- ceiling(Vis$nj_min_x)
-      }
-      sliderInput(
-        "nj_treescale_x",
-        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-        min = floor,
-        max = round(floor(Vis$nj_max_x)),
-        value = round(ceiling(Vis$nj_max_x) * 0.2, 0),
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_treescale_x",
-        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        value = 2,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_treescale_x <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(ceiling(Vis$upgma_min_x) < 1) {
-        floor <- 1
-      } else {
-        floor <- ceiling(Vis$upgma_min_x)
-      }
-      sliderInput(
-        "upgma_treescale_x",
-        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-        min = floor,
-        max = round(floor(Vis$upgma_max_x)),
-        value = round(ceiling(Vis$upgma_max_x) * 0.2, 0),
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_treescale_x",
-        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
-        min = 1,
-        max = 10,
-        value = 2,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$nj_treescale_y <- renderUI({
-    if(!is.null(sum(DB$data$Include))) {
-      sliderInput(
-        "nj_treescale_y",
-        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-        min = 0,
-        max = sum(DB$data$Include),
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_treescale_y",
-        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-        min = 0,
-        max = 10,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_treescale_y <- renderUI({
-    if(!is.null(sum(DB$data$Include))) {
-      sliderInput(
-        "upgma_treescale_y",
-        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-        min = 0,
-        max = sum(DB$data$Include),
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_treescale_y",
-        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
-        min = 0,
-        max = 10,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  ### Heatmap 
-  # Heatmap picker
-  output$nj_heatmap_sel <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      meta <- select(Vis$meta_nj, -c(taxa, Index, `Assembly ID`, `Assembly Name`,
-                                     Scheme, `Typing Date`, Successes, Errors))
-      
-      # Identify numeric columns
-      numeric_columns <- sapply(meta, is.numeric)
-      
-      numeric_column_names <- names(meta[numeric_columns])
-      
-      non_numeric_column_names <- names(meta)[!numeric_columns]
-      
-      choices <- list()
-      
-      # Add Continuous list only if there are numeric columns
-      if (length(numeric_column_names) > 0) {
-        choices$Continuous <- as.list(setNames(numeric_column_names, numeric_column_names))
-      }
-      
-      # Add Diverging list
-      choices$Categorical <- as.list(setNames(non_numeric_column_names, non_numeric_column_names))
-      
-      div(
-        class = "heatmap-picker",
-        shinyjs::disabled(
-          pickerInput(
-            inputId = "nj_heatmap_select",
-            label = "",
-            width = "100%",
-            choices = if(ncol(Vis$meta_nj) == 11) {
-              c(
-                `Isolation Date` = "Isolation Date",
-                Host = "Host",
-                Country = "Country",
-                City = "City"
-              )
-            } else {choices},
-            options = list(
-              `dropdown-align-center` = TRUE,
-              size = 10,
-              style = "background-color: white; border-radius: 5px;"
-            ),
-            multiple = TRUE
-          )
-        )
-      )
-    } else {
-      div(
-        class = "heatmap-picker",
-        shinyjs::disabled(
-          pickerInput(
-            inputId = "nj_heatmap_select",
-            label = "",
-            width = "100%",
-            choices = c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            ),
-            multiple = TRUE
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_heatmap_sel <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      meta <- select(Vis$meta_upgma, -c(taxa, Index, `Assembly ID`, `Assembly Name`,
-                                        Scheme, `Typing Date`, Successes, Errors))
-      
-      # Identify numeric columns
-      numeric_columns <- sapply(meta, is.numeric)
-      
-      numeric_column_names <- names(meta[numeric_columns])
-      
-      non_numeric_column_names <- names(meta)[!numeric_columns]
-      
-      choices <- list()
-      
-      # Add Continuous list only if there are numeric columns
-      if (length(numeric_column_names) > 0) {
-        choices$Continuous <- as.list(setNames(numeric_column_names, numeric_column_names))
-      }
-      
-      # Add Diverging list
-      choices$Categorical <- as.list(setNames(non_numeric_column_names, non_numeric_column_names))
-      
-      div(
-        class = "heatmap-picker",
-        shinyjs::disabled(
-          pickerInput(
-            inputId = "upgma_heatmap_select",
-            label = "",
-            width = "100%",
-            choices = if(ncol(Vis$meta_upgma) == 11) {
-              c(
-                `Isolation Date` = "Isolation Date",
-                Host = "Host",
-                Country = "Country",
-                City = "City"
-              )
-            } else {choices},
-            options = list(
-              `dropdown-align-center` = TRUE,
-              size = 10,
-              style = "background-color: white; border-radius: 5px;"
-            ),
-            multiple = TRUE
-          )
-        )
-      )
-    } else {
-      div(
-        class = "heatmap-picker",
-        shinyjs::disabled(
-          pickerInput(
-            inputId = "upgma_heatmap_select",
-            label = "",
-            width = "100%",
-            choices = c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            ),
-            multiple = TRUE
-          )
-        )
-      )
-    }
-  })
-  
-  # Heatmap offset
-  output$nj_heatmap_offset <- renderUI({
-    if(!is.null(Vis$nj_max_x)) {
-      sliderInput(
-        "nj_heatmap_offset",
-        label = "",
-        min = 0,
-        max = round(ceiling(Vis$nj_max_x)*1.5, 0),
-        step = 1,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "nj_heatmap_offset",
-        label = "",
-        min = 0,
-        max = 10,
-        step = 1,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  output$upgma_heatmap_offset <- renderUI({
-    if(!is.null(Vis$upgma_max_x)) {
-      sliderInput(
-        "upgma_heatmap_offset",
-        label = "",
-        min = 0,
-        max = round(ceiling(Vis$upgma_max_x)*1.5, 0),
-        step = 1,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      sliderInput(
-        "upgma_heatmap_offset",
-        label = "",
-        min = 0,
-        max = 10,
-        step = 1,
-        value = 0,
-        width = "150px",
-        ticks = FALSE
-      )
-    }
-  })
-  
-  ### Tiling 
-  # Geom Fruit select Variable
-  output$nj_fruit_variable <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$nj_fruit_variable2 <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_2",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_2",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$nj_fruit_variable3 <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_3",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_3",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$nj_fruit_variable4 <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_4",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_4",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$nj_fruit_variable5 <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_5",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_fruit_variable_5",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_fruit_variable <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_fruit_variable2 <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_2",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_2",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_fruit_variable3 <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(selectInput(
-        "upgma_fruit_variable_3",
-        "",
-        choices = if(ncol(Vis$meta_upgma) == 11) {
-          c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        } else {
-          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-        },
-        selected = c(`Isolation Date` = "Isolation Date"),
-        width = "100%"
-      ))
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_3",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_fruit_variable4 <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_4",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_4",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  output$upgma_fruit_variable5 <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_5",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(`Isolation Date` = "Isolation Date"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_fruit_variable_5",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        )
-      )
-    }
-  })
-  
-  # Geom Fruit Width
-  output$nj_fruit_width <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "nj_fruit_width_circ",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        sliderInput(
-          "nj_fruit_width_circ",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "nj_fruit_width_circ",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$nj_fruit_width2 <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "nj_fruit_width_circ_2",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        sliderInput(
-          "nj_fruit_width_circ_2",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "nj_fruit_width_circ_2",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$nj_fruit_width3 <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "nj_fruit_width_circ_3",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        sliderInput(
-          "nj_fruit_width_circ_3",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "nj_fruit_width_circ_3",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$nj_fruit_width4 <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "nj_fruit_width_circ_4",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        sliderInput(
-          "nj_fruit_width_circ_4",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "nj_fruit_width_circ_4",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$nj_fruit_width5 <- renderUI({
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "nj_fruit_width_circ_5",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-        sliderInput(
-          "nj_fruit_width_circ_5",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "nj_fruit_width_circ_5",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$upgma_fruit_width <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "upgma_fruit_width_circ",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        sliderInput(
-          "upgma_fruit_width_circ",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "upgma_fruit_width_circ",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$upgma_fruit_width2 <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "upgma_fruit_width_circ_2",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        sliderInput(
-          "upgma_fruit_width_circ_2",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "upgma_fruit_width_circ_2",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$upgma_fruit_width3 <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "upgma_fruit_width_circ_3",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        sliderInput(
-          "upgma_fruit_width_circ_3",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "upgma_fruit_width_circ_3",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$upgma_fruit_width4 <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "upgma_fruit_width_circ_4",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        sliderInput(
-          "upgma_fruit_width_circ_4",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "upgma_fruit_width_circ_4",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  output$upgma_fruit_width5 <- renderUI({
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-          if(width_calc < 1) {width <- 1}
-        } else {
-          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          if(width_calc < 1) {width <- 1}
-        }
-      }
-      sliderInput(
-        "upgma_fruit_width_circ_5",
-        label = "",
-        min = 1,
-        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
-        value = width,
-        width = "150px",
-        ticks = FALSE
-      )
-    } else {
-      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-        sliderInput(
-          "upgma_fruit_width_circ_5",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 3,
-          width = "150px",
-          ticks = FALSE
-        )
-      } else {
-        sliderInput(
-          "upgma_fruit_width_circ_5",
-          label = "",
-          min = 1,
-          max = 10,
-          value = 1,
-          width = "150px",
-          ticks = FALSE
-        )
-      }
-    }
-  })
-  
-  # For Layout change update tiles 
-  observeEvent(input$nj_layout, {
-    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
-      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          width <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
-        } else {
-          width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-        }
-      }
-      
-      updateSliderInput(session, "nj_fruit_width_circ", value = width)
-      updateSliderInput(session, "nj_fruit_width_circ_2", value = width)
-      updateSliderInput(session, "nj_fruit_width_circ_3", value = width)
-      updateSliderInput(session, "nj_fruit_width_circ_4", value = width)
-      updateSliderInput(session, "nj_fruit_width_circ_5", value = width) 
-    }
-  })
-  
-  observeEvent(input$upgma_layout, {
-    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
-      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- 3
-        } else {
-          width <- 1
-        }
-      } else {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
-        } else {
-          width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-        }
-      }
-      
-      updateSliderInput(session, "upgma_fruit_width_circ", value = width)
-      updateSliderInput(session, "upgma_fruit_width_circ_2", value = width)
-      updateSliderInput(session, "upgma_fruit_width_circ_3", value = width)
-      updateSliderInput(session, "upgma_fruit_width_circ_4", value = width)
-      updateSliderInput(session, "upgma_fruit_width_circ_5", value = width) 
-    }
-  })
-  
-  # Tip color mapping 
-  output$nj_tipcolor_mapping <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tipcolor_mapping",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Assembly Name` = "Assembly Name",
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Assembly Name` = "Assembly Name", `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(City = "City"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tipcolor_mapping",
-          "",
-          choices = c(
-            `Assembly Name` = "Assembly Name",
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c(City = "City")
-        )
-      )
-    }
-  })
-  
-  output$upgma_tipcolor_mapping <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tipcolor_mapping",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Assembly Name` = "Assembly Name",
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Assembly Name` = "Assembly Name", `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(City = "City"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tipcolor_mapping",
-          "",
-          choices = c(
-            `Assembly Name` = "Assembly Name",
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c(City = "City")
-        )
-      )
-    }
-  })
-  
-  # Tip shape Mapping 
-  output$nj_tipshape_mapping <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tipshape_mapping",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c("Host" = "Host"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_tipshape_mapping",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c("Host" = "Host"),
-          width = "100%"
-        )
-      )
-    }
-  })
-  
-  output$upgma_tipshape_mapping <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tipshape_mapping",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c("Host" = "Host"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_tipshape_mapping",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c("Host" = "Host"),
-          width = "100%"
-        )
-      )
-    }
-  })
-  
-  # Branch label 
-  output$nj_branch_label <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      selectInput(
-        "nj_branch_label",
-        "",
-        choices = if(ncol(Vis$meta_nj) == 11) {
-          c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        } else {
-          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                 names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-        },
-        selected = c("Host" = "Host"),
-        width = "100%"
-      )
-    } else {
-      selectInput(
-        "nj_branch_label",
-        "",
-        choices = c(
-          `Isolation Date` = "Isolation Date",
-          Host = "Host",
-          Country = "Country",
-          City = "City"
-        ),
-        selected = c("Host" = "Host"),
-        width = "100%"
-      )
-    }
-  })
-  
-  output$upgma_branch_label <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      selectInput(
-        "upgma_branch_label",
-        "",
-        choices = if(ncol(Vis$meta_upgma) == 11) {
-          c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        } else {
-          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-        },
-        selected = c("Host" = "Host"),
-        width = "100%"
-      )
-    } else {
-      selectInput(
-        "upgma_branch_label",
-        "",
-        choices = c(
-          `Isolation Date` = "Isolation Date",
-          Host = "Host",
-          Country = "Country",
-          City = "City"
-        ),
-        selected = c("Host" = "Host"),
-        width = "100%"
-      )
-    }
-  })
-  
-  # Color mapping 
-  output$nj_color_mapping <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      shinyjs::disabled(
-        selectInput(
-          "nj_color_mapping",
-          "",
-          choices = if(ncol(Vis$meta_nj) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-          },
-          selected = c(Country = "Country"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "nj_color_mapping",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c(Country = "Country"),
-          width = "100%"
-        )
-      )
-    }
-  })
-  
-  output$upgma_color_mapping <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_color_mapping",
-          "",
-          choices = if(ncol(Vis$meta_upgma) == 11) {
-            c(
-              `Isolation Date` = "Isolation Date",
-              Host = "Host",
-              Country = "Country",
-              City = "City"
-            )
-          } else {
-            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-          },
-          selected = c(Country = "Country"),
-          width = "100%"
-        )
-      )
-    } else {
-      shinyjs::disabled(
-        selectInput(
-          "upgma_color_mapping",
-          "",
-          choices = c(
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          ),
-          selected = c(Country = "Country"),
-          width = "100%"
-        )
-      )
-    }
-  })
-  
-  # Tip labels 
-  output$nj_tiplab <- renderUI({
-    if(!is.null(Vis$meta_nj)) {
-      selectInput(
-        "nj_tiplab",
-        label = "",
-        choices = if(ncol(Vis$meta_nj) == 11) {
-          c(
-            Index = "Index",
-            `Assembly ID` = "Assembly ID",
-            `Assembly Name` = "Assembly Name",
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        } else {
-          append(c(Index = "Index", `Assembly ID` = "Assembly ID", `Assembly Name` = "Assembly Name",
-                   `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                 names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
-        },
-        selected = c(`Assembly Name` = "Assembly Name"),
-        width = "100%"
-      )
-    } else {
-      selectInput(
-        "nj_tiplab",
-        label = "",
-        choices = c(
-          Index = "Index",
-          `Assembly ID` = "Assembly ID",
-          `Assembly Name` = "Assembly Name",
-          `Isolation Date` = "Isolation Date",
-          Host = "Host",
-          Country = "Country",
-          City = "City"
-        ),
-        selected = c(`Assembly Name` = "Assembly Name"),
-        width = "100%"
-      )
-    }
-  })
-  
-  output$upgma_tiplab <- renderUI({
-    if(!is.null(Vis$meta_upgma)) {
-      selectInput(
-        "upgma_tiplab",
-        label = "",
-        choices = if(ncol(Vis$meta_upgma) == 11) {
-          c(
-            Index = "Index",
-            `Assembly ID` = "Assembly ID",
-            `Assembly Name` = "Assembly Name",
-            `Isolation Date` = "Isolation Date",
-            Host = "Host",
-            Country = "Country",
-            City = "City"
-          )
-        } else {
-          append(c(Index = "Index", `Assembly ID` = "Assembly ID", `Assembly Name` = "Assembly Name",
-                   `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
-                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
-        },
-        selected = c(`Assembly Name` = "Assembly Name"),
-        width = "100%"
-      )
-    } else {
-      selectInput(
-        "upgma_tiplab",
-        label = "",
-        choices = c(
-          Index = "Index",
-          `Assembly ID` = "Assembly ID",
-          `Assembly Name` = "Assembly Name",
-          `Isolation Date` = "Isolation Date",
-          Host = "Host",
-          Country = "Country",
-          City = "City"
-        ),
-        selected = c(`Assembly Name` = "Assembly Name"),
-        width = "100%"
-      )
-    }
-  })
-  
-  #### MST controls ----
-  
-  # Clustering UI
-  output$mst_cluster <- renderUI({
-    req(DB$schemeinfo)
-    numericInput(
-      inputId = "mst_cluster_threshold",
-      label = NULL,
-      value = as.numeric(DB$schemeinfo[7, 2]),
-      min = 1,
-      max = 99
-    )
-  })
-  
-  # MST color mapping
-  output$mst_color_mapping <- renderUI({
-    if(input$mst_color_var == FALSE) {
-      fluidRow(
-        column(
-          width = 7,
-          div(
-            class = "node_color",
-            colorPickr(
-              inputId = "mst_color_node",
-              width = "100%",
-              selected = "#B2FACA",
-              label = "",
-              update = "changestop",
-              interaction = list(clear = FALSE,
-                                 save = FALSE),
-              position = "right-start"
-            )
-          )
-        ),
-        column(
-          width = 5,
-          dropMenu(
-            actionBttn(
-              "mst_node_menu",
-              label = "",
-              color = "default",
-              size = "sm",
-              style = "material-flat",
-              icon = icon("sliders")
-            ),
-            placement = "top-start",
-            theme = "translucent",
-            width = 5,
-            numericInput(
-              "node_opacity",
-              label = h5("Opacity", style = "color:white; margin-bottom: 0px;"),
-              value = 1,
-              step = 0.1,
-              min = 0,
-              max = 1,
-              width = "80px"
-            )
-          )
-        )
-      ) 
-    } else {
-      fluidRow(
-        column(
-          width = 9,
-          div(
-            class = "mst_col_sel",
-            selectInput(
-              "mst_col_var",
-              label = "",
-              choices = if(any(DB$cust_var[DB$cust_var$Variable[which(DB$cust_var$Variable %in% c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)]))],]$Type != "categ")) {
-                selection <- c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)])
-                cust_vars <- DB$cust_var$Variable[which(DB$cust_var$Variable %in% selection)]
-                selection[-which(selection == cust_vars[DB$cust_var[cust_vars,]$Type != "categ"])]
-              } else {c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)])},
-              width = "100%"
-            )
-          )
-        ),
-        column(
-          width = 3,
-          dropMenu(
-            actionBttn(
-              "mst_col_menu",
-              label = "",
-              color = "default",
-              size = "sm",
-              style = "material-flat",
-              icon = icon("sliders")
-            ),
-            placement = "top-start",
-            theme = "translucent",
-            width = 5,
-            selectInput(
-              "mst_col_scale",
-              label = h5("Color Scale", style = "color:white; margin-bottom: 0px;"),
-              choices = c("Viridis", "Rainbow"),
-              width = "150px"
-            ),
-            br(), br(), br(), br()
-          )
-        )
-      ) 
-    }
-  })
-  
-  observeEvent(input$mst_color_var, {
-    
-    if(input$mst_color_var == TRUE) {
-      updateSelectizeInput(session, inputId = "mst_node_shape", choices = c("Pie Nodes" = "custom"))
-      updateSelectizeInput(session, inputId = "mst_node_label", choices = c("Assembly Name"))
-    } else {
-      updateSelectizeInput(session, inputId = "mst_node_shape", 
-                           choices = list(`Label inside` = c("Circle" = "circle", "Box" = "box", "Text" = "text"),
-                                          `Label outside` = c("Diamond" = "diamond", "Hexagon" = "hexagon","Dot" = "dot", "Square" = "square")),
-                           selected = c("Dot" = "dot"))
-      updateSelectizeInput(session, inputId = "mst_node_label",
-                           choices = names(DB$meta)[c(1, 3, 4, 6, 7, 8, 9)],
-                           selected = "Assembly Name")
-    }
-  })
-  
-  # MST node labels 
-  output$mst_node_label <- renderUI({
-    selectInput(
-      "mst_node_label",
-      label = "",
-      choices = names(DB$meta)[c(1, 3, 4, 6, 7, 8, 9)],
-      selected = "Assembly Name",
-      width = "100%"
-    )
-  })
-  
-  ### Plot Reactives ----
-  
-  #### MST ----
-  
-  mst_tree <- reactive({
-    data <- toVisNetworkData(Vis$ggraph_1)
-    data$nodes <- mutate(data$nodes, 
-                                label = label_mst(),
-                                value = mst_node_scaling(),
-                                opacity = node_opacity())
-    
-    ctxRendererJS <- htmlwidgets::JS("({ctx, id, x, y, state: { selected, hover }, style, font, label, metadata}) => {
-                            var pieData = JSON.parse(metadata);
-                            var radius = style.size;
-                            var centerX = x;
-                            var centerY = y;
-                            var total = pieData.reduce((sum, slice) => sum + slice.value, 0)
-                            var startAngle = 0;
-
-                            const drawNode = () => {
-                                // Set shadow properties
-                                if (style.shadow) {
-                                  var shadowSize = style.shadowSize;
-                                  ctx.shadowColor = style.shadowColor;
-                                  ctx.shadowBlur = style.shadowSize;
-                                  ctx.shadowOffsetX = style.shadowX;
-                                  ctx.shadowOffsetY = style.shadowY;
-                                  
-                                  ctx.beginPath();
-                                  ctx.arc(centerX, centerY, radius, 0, 2 * Math.PI);
-                                  ctx.fill();
-                                  
-                                  ctx.shadowColor = 'transparent';
-                                  ctx.shadowBlur = 0;
-                                  ctx.shadowOffsetX = 0;
-                                  ctx.shadowOffsetY = 0;
-                                }
-
-                                pieData.forEach(slice => {
-                                    var sliceAngle = 2 * Math.PI * (slice.value / total);
-                                    ctx.beginPath();
-                                    ctx.moveTo(centerX, centerY);
-                                    ctx.arc(centerX, centerY, radius, startAngle, startAngle + sliceAngle);
-                                    ctx.closePath();
-                                    ctx.fillStyle = slice.color;
-                                    ctx.fill();
-                                     if (pieData.length > 1) {
-                ctx.strokeStyle = 'black';
-                ctx.lineWidth = 1;
-                ctx.stroke();
-            }
-                                    startAngle += sliceAngle;
-                                });
-                    
-                                // Draw a border
-                                ctx.beginPath();
-                                ctx.arc(centerX, centerY, radius, 0, 2 * Math.PI);
-                                ctx.strokeStyle = 'black';
-                                ctx.lineWidth = 1;
-                                ctx.stroke();
-                            };
-                            drawLabel = () => {
-                              //Draw the label
-                              var lines = label.split(`\n`);
-                              var lineHeight = font.size;
-                              ctx.font = `${font.size}px ${font.face}`;
-                              ctx.fillStyle = font.color;
-                              ctx.textAlign = 'center';
-                              ctx.textBaseline = 'middle';
-                              lines.forEach((line, index) => {
-                                ctx.fillText(line, centerX, 
-                                centerY + radius + (index + 1) * lineHeight);
-                              })
-                            }
-                            
-                            return {
-                                drawNode,
-                                drawExternalLabel: drawLabel,
-                                nodeDimensions: { width: 2 * radius, height: 2 * radius },
-                            };
-                        }")
-    
-    Vis$var_cols <- NULL
-    
-    # Generate pie charts as nodes
-    if(input$mst_color_var == TRUE & (!is.null(input$mst_col_var))) {
-      
-      group <- character(nrow(data$nodes))
-      for (i in 1:length(unique(Vis$meta_mst[[input$mst_col_var]]))) {
-        group[i] <- unique(Vis$meta_mst[[input$mst_col_var]])[i]
-      }
-      
-      data$nodes <- cbind(data$nodes, data.frame(metadata = character(nrow(data$nodes))))
-      
-      if(length(which(data$nodes$group == "")) != 0) {
-        data$nodes$group[which(data$nodes$group == "")] <- data$nodes$group[1]
-      }
-      
-      if(is.null(input$mst_col_scale)) {
-        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
-                                      color = viridis(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
-      } else if (input$mst_col_scale == "Rainbow") {
-        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
-                                      color = rainbow(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
-      } else if (input$mst_col_scale == "Viridis") {
-        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
-                                      color = viridis(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
-      }
-      
-      for(i in 1:nrow(data$nodes)) {
-        
-        iso_subset <- strsplit(data$nodes$label[i], split = "\n")[[1]]
-        variable <- Vis$meta_mst[[input$mst_col_var]]
-        values <- variable[which(Vis$meta_mst$`Assembly Name` %in% iso_subset)]
-        
-        for(j in 1:length(unique(values))) {
-          
-          share <- sum(unique(values)[j] == values) / length(values) * 100
-          color <- Vis$var_cols$color[Vis$var_cols$value == unique(values)[j]]
-          
-          if(j == 1) {
-            pie_vec <- paste0('{"value":', share,',"color":"', color,'"}')
-          } else {
-            pie_vec <- paste0(pie_vec, ',{"value":', share,',"color":"', color,'"}')
-          }
-        }
-        
-        data$nodes$metadata[i] <- paste0('[', pie_vec, ']')
-      }
-    }
-    
-    data$edges <- mutate(data$edges,
-                                length = if(input$mst_scale_edges == FALSE) {
-                                  input$mst_edge_length
-                                } else {
-                                  data$edges$weight * input$mst_edge_length_scale
-                                },
-                                label = as.character(data$edges$weight),
-                                opacity = input$mst_edge_opacity)
-    
-    if (input$mst_show_clusters) {
-      clusters <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
-      if (input$mst_cluster_type == "Type 1") {
-        data$nodes$group <- clusters$group
-      }
-    }
-    
-    visNetwork_graph <- visNetwork(data$nodes, data$edges,
-                                   main = mst_title(),
-                                   background = mst_background_color(),
-                                   submain = mst_subtitle()) %>%
-      visNodes(size = mst_node_size(),
-               shape = input$mst_node_shape,
-               shadow = input$mst_shadow,
-               color = mst_color_node(),
-               ctxRenderer = ctxRendererJS,
-               scaling = list(min = mst_node_size_min(),
-                              max = mst_node_size_max()),
-               font = list(color = node_font_color(),
-                           size = input$node_label_fontsize)) %>%
-      visEdges(color = mst_color_edge(),
-               font = list(color = mst_edge_font_color(),
-                           size = mst_edge_font_size(),
-                           strokeWidth = 4)) %>%
-      visOptions(collapse = TRUE) %>%
-      visInteraction(hover = TRUE) %>%
-      visLayout(randomSeed = 1) %>%
-      visLegend(useGroups = FALSE,
-                zoom = TRUE,
-                width = legend_width(),
-                position = input$mst_legend_ori,
-                ncol = legend_col(),
-                addNodes = mst_legend())
-    
-    if (input$mst_show_clusters) {
-      if (input$mst_cluster_col_scale == "Viridis") {
-        color_palette <- viridis(length(unique(data$nodes$group)))
-      } else {
-        color_palette <- rainbow(length(unique(data$nodes$group)))
-      }
-      
-      if (input$mst_cluster_type == "Type 1") {
-        for (i in 1:length(unique(data$nodes$group))) {
-          visNetwork_graph <- visNetwork_graph %>% 
-            visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
-        }
-      } else {
-        thin_edges <- data$edges
-        thin_edges$width <- 1
-        thin_edges$color <- "black"
-        
-        thick_edges <- data$edges
-        thick_edges$width <- 24
-        
-        thick_edges$color <- rep("rgba(0, 0, 0, 0)", length(data$edges$from))
-        color_palette <- rainbow(length(unique(clusters$edges)))
-        for (i in 1:length(unique(clusters$edges))) {
-          print(clusters$edges)
-          if (unique(clusters$edges)[i] != "0") {
-            edge_color <- paste(col2rgb(color_palette[i]), collapse=", ")
-            thick_edges$color[clusters$edges == unique(clusters$edges)[i]] <- paste0("rgba(", edge_color, ", 0.5)")
-          }
-        }
-        merged_edges <- rbind(thick_edges, thin_edges)
-        data$edges <- merged_edges
-        visNetwork_graph <- visNetwork(data$nodes, data$edges,
-                                       main = mst_title(),
-                                       background = mst_background_color(),
-                                       submain = mst_subtitle()) %>%
-          visNodes(size = mst_node_size(),
-                   shape = input$mst_node_shape,
-                   shadow = input$mst_shadow,
-                   color = mst_color_node(),
-                   ctxRenderer = ctxRendererJS,
-                   scaling = list(min = mst_node_size_min(),
-                                  max = mst_node_size_max()),
-                   font = list(color = node_font_color(),
-                               size = input$node_label_fontsize)) %>%
-          visEdges(color = mst_color_edge(),
-                   font = list(color = mst_edge_font_color(),
-                               size = mst_edge_font_size(),
-                               strokeWidth = 4),
-                   smooth = FALSE,
-                   physics = FALSE) %>%
-          visOptions(collapse = TRUE) %>%
-          visInteraction(hover = TRUE) %>%
-          visLayout(randomSeed = 1) %>%
-          visLegend(useGroups = FALSE,
-                    zoom = TRUE,
-                    width = legend_width(),
-                    position = input$mst_legend_ori,
-                    ncol = legend_col(),
-                    addNodes = mst_legend())
-      }
-    }
-    visNetwork_graph
-  })
-  
-  # MST legend
-  legend_col <- reactive({
-    if(!is.null(Vis$var_cols)) {
-      if(nrow(Vis$var_cols) > 10) {
-        3
-      } else if(nrow(Vis$var_cols) > 5) {
-        2
-      } else {
-        1
-      }
-    } else {1}
-  })
-  
-  mst_legend <- reactive({
-    if(is.null(Vis$var_cols)) {
-      NULL
-    } else {
-      legend <- Vis$var_cols
-      names(legend)[1] <- "label"
-      mutate(legend, shape = "dot",
-             font.color = input$mst_legend_color,
-             size = input$mst_symbol_size,
-             font.size = input$mst_font_size)
-    }
-  })
-  
-  # Set MST legend width
-  legend_width <- reactive({
-    0.2
-  })
-  
-  # Set MST node shape
-  mst_node_shape <- reactive({
-    if(input$mst_node_shape == "Pie Nodes"){
-      "dot"
-    } else if(input$mst_node_shape %in% c("circle", "database", "box", "text")) {
-      shinyjs::disable('scale_nodes') 
-      updateCheckboxInput(session, "scale_nodes", value = FALSE)
-      shinyjs::disable('mst_node_size') 
-      shinyjs::disable('mst_node_scale')
-      input$mst_node_shape
-    } else {
-      shinyjs::enable('scale_nodes') 
-      shinyjs::enable('mst_node_size') 
-      shinyjs::enable('mst_node_scale')
-      input$mst_node_shape
-    }
-  })
-  
-  # Set MST label
-  label_mst <- reactive({
-    Vis$unique_meta[, colnames(Vis$unique_meta) %in% input$mst_node_label]
-  })
-  
-  # Set node color
-  mst_color_node <- reactive({
-    input$mst_color_node
-  })
-  
-  # Node Label Color
-  node_font_color <- reactive({
-    input$node_font_color
-  })
-  
-  
-  # Node Size Scaling
-  mst_node_scaling <- reactive({
-    if(input$scale_nodes == TRUE){
-      Vis$unique_meta$size
-    } else {NULL}
-  })
-  
-  # Node Size Min/May
-  mst_node_size_min <- reactive({
-    input$mst_node_scale[1]
-  })
-  
-  mst_node_size_max <- reactive({
-    input$mst_node_scale[2]
-  })
-  
-  # Node Size
-  mst_node_size <- reactive({
-    input$mst_node_size
-  })
-  
-  # Node Alpha/Opacity
-  node_opacity <- reactive({
-    input$node_opacity
-  })
-  
-  # Set Title
-  mst_title <- reactive({
-    if(!is.null(input$mst_title)) {
-      if(nchar(input$mst_title) < 1) {
-        list(text = "title",
-             style = paste0(
-               "font-family:Georgia, Times New Roman, Times, serif;",
-               "text-align:center;",
-               "font-size: ", as.character(input$mst_title_size), "px", 
-               "; color: ", as.character(mst_background_color()))
-        )
-      } else {
-        list(text = input$mst_title,
-             style = paste0(
-               "font-family:Georgia, Times New Roman, Times, serif;",
-               "text-align:center;",
-               "font-size: ", as.character(input$mst_title_size), "px", 
-               "; color: ", as.character(input$mst_title_color))
-        )
-      }
-    } else {
-      list(text = "title",
-           style = paste0(
-             "font-family:Georgia, Times New Roman, Times, serif;",
-             "text-align:center;",
-             "font-size: ", as.character(input$mst_title_size), "px", 
-             "; color: ", as.character(mst_background_color()))
-      )
-    }
-  })
-  
-  # Set Subtitle
-  mst_subtitle <- reactive({
-    list(text = input$mst_subtitle,
-         style = paste0(
-           "font-family:Georgia, Times New Roman, Times, serif;",
-           "text-align:center;",
-           "font-size: ", as.character(input$mst_subtitle_size), "px", 
-           "; color: ", as.character(input$mst_subtitle_color))
-    )
-  })
-  
-  # Background color
-  
-  mst_background_color <- reactive({
-    if(input$mst_background_transparent == TRUE) {
-      'rgba(0, 0, 0, 0)'
-    } else{
-      input$mst_background_color
-    }
-  })
-  
-  # Edge font color
-  mst_edge_font_color <- reactive({
-    input$mst_edge_font_color
-  })
-  
-  # Edge color
-  mst_color_edge <- reactive({
-    input$mst_color_edge
-  })
-  
-  # Edge font size
-  mst_edge_font_size <- reactive({
-    input$mst_edge_font_size
-  })
-  
-  #### NJ ----
-  
-  nj_tree <- reactive({
-    
-    # Convert negative edges 
-    Vis$nj[["edge.length"]] <- abs(Vis$nj[["edge.length"]])
-    
-    if(input$nj_nodelabel_show == TRUE) {
-      ggtree(Vis$nj, alpha = 0.2, layout = layout_nj()) + 
-        geom_nodelab(aes(label = node), color = "#29303A", size = nj_tiplab_size() + 1, hjust = 0.7) +
-        nj_limit() +
-        nj_inward() 
-    } else {
-      tree <- 
-        ggtree(Vis$nj, 
-               color = input$nj_color,
-               layout = layout_nj(),
-               ladderize = input$nj_ladder) %<+% Vis$meta_nj +
-        nj_clades() +
-        nj_tiplab() +
-        nj_tiplab_scale() + 
-        new_scale_color() +
-        nj_limit() +
-        nj_inward() +
-        nj_label_branch() +
-        nj_treescale() +
-        nj_nodepoint() +
-        nj_tippoint() +
-        nj_tippoint_scale() + 
-        new_scale_color() +
-        nj_clip_label() +
-        nj_rootedge() +
-        ggtitle(label = input$nj_title,
-                subtitle = input$nj_subtitle) +
-        theme_tree(bgcolor = input$nj_bg) +
-        theme(plot.title = element_text(colour = input$nj_title_color,
-                                        size = input$nj_title_size),
-              plot.subtitle = element_text(colour = input$nj_title_color,
-                                           size = input$nj_subtitle_size),
-              legend.background = element_rect(fill = input$nj_bg),
-              legend.direction = input$nj_legend_orientation,
-              legend.title = element_text(color = input$nj_color,
-                                          size = input$nj_legend_size*1.2),
-              legend.title.align = 0.5,
-              legend.position = nj_legend_pos(),
-              legend.text = element_text(color = input$nj_color, 
-                                         size = input$nj_legend_size),
-              legend.key = element_rect(fill = input$nj_bg),
-              legend.box.spacing = unit(1.5, "cm"),
-              legend.key.size = unit(0.05*input$nj_legend_size, 'cm'),
-              plot.background = element_rect(fill = input$nj_bg, color = input$nj_bg)) +
-        new_scale_fill() +
-        nj_fruit() +
-        nj_gradient() +
-        new_scale_fill() +
-        nj_fruit2() +
-        nj_gradient2() +
-        new_scale_fill() +
-        nj_fruit3() +
-        nj_gradient3() +
-        new_scale_fill() +
-        nj_fruit4() +
-        nj_gradient4() +
-        new_scale_fill() +
-        nj_fruit5() +
-        nj_gradient5() +
-        new_scale_fill() 
-      
-      # Add custom labels
-      if(length(Vis$custom_label_nj) > 0) {
-        
-        for(i in Vis$custom_label_nj[,1]) {
-          
-          if(!is.null(Vis$nj_label_pos_x[[i]])) {
-            x_pos <- Vis$nj_label_pos_x[[i]]
-          } else {
-            x_pos <- round(Vis$nj_max_x / 2, 0)
-          }
-          
-          if(!is.null(Vis$nj_label_pos_y[[i]])) {
-            y_pos <- Vis$nj_label_pos_y[[i]]
-          } else {
-            y_pos <- sum(DB$data$Include) / 2
-          }
-          
-          if(!is.null(Vis$nj_label_size[[i]])) {
-            size <- Vis$nj_label_size[[i]]
-          } else {
-            size <- 5
-          }
-          
-          tree <- tree + annotate("text",
-                                  x = x_pos,
-                                  y = y_pos, 
-                                  label = i,
-                                  size = size)
-        }
-      }
-      
-      # Add heatmap
-      if(input$nj_heatmap_show == TRUE & length(input$nj_heatmap_select) > 0) {
-        if (!(any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)) & 
-              any(!sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)))) {
-          tree <- gheatmap.mod(tree, 
-                               data = select(Vis$meta_nj, input$nj_heatmap_select),
-                               offset = nj_heatmap_offset(),
-                               width = nj_heatmap_width(),
-                               legend_title = input$nj_heatmap_title,
-                               colnames_angle = -nj_colnames_angle(),
-                               colnames_offset_y = nj_colnames_y(),
-                               colnames_color = input$nj_color) +
-            nj_heatmap_scale()
-        }
-      } 
-      
-      # Sizing control
-      Vis$nj_plot <- ggplotify::as.ggplot(tree, 
-                                          scale = input$nj_zoom,
-                                          hjust = input$nj_h,
-                                          vjust = input$nj_v)  
-      
-      Vis$nj_true <- TRUE
-      
-      # Correct background color if zoomed out
-      cowplot::ggdraw(Vis$nj_plot) + 
-        theme(plot.background = element_rect(fill = input$nj_bg, color = input$nj_bg))
-    }
-  })
-  
-  # Heatmap width
-  nj_heatmap_width <- reactive({
-    if(!is.null(input$nj_heatmap_width)) {
-      input$nj_heatmap_width
-    } else {
-      length_input <- length(input$nj_heatmap_select)
-      if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
-        if(length_input < 3) {
-          0.1
-        } else {
-          if (length_input >= 3 && length_input <= 50) {
-            min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-          } else {
-            1.5
-          }   
-        }
-      } else {
-        if(length_input < 3) {
-          0.3
-        } else if (length_input >= 3 && length_input <= 27) {
-          min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          3
-        }
-      }
-    }
-  })
-  
-  # Heatmap column titles position
-  nj_colnames_y <- reactive({
-    if(!is.null(input$nj_colnames_y)) {
-      input$nj_colnames_y
-    } else {
-      if(input$nj_layout == "inward" | input$nj_layout == "circular") {
-        0
-      } else {-1}
-    }
-  })
-  
-  # Heatmap column titles angle
-  nj_colnames_angle <- reactive({
-    if(!is.null(input$nj_colnames_angle)) {
-      input$nj_colnames_angle
-    } else {
-      if(!is.null(input$nj_layout)) {
-        if(input$nj_layout == "inward" | input$nj_layout == "circular") {
-          90
-        } else {-90}
-      } else {-90}
-    }
-  })
-  
-  # Heatmap scale
-  nj_heatmap_scale <- reactive({
-    if(!is.null(input$nj_heatmap_scale) & !is.null(input$nj_heatmap_div_mid)) {
-      if(input$nj_heatmap_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$nj_heatmap_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$nj_heatmap_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_heatmap_select]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_heatmap_select]), na.rm = TRUE)
-        }
-        scale_fill_gradient2(low = brewer.pal(3, input$nj_heatmap_scale)[1],
-                             mid = brewer.pal(3, input$nj_heatmap_scale)[2],
-                             high = brewer.pal(3, input$nj_heatmap_scale)[3],
-                             midpoint = midpoint,
-                             name = input$nj_heatmap_title)
-      } else {
-        if(input$nj_heatmap_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_nj[input$nj_heatmap_select])) == "numeric") {
-            if(input$nj_heatmap_scale == "magma") {
-              scale_fill_viridis(option = "A",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "inferno") {
-              scale_fill_viridis(option = "B",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "plasma") {
-              scale_fill_viridis(option = "C",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "viridis") {
-              scale_fill_viridis(option = "D",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "cividis") {
-              scale_fill_viridis(option = "E",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "rocket") {
-              scale_fill_viridis(option = "F",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "mako") {
-              scale_fill_viridis(option = "G",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "turbo") {
-              scale_fill_viridis(option = "H",
-                                 name = input$nj_heatmap_title)
-            } 
-          } else {
-            if(input$nj_heatmap_scale == "magma") {
-              scale_fill_viridis(discrete = TRUE, option = "A",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "inferno") {
-              scale_fill_viridis(discrete = TRUE, option = "B",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "plasma") {
-              scale_fill_viridis(discrete = TRUE, option = "C",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "viridis") {
-              scale_fill_viridis(discrete = TRUE, option = "D",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "cividis") {
-              scale_fill_viridis(discrete = TRUE, option = "E",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "rocket") {
-              scale_fill_viridis(discrete = TRUE, option = "F",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "mako") {
-              scale_fill_viridis(discrete = TRUE, option = "G",
-                                 name = input$nj_heatmap_title)
-            } else if(input$nj_heatmap_scale == "turbo") {
-              scale_fill_viridis(discrete = TRUE, option = "H",
-                                 name = input$nj_heatmap_title)
-            } 
-          }
-        } else {
-          scale_fill_brewer(palette = input$nj_heatmap_scale,
-                            name = input$nj_heatmap_title)
-        }
-      }
-    }
-  })
-  
-  # Tippoint Scale
-  nj_tippoint_scale <- reactive({
-    if(!is.null(input$nj_tippoint_scale) & !is.null(input$nj_tipcolor_mapping_div_mid)) {
-      if(input$nj_tippoint_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$nj_tipcolor_mapping_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$nj_tipcolor_mapping_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_tipcolor_mapping]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_tipcolor_mapping]), na.rm = TRUE)
-        }
-        scale_color_gradient2(low = brewer.pal(3, input$nj_tippoint_scale)[1],
-                              mid = brewer.pal(3, input$nj_tippoint_scale)[2],
-                              high = brewer.pal(3, input$nj_tippoint_scale)[3],
-                              midpoint = midpoint)
-      } else {
-        if(input$nj_tippoint_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_nj[input$nj_tipcolor_mapping])) == "numeric") {
-            if(input$nj_tippoint_scale == "magma") {
-              scale_color_viridis(option = "A")
-            } else if(input$nj_tippoint_scale == "inferno") {
-              scale_color_viridis(option = "B")
-            } else if(input$nj_tippoint_scale == "plasma") {
-              scale_color_viridis(option = "C")
-            } else if(input$nj_tippoint_scale == "viridis") {
-              scale_color_viridis(option = "D")
-            } else if(input$nj_tippoint_scale == "cividis") {
-              scale_color_viridis(option = "E")
-            } else if(input$nj_tippoint_scale == "rocket") {
-              scale_color_viridis(option = "F")
-            } else if(input$nj_tippoint_scale == "mako") {
-              scale_color_viridis(option = "G")
-            } else if(input$nj_tippoint_scale == "turbo") {
-              scale_color_viridis(option = "H")
-            } 
-          } else {
-            if(input$nj_tippoint_scale == "magma") {
-              scale_color_viridis(discrete = TRUE, option = "A")
-            } else if(input$nj_tippoint_scale == "inferno") {
-              scale_color_viridis(discrete = TRUE, option = "B")
-            } else if(input$nj_tippoint_scale == "plasma") {
-              scale_color_viridis(discrete = TRUE, option = "C")
-            } else if(input$nj_tippoint_scale == "viridis") {
-              scale_color_viridis(discrete = TRUE, option = "D")
-            } else if(input$nj_tippoint_scale == "cividis") {
-              scale_color_viridis(discrete = TRUE, option = "E")
-            } else if(input$nj_tippoint_scale == "rocket") {
-              scale_color_viridis(discrete = TRUE, option = "F")
-            } else if(input$nj_tippoint_scale == "mako") {
-              scale_color_viridis(discrete = TRUE, option = "G")
-            } else if(input$nj_tippoint_scale == "turbo") {
-              scale_color_viridis(discrete = TRUE, option = "H")
-            } 
-          }
-        } else {
-          scale_color_brewer(palette = input$nj_tippoint_scale)
-        }
-      }
-    }
-  })
-  
-  # Tiplab Scale
-  nj_tiplab_scale <- reactive({
-    if(!is.null(input$nj_tiplab_scale) & !is.null(input$nj_color_mapping_div_mid)) {
-      if(input$nj_tiplab_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$nj_color_mapping_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$nj_color_mapping_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_color_mapping]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_color_mapping]), na.rm = TRUE)
-        }
-        scale_color_gradient2(low = brewer.pal(3, input$nj_tiplab_scale)[1],
-                              mid = brewer.pal(3, input$nj_tiplab_scale)[2],
-                              high = brewer.pal(3, input$nj_tiplab_scale)[3],
-                              midpoint = midpoint)
-      } else {
-        if(input$nj_tiplab_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_nj[input$nj_color_mapping])) == "numeric") {
-            if(input$nj_tiplab_scale == "magma") {
-              scale_color_viridis(option = "A")
-            } else if(input$nj_tiplab_scale == "inferno") {
-              scale_color_viridis(option = "B")
-            } else if(input$nj_tiplab_scale == "plasma") {
-              scale_color_viridis(option = "C")
-            } else if(input$nj_tiplab_scale == "viridis") {
-              scale_color_viridis(option = "D")
-            } else if(input$nj_tiplab_scale == "cividis") {
-              scale_color_viridis(option = "E")
-            } else if(input$nj_tiplab_scale == "rocket") {
-              scale_color_viridis(option = "F")
-            } else if(input$nj_tiplab_scale == "mako") {
-              scale_color_viridis(option = "G")
-            } else if(input$nj_tiplab_scale == "turbo") {
-              scale_color_viridis(option = "H")
-            } 
-          } else {
-            if(input$nj_tiplab_scale == "magma") {
-              scale_color_viridis(discrete = TRUE, option = "A")
-            } else if(input$nj_tiplab_scale == "inferno") {
-              scale_color_viridis(discrete = TRUE, option = "B")
-            } else if(input$nj_tiplab_scale == "plasma") {
-              scale_color_viridis(discrete = TRUE, option = "C")
-            } else if(input$nj_tiplab_scale == "viridis") {
-              scale_color_viridis(discrete = TRUE, option = "D")
-            } else if(input$nj_tiplab_scale == "cividis") {
-              scale_color_viridis(discrete = TRUE, option = "E")
-            } else if(input$nj_tiplab_scale == "rocket") {
-              scale_color_viridis(discrete = TRUE, option = "F")
-            } else if(input$nj_tiplab_scale == "mako") {
-              scale_color_viridis(discrete = TRUE, option = "G")
-            } else if(input$nj_tiplab_scale == "turbo") {
-              scale_color_viridis(discrete = TRUE, option = "H")
-            } 
-          }
-        } else {
-          scale_color_brewer(palette = input$nj_tiplab_scale)
-        }
-      }
-    }
-  })
-  
-  # Clade Highlight
-  nj_clades <- reactive({
-    if(!is.null(input$nj_parentnode)) {
-      if(!length(input$nj_parentnode) == 0) {
-        if(length(input$nj_parentnode) == 1) {
-          fill <- input$nj_clade_scale
-        } else if (length(input$nj_parentnode) == 2) {
-          if(startsWith(input$nj_clade_scale, "#")) {
-            fill <- brewer.pal(3, "Set1")[1:2]
-          } else {
-            fill <- brewer.pal(3, input$nj_clade_scale)[1:2]
-          }
-        } else {
-          fill <- brewer.pal(length(input$nj_parentnode), input$nj_clade_scale)
-        }
-        geom_hilight(node = as.numeric(input$nj_parentnode),
-                     fill = fill,
-                     type = input$nj_clade_type,
-                     to.bottom = TRUE
-        )
-      } else {NULL}
-    }
-  })
-  
-  # Legend Position
-  nj_legend_pos <- reactive({
-    if(!is.null(input$nj_legend_x) & !is.null(input$nj_legend_y)) {
-      c(input$nj_legend_x, input$nj_legend_y)
-    } else {
-      c(0.1, 1)
-    }
-  })
-  
-  # Heatmap offset
-  nj_heatmap_offset <- reactive({
-    if(is.null(input$nj_heatmap_offset)) {
-      0
-    } else {input$nj_heatmap_offset}
-  })
-  
-  # Tiles fill color gradient
-  nj_gradient <- reactive({
-    if(!is.null(input$nj_tiles_show_1) & 
-       !is.null(input$nj_fruit_variable) & 
-       !is.null(input$nj_tiles_scale_1) & 
-       !is.null(input$nj_tiles_mapping_div_mid_1)) {
-      if(input$nj_tiles_show_1 == TRUE) {
-        if(input$nj_tiles_scale_1 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$nj_tiles_mapping_div_mid_1 == "Zero") {
-            midpoint <- 0
-          } else if(input$nj_tiles_mapping_div_mid_1 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable]), na.rm = TRUE)
-          }
-          scale_fill_gradient2(low = brewer.pal(3, input$nj_tiles_scale_1)[1],
-                               mid = brewer.pal(3, input$nj_tiles_scale_1)[2],
-                               high = brewer.pal(3, input$nj_tiles_scale_1)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$nj_tiles_scale_1 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
-              if(input$nj_tiles_scale_1 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$nj_tiles_scale_1 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$nj_tiles_scale_1 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$nj_tiles_scale_1 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$nj_tiles_scale_1 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$nj_tiles_scale_1 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$nj_tiles_scale_1 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$nj_tiles_scale_1 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$nj_tiles_scale_1 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$nj_tiles_scale_1 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$nj_tiles_scale_1 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$nj_tiles_scale_1 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$nj_tiles_scale_1 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$nj_tiles_scale_1 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$nj_tiles_scale_1 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$nj_tiles_scale_1 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$nj_tiles_scale_1)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_gradient2 <- reactive({
-    if(!is.null(input$nj_tiles_show_2) & 
-       !is.null(input$nj_fruit_variable_2) & 
-       !is.null(input$nj_tiles_scale_2) & 
-       !is.null(input$nj_tiles_mapping_div_mid_2)) {
-      if(input$nj_tiles_show_2 == TRUE) {
-        if(input$nj_tiles_scale_2 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$nj_tiles_mapping_div_mid_2 == "Zero") {
-            midpoint <- 0
-          } else if(input$nj_tiles_mapping_div_mid_2 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_2]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_2]), na.rm = TRUE)
-          }
-          scale_fill_gradient2(low = brewer.pal(3, input$nj_tiles_scale_2)[1],
-                               mid = brewer.pal(3, input$nj_tiles_scale_2)[2],
-                               high = brewer.pal(3, input$nj_tiles_scale_2)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$nj_tiles_scale_2 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_2])) == "numeric") {
-              if(input$nj_tiles_scale_2 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$nj_tiles_scale_2 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$nj_tiles_scale_2 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$nj_tiles_scale_2 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$nj_tiles_scale_2 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$nj_tiles_scale_2 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$nj_tiles_scale_2 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$nj_tiles_scale_2 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$nj_tiles_scale_2 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$nj_tiles_scale_2 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$nj_tiles_scale_2 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$nj_tiles_scale_2 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$nj_tiles_scale_2 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$nj_tiles_scale_2 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$nj_tiles_scale_2 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$nj_tiles_scale_2 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$nj_tiles_scale_2)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_gradient3 <- reactive({
-    if(!is.null(input$nj_tiles_show_3) & 
-       !is.null(input$nj_fruit_variable_3) & 
-       !is.null(input$nj_tiles_scale_3 & 
-                !is.null(input$nj_tiles_mapping_div_mid_3))) {
-      if(input$nj_tiles_show_3 == TRUE) {
-        if(input$nj_tiles_scale_3 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$nj_tiles_mapping_div_mid_3 == "Zero") {
-            midpoint <- 0
-          } else if(input$nj_tiles_mapping_div_mid_3 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_3]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_3]), na.rm = TRUE)
-          }
-          scale_fill_gradient3(low = brewer.pal(3, input$nj_tiles_scale_3)[1],
-                               mid = brewer.pal(3, input$nj_tiles_scale_3)[2],
-                               high = brewer.pal(3, input$nj_tiles_scale_3)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$nj_tiles_scale_3 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_3])) == "numeric") {
-              if(input$nj_tiles_scale_3 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$nj_tiles_scale_3 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$nj_tiles_scale_3 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$nj_tiles_scale_3 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$nj_tiles_scale_3 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$nj_tiles_scale_3 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$nj_tiles_scale_3 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$nj_tiles_scale_3 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$nj_tiles_scale_3 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$nj_tiles_scale_3 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$nj_tiles_scale_3 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$nj_tiles_scale_3 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$nj_tiles_scale_3 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$nj_tiles_scale_3 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$nj_tiles_scale_3 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$nj_tiles_scale_3 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$nj_tiles_scale_3)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_gradient4 <- reactive({
-    if(!is.null(input$nj_tiles_show_4) & 
-       !is.null(input$nj_fruit_variable_4) & 
-       !is.null(input$nj_tiles_scale_4) & 
-       !is.null(input$nj_tiles_mapping_div_mid_4)) {
-      if(input$nj_tiles_show_4 == TRUE) {
-        if(input$nj_tiles_scale_4 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$nj_tiles_mapping_div_mid_4 == "Zero") {
-            midpoint <- 0
-          } else if(input$nj_tiles_mapping_div_mid_4 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_4]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_4]), na.rm = TRUE)
-          }
-          scale_fill_gradient4(low = brewer.pal(3, input$nj_tiles_scale_4)[1],
-                               mid = brewer.pal(3, input$nj_tiles_scale_4)[2],
-                               high = brewer.pal(3, input$nj_tiles_scale_4)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$nj_tiles_scale_4 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
-              if(input$nj_tiles_scale_4 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$nj_tiles_scale_4 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$nj_tiles_scale_4 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$nj_tiles_scale_4 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$nj_tiles_scale_4 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$nj_tiles_scale_4 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$nj_tiles_scale_4 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$nj_tiles_scale_4 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$nj_tiles_scale_4 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$nj_tiles_scale_4 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$nj_tiles_scale_4 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$nj_tiles_scale_4 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$nj_tiles_scale_4 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$nj_tiles_scale_4 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$nj_tiles_scale_4 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$nj_tiles_scale_4 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$nj_tiles_scale_4)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_gradient5 <- reactive({
-    if(!is.null(input$nj_tiles_show_5) & 
-       !is.null(input$nj_fruit_variable_5) & 
-       !is.null(input$nj_tiles_scale_5) & 
-       !is.null(input$nj_tiles_mapping_div_mid_5)) {
-      if(input$nj_tiles_show_5 == TRUE) {
-        if(input$nj_tiles_scale_5 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$nj_tiles_mapping_div_mid_5 == "Zero") {
-            midpoint <- 0
-          } else if(input$nj_tiles_mapping_div_mid_5 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_5]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_5]), na.rm = TRUE)
-          }
-          scale_fill_gradient5(low = brewer.pal(3, input$nj_tiles_scale_5)[1],
-                               mid = brewer.pal(3, input$nj_tiles_scale_5)[2],
-                               high = brewer.pal(3, input$nj_tiles_scale_5)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$nj_tiles_scale_5 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_5])) == "numeric") {
-              if(input$nj_tiles_scale_5 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$nj_tiles_scale_5 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$nj_tiles_scale_5 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$nj_tiles_scale_5 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$nj_tiles_scale_5 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$nj_tiles_scale_5 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$nj_tiles_scale_5 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$nj_tiles_scale_5 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$nj_tiles_scale_5 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$nj_tiles_scale_5 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$nj_tiles_scale_5 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$nj_tiles_scale_5 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$nj_tiles_scale_5 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$nj_tiles_scale_5 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$nj_tiles_scale_5 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$nj_tiles_scale_5 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$nj_tiles_scale_5)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  # No label clip off for linear NJ tree
-  nj_clip_label <- reactive({
-    if(!(input$nj_layout == "circular" | input$nj_layout == "inward")) {
-      coord_cartesian(clip = "off")
-    } else {NULL}
-  })
-  
-  # Geom Fruit
-  nj_fruit <- reactive({
-    if((!is.null(input$nj_tiles_show_1)) & 
-       (!is.null(input$nj_fruit_variable)) & 
-       (!is.null(input$nj_layout)) & 
-       (!is.null(input$nj_fruit_offset_circ)) & 
-       (!is.null(input$nj_fruit_width_circ)) & 
-       (!is.null(input$nj_fruit_alpha))) {
-      if(input$nj_tiles_show_1 == TRUE) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
-            offset = input$nj_fruit_offset_circ,
-            width = input$nj_fruit_width_circ,
-            alpha = input$nj_fruit_alpha
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
-            offset = input$nj_fruit_offset_circ,
-            width = input$nj_fruit_width_circ,
-            alpha = input$nj_fruit_alpha
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$nj_tiles_show_1 == TRUE) {
-        if(!is.null(Vis$nj_max_x)) {
-          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
-            offset = 0,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
-            offset = 0,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  # Geom Fruit
-  nj_fruit2 <- reactive({
-    if((!is.null(input$nj_tiles_show_2)) & 
-       (!is.null(input$nj_fruit_variable_2)) & 
-       (!is.null(input$nj_layout)) & 
-       (!is.null(input$nj_fruit_offset_circ_2)) & 
-       (!is.null(input$nj_fruit_width_circ_2)) & 
-       (!is.null(input$nj_fruit_alpha_2))) {
-      if(input$nj_tiles_show_2 == TRUE) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_2)),
-            offset = input$nj_fruit_offset_circ_2,
-            width = input$nj_fruit_width_circ_2,
-            alpha = input$nj_fruit_alpha_2
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_2)),
-            offset = input$nj_fruit_offset_circ_2,
-            width = input$nj_fruit_width_circ_2,
-            alpha = input$nj_fruit_alpha_2
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$nj_tiles_show_2 == TRUE) {
-        if(!is.null(Vis$nj_max_x)) {
-          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_2)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_2)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_fruit3 <- reactive({
-    if((!is.null(input$nj_tiles_show_3)) & 
-       (!is.null(input$nj_fruit_variable_3)) & 
-       (!is.null(input$nj_layout)) & 
-       (!is.null(input$nj_fruit_offset_circ_3)) & 
-       (!is.null(input$nj_fruit_width_circ_3)) & 
-       (!is.null(input$nj_fruit_alpha_3))) {
-      if(input$nj_tiles_show_3 == TRUE) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_3)),
-            offset = input$nj_fruit_offset_circ_3,
-            width = input$nj_fruit_width_circ_3,
-            alpha = input$nj_fruit_alpha_3
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_3)),
-            offset = input$nj_fruit_offset_circ_3,
-            width = input$nj_fruit_width_circ_3,
-            alpha = input$nj_fruit_alpha_3
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$nj_tiles_show_3 == TRUE) {
-        if(!is.null(Vis$nj_max_x)) {
-          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_3)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_3)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  nj_fruit4 <- reactive({
-    if((!is.null(input$nj_tiles_show_4)) & 
-       (!is.null(input$nj_fruit_variable_4)) & 
-       (!is.null(input$nj_layout)) & 
-       (!is.null(input$nj_fruit_offset_circ_4)) & 
-       (!is.null(input$nj_fruit_width_circ_4)) & 
-       (!is.null(input$nj_fruit_alpha_4))) {
-      if(input$nj_tiles_show_4 == TRUE) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_4)),
-            offset = input$nj_fruit_offset_circ_4,
-            width = input$nj_fruit_width_circ_4,
-            alpha = input$nj_fruit_alpha_4
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_4)),
-            offset = input$nj_fruit_offset_circ_4,
-            width = input$nj_fruit_width_circ_4,
-            alpha = input$nj_fruit_alpha_4
-          )
-        }
-      } else {
-        if(input$nj_tiles_show_4 == TRUE) {
-          if(!is.null(Vis$nj_max_x)) {
-            if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-              width <- 1
-            } else {
-              width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-            }
-          } else {
-            width <- 2
-          }
-          if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-            geom_fruit(
-              geom = geom_tile,
-              mapping = aes(fill= !!sym(input$nj_fruit_variable_4)),
-              offset = 0.15,
-              width = width * 3,
-              alpha = 1
-            )
-          } else {
-            geom_fruit(
-              geom = geom_tile,
-              mapping = aes(fill= !!sym(input$nj_fruit_variable_4)),
-              offset = 0.05,
-              width = width,
-              alpha = 1
-            )
-          }
-        } else {NULL}
-      }
-    }
-  })
-  
-  nj_fruit5 <- reactive({
-    if((!is.null(input$nj_tiles_show_5)) & 
-       (!is.null(input$nj_fruit_variable_5)) & 
-       (!is.null(input$nj_layout)) & 
-       (!is.null(input$nj_fruit_offset_circ_5)) & 
-       (!is.null(input$nj_fruit_width_circ_5)) & 
-       (!is.null(input$nj_fruit_alpha_5))) {
-      if(input$nj_tiles_show_5 == TRUE) {
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_5)),
-            offset = input$nj_fruit_offset_circ_5,
-            width = input$nj_fruit_width_circ_5,
-            alpha = input$nj_fruit_alpha_5
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$nj_fruit_variable_5)),
-            offset = input$nj_fruit_offset_circ_5,
-            width = input$nj_fruit_width_circ_5,
-            alpha = input$nj_fruit_alpha_5
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$nj_tiles_show_5 == TRUE) {
-        if(!is.null(Vis$nj_max_x)) {
-          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_5)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$nj_fruit_variable_5)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  # Xlim
-  nj_limit <- reactive({
-    if(input$nj_layout == "circular") {
-      xlim(input$nj_xlim, NA)
-    } else {NULL}
-  })
-  
-  # Treescale
-  nj_treescale <- reactive({
-    if(!input$nj_layout == "circular") {
-      if(input$nj_treescale_show == TRUE) {
-        geom_treescale(x = nj_treescale_x(),
-                       y = nj_treescale_y(),
-                       width = nj_treescale_width(),
-                       color = input$nj_color,
-                       fontsize = 4)
-      } else {NULL}
-    } else {NULL}
-  }) 
-  
-  # Treescale Y Position
-  nj_treescale_y <- reactive({
-    if(is.null(input$nj_treescale_y)) {
-      0
-    } else {input$nj_treescale_y}
-  })
-  
-  # Treescale X Position
-  nj_treescale_x <- reactive({
-    if(is.null(input$nj_treescale_x)) {
-      round(ceiling(Vis$nj_max_x) * 0.2, 0)
-    } else {input$nj_treescale_x}
-  })
-  
-  # Treescale width
-  nj_treescale_width <- reactive({
-    if(!is.null(input$nj_treescale_width)) {
-      input$nj_treescale_width
-    } else {
-      round(ceiling(Vis$nj_max_x) * 0.1, 0)
-    }
-  })
-  
-  # Label branches
-  nj_label_branch <- reactive({
-    if(!input$nj_layout == "circular" | !input$nj_layout == "inward") {
-      if(input$nj_show_branch_label == TRUE) {
-        geom_label(
-          aes(
-            x=!!sym("branch"), 
-            label= !!sym(input$nj_branch_label)),
-          fill = input$nj_branch_label_color,
-          size = nj_branch_size(),
-          label.r = unit(input$nj_branch_labelradius, "lines"),
-          nudge_x = input$nj_branch_x,
-          nudge_y = input$nj_branch_y,
-          fontface = input$nj_branchlab_fontface,
-          alpha = input$nj_branchlab_alpha
-        )
-      } else {NULL}
-    } else {NULL}
-  })
-  
-  # Branch label size
-  nj_branch_size <- reactive({
-    if(!is.null(input$nj_branch_size)) {
-      input$nj_branch_size
-    } else {
-      Vis$branch_size_nj
-    }
-  })
-  
-  # Rootedge
-  nj_rootedge <- reactive({
-    if(input$nj_rootedge_show == TRUE) {
-      if(is.null(input$nj_rootedge_length)) {
-        geom_rootedge(rootedge = round(ceiling(Vis$nj_max_x) * 0.05, 0),
-                      linetype = input$nj_rootedge_line)
-      } else {
-        geom_rootedge(rootedge = input$nj_rootedge_length,
-                      linetype = input$nj_rootedge_line)
-      }
-    } else {NULL}
-  })
-  
-  # Tippoints
-  nj_tippoint <- reactive({
-    if(input$nj_tippoint_show == TRUE | input$nj_tipcolor_mapping_show == TRUE | input$nj_tipshape_mapping_show == TRUE) {
-      if(input$nj_tipcolor_mapping_show == TRUE & input$nj_tipshape_mapping_show == FALSE) {
-        geom_tippoint(
-          aes(color = !!sym(input$nj_tipcolor_mapping)),
-          alpha = input$nj_tippoint_alpha,
-          shape = input$nj_tippoint_shape,
-          size = nj_tippoint_size()
-        )
-      } else if (input$nj_tipcolor_mapping_show == FALSE & input$nj_tipshape_mapping_show == TRUE) {
-        geom_tippoint(
-          aes(shape = !!sym(input$nj_tipshape_mapping)),
-          alpha = input$nj_tippoint_alpha,
-          color = input$nj_tippoint_color,
-          size = nj_tippoint_size()
-        )
-      } else if (input$nj_tipcolor_mapping_show == TRUE & input$nj_tipshape_mapping_show == TRUE) {
-        geom_tippoint(
-          aes(shape = !!sym(input$nj_tipshape_mapping),
-              color = !!sym(input$nj_tipcolor_mapping)),
-          alpha = input$nj_tippoint_alpha,
-          size = nj_tippoint_size()
-        )
-      } else {
-        geom_tippoint(
-          alpha = input$nj_tippoint_alpha,
-          colour = input$nj_tippoint_color,
-          fill = input$nj_tippoint_color,
-          shape = input$nj_tippoint_shape,
-          size = nj_tippoint_size()
-        )
-      } 
-    } else {NULL}
-  })
-  
-  # Nodepoints
-  nj_nodepoint <- reactive({
-    if(input$nj_nodepoint_show == TRUE) {
-      geom_nodepoint(
-        alpha = input$nj_nodepoint_alpha,
-        color = input$nj_nodepoint_color,
-        shape = input$nj_nodepoint_shape,
-        size = nj_nodepoint_size()
-      )
-    } else {NULL}
-  })
-  
-  # Nodepoint size
-  nj_nodepoint_size <- reactive({
-    if(!is.null(input$nj_nodepoint_size)) {
-      input$nj_nodepoint_size
-    } else {
-      Vis$nodepointsize_nj
-    }
-  })
-  
-  # NJ circular or not
-  nj_tiplab <- reactive({
-    if(input$nj_tiplab_show == TRUE) {
-      if(input$nj_layout == "circular") {
-        if(input$nj_mapping_show == TRUE) {
-          geom_tiplab(
-            nj_mapping_tiplab(), 
-            geom = "text",
-            size = nj_tiplab_size(),
-            alpha = input$nj_tiplab_alpha,
-            fontface = input$nj_tiplab_fontface,
-            align = as.logical(input$nj_align),
-            hjust = as.numeric(input$nj_tiplab_position),
-            check.overlap = input$nj_tiplab_overlap
-          )
-        } else {
-          geom_tiplab(
-            nj_mapping_tiplab(),
-            color = input$nj_tiplab_color,
-            geom = "text",
-            size = nj_tiplab_size(),
-            alpha = input$nj_tiplab_alpha,
-            fontface = input$nj_tiplab_fontface,
-            align = as.logical(input$nj_align),
-            hjust = as.numeric(input$nj_tiplab_position),
-            check.overlap = input$nj_tiplab_overlap
-          )
-        }
-      } else if (input$nj_layout == "inward") {
-        if(input$nj_mapping_show == TRUE) {
-          geom_tiplab(
-            nj_mapping_tiplab(), 
-            geom = "text",
-            size = nj_tiplab_size(),
-            alpha = input$nj_tiplab_alpha,
-            fontface = input$nj_tiplab_fontface,
-            align = as.logical(input$nj_align),
-            hjust = as.numeric(input$nj_tiplab_position_inw),
-            check.overlap = input$nj_tiplab_overlap
-          )
-        } else {
-          geom_tiplab(
-            nj_mapping_tiplab(),
-            color = input$nj_tiplab_color,
-            geom = "text",
-            size = nj_tiplab_size(),
-            alpha = input$nj_tiplab_alpha,
-            fontface = input$nj_tiplab_fontface,
-            align = as.logical(input$nj_align),
-            hjust = as.numeric(input$nj_tiplab_position_inw),
-            check.overlap = input$nj_tiplab_overlap
-          )
-        }
-      } else {
-        if(input$nj_mapping_show == TRUE) {
-          if(input$nj_geom == TRUE) {
-            geom_tiplab(
-              nj_mapping_tiplab(), 
-              geom = nj_geom(),
-              angle = input$nj_tiplab_angle,
-              size = nj_tiplab_size(),
-              alpha = input$nj_tiplab_alpha,
-              fontface = input$nj_tiplab_fontface,
-              align = as.logical(input$nj_align),
-              nudge_x = input$nj_tiplab_nudge_x,
-              check.overlap = input$nj_tiplab_overlap,
-              label.padding = unit(nj_tiplab_padding(), "lines"),
-              label.r = unit(input$nj_tiplab_labelradius, "lines"), 
-              fill = input$nj_tiplab_fill
-            )
-          } else {
-            geom_tiplab(
-              nj_mapping_tiplab(), 
-              geom = nj_geom(),
-              angle = input$nj_tiplab_angle,
-              size = nj_tiplab_size(),
-              alpha = input$nj_tiplab_alpha,
-              fontface = input$nj_tiplab_fontface,
-              align = as.logical(input$nj_align),
-              nudge_x = input$nj_tiplab_nudge_x,
-              check.overlap = input$nj_tiplab_overlap
-            )
-          }
-        } else {
-          if(input$nj_geom == TRUE) {
-            geom_tiplab(
-              nj_mapping_tiplab(), 
-              geom = nj_geom(),
-              color = input$nj_tiplab_color,
-              angle = input$nj_tiplab_angle,
-              size = nj_tiplab_size(),
-              alpha = input$nj_tiplab_alpha,
-              fontface = input$nj_tiplab_fontface,
-              align = as.logical(input$nj_align),
-              nudge_x = input$nj_tiplab_nudge_x,
-              check.overlap = input$nj_tiplab_overlap,
-              label.padding = unit(nj_tiplab_padding(), "lines"),
-              label.r = unit(input$nj_tiplab_labelradius, "lines"), 
-              fill = input$nj_tiplab_fill
-            )
-          } else {
-            geom_tiplab(
-              nj_mapping_tiplab(), 
-              geom = nj_geom(),
-              color = input$nj_tiplab_color,
-              angle = input$nj_tiplab_angle,
-              size = nj_tiplab_size(),
-              alpha = input$nj_tiplab_alpha,
-              fontface = input$nj_tiplab_fontface,
-              align = as.logical(input$nj_align),
-              nudge_x = input$nj_tiplab_nudge_x,
-              check.overlap = input$nj_tiplab_overlap
-            )
-          }
-        }
-      }
-    } else {NULL}
-  })
-  
-  # Tip panel size
-  nj_tiplab_padding <- reactive({
-    if(!is.null(input$nj_tiplab_padding)) {
-      input$nj_tiplab_padding
-    } else {
-      Vis$tiplab_padding_nj
-    }
-  })
-  
-  # Tiplab size
-  nj_tiplab_size <- reactive({
-    if(!is.null(input$nj_tiplab_size)) {
-      input$nj_tiplab_size
-    } else {
-      Vis$labelsize_nj
-    }
-  })
-  
-  # Tippoint size
-  nj_tippoint_size <- reactive({
-    if(!is.null(input$nj_tippoint_size)) {
-      input$nj_tippoint_size
-    } else {
-      Vis$tippointsize_nj
-    }
-  })
-  
-  # Show Label Panels?
-  nj_geom <- reactive({
-    if(input$nj_geom == TRUE) {
-      "label"
-    } else {"text"}
-  })
-  
-  # NJ Tiplab color
-  nj_mapping_tiplab <- reactive({
-    if(input$nj_mapping_show == TRUE) {
-      if(!is.null(input$nj_tiplab)) {
-        aes(label = !!sym(input$nj_tiplab),
-            color = !!sym(input$nj_color_mapping))
-      } else {
-        aes(label = !!sym("Assembly Name"),
-            color = !!sym(input$nj_color_mapping))
-      }
-    } else {
-      if(!is.null(input$nj_tiplab)) {
-        aes(label = !!sym(input$nj_tiplab))
-      } else {
-        aes(label = !!sym("Assembly Name"))
-      }
-    }
-  })
-  
-  # NJ Tree Layout
-  layout_nj <- reactive({
-    if(input$nj_layout == "inward") {
-      "circular"
-    } else {input$nj_layout}
-  })
-  
-  # NJ inward circular
-  nj_inward <- reactive({
-    if (input$nj_layout == "inward") {
-      layout_inward_circular(xlim = input$nj_inward_xlim)
-    } else {
-      NULL
-    }
-  })
-  
-  #### UPGMA ----
-  
-  upgma_tree <- reactive({
-    if(input$upgma_nodelabel_show == TRUE) {
-      ggtree(Vis$upgma, alpha = 0.2, layout = layout_upgma()) + 
-        geom_nodelab(aes(label = node), color = "#29303A", size = upgma_tiplab_size() + 1, hjust = 0.7) +
-        upgma_limit() +
-        upgma_inward() 
-    } else {
-      tree <-
-        ggtree(Vis$upgma, 
-               color = input$upgma_color,
-               layout = layout_upgma(),
-               ladderize = input$upgma_ladder) %<+% Vis$meta_upgma +
-        upgma_tiplab() +
-        upgma_tiplab_scale() + 
-        new_scale_color() +
-        upgma_limit() +
-        upgma_inward() +
-        upgma_label_branch() +
-        upgma_treescale() +
-        upgma_nodepoint() +
-        upgma_tippoint() +
-        upgma_tippoint_scale() + 
-        new_scale_color() +
-        upgma_clip_label() +
-        upgma_rootedge() +
-        upgma_clades() +
-        ggtitle(label = input$upgma_title,
-                subtitle = input$upgma_subtitle) +
-        theme_tree(bgcolor = input$upgma_bg) +
-        theme(plot.title = element_text(colour = input$upgma_title_color,
-                                        size = input$upgma_title_size),
-              plot.subtitle = element_text(colour = input$upgma_title_color,
-                                           size = input$upgma_subtitle_size),
-              legend.background = element_rect(fill = input$upgma_bg),
-              legend.direction = input$upgma_legend_orientation,
-              legend.title = element_text(color = input$upgma_color,
-                                          size = input$upgma_legend_size*1.2),
-              legend.title.align = 0.5,
-              legend.position = upgma_legend_pos(),
-              legend.text = element_text(color = input$upgma_color, 
-                                         size = input$upgma_legend_size),
-              legend.key = element_rect(fill = input$upgma_bg),
-              legend.box.spacing = unit(1.5, "cm"),
-              legend.key.size = unit(0.05*input$upgma_legend_size, 'cm'),
-              plot.background = element_rect(fill = input$upgma_bg, color = input$upgma_bg)) +
-        new_scale_fill() +
-        upgma_fruit() +
-        upgma_gradient() +
-        new_scale_fill() +
-        upgma_fruit2() +
-        upgma_gradient2() +
-        new_scale_fill() +
-        upgma_fruit3() +
-        upgma_gradient3() +
-        new_scale_fill() +
-        upgma_fruit4() +
-        upgma_gradient4() +
-        new_scale_fill() +
-        upgma_fruit5() +
-        upgma_gradient5() +
-        new_scale_fill() 
-      
-      # Add custom labels
-      if(length(Vis$custom_label_upgma) > 0) {
-        
-        for(i in Vis$custom_label_upgma[,1]) {
-          
-          if(!is.null(Vis$upgma_label_pos_x[[i]])) {
-            x_pos <- Vis$upgma_label_pos_x[[i]]
-          } else {
-            x_pos <- round(Vis$upgma_max_x / 2, 0)
-          }
-          
-          if(!is.null(Vis$upgma_label_pos_y[[i]])) {
-            y_pos <- Vis$upgma_label_pos_y[[i]]
-          } else {
-            y_pos <- sum(DB$data$Include) / 2
-          }
-          
-          if(!is.null(Vis$upgma_label_size[[i]])) {
-            size <- Vis$upgma_label_size[[i]]
-          } else {
-            size <- 5
-          }
-          
-          tree <- tree + annotate("text",
-                                  x = x_pos,
-                                  y = y_pos, 
-                                  label = i,
-                                  size = size)
-        }
-      }
-      
-      # Add heatmap
-      if(input$upgma_heatmap_show == TRUE & length(input$upgma_heatmap_select) > 0) {
-        if (!(any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)) & 
-              any(!sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)))) {
-          tree <- gheatmap.mod(tree, 
-                               data = select(Vis$meta_upgma, input$upgma_heatmap_select),
-                               offset = upgma_heatmap_offset(),
-                               width = upgma_heatmap_width(),
-                               legend_title = input$upgma_heatmap_title,
-                               colnames_angle = -upgma_colnames_angle(),
-                               colnames_offset_y = upgma_colnames_y(),
-                               colnames_color = input$upgma_color) +
-            upgma_heatmap_scale()
-        }
-      } 
-      
-      # Sizing control
-      Vis$upgma_plot <- ggplotify::as.ggplot(tree, 
-                                             scale = input$upgma_zoom,
-                                             hjust = input$upgma_h,
-                                             vjust = input$upgma_v)  
-      
-      # Correct background color if zoomed out
-      cowplot::ggdraw(Vis$upgma_plot) + 
-        theme(plot.background = element_rect(fill = input$upgma_bg, color = input$upgma_bg))
-    }
-  })
-  
-  # Heatmap width
-  upgma_heatmap_width <- reactive({
-    if(!is.null(input$upgma_heatmap_width)) {
-      input$upgma_heatmap_width
-    } else {
-      length_input <- length(input$upgma_heatmap_select)
-      if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
-        if(length_input < 3) {
-          0.1
-        } else {
-          if (length_input >= 3 && length_input <= 50) {
-            min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
-          } else {
-            1.5
-          }   
-        }
-      } else {
-        if(length_input < 3) {
-          0.3
-        } else if (length_input >= 3 && length_input <= 27) {
-          min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
-        } else {
-          3
-        }
-      }
-    }
-  })
-  
-  # Heatmap column titles position
-  upgma_colnames_y <- reactive({
-    if(!is.null(input$upgma_colnames_y)) {
-      input$upgma_colnames_y
-    } else {
-      if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
-        0
-      } else {-1}
-    }
-  })
-  
-  # Heatmap column titles angle
-  upgma_colnames_angle <- reactive({
-    if(!is.null(input$upgma_colnames_angle)) {
-      input$upgma_colnames_angle
-    } else {
-      if(!is.null(input$upgma_layout)) {
-        if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
-          90
-        } else {-90}
-      } else {-90}
-    }
-  })
-  
-  # Heatmap scale
-  upgma_heatmap_scale <- reactive({
-    if(!is.null(input$upgma_heatmap_scale) & !is.null(input$upgma_heatmap_div_mid)) {
-      if(input$upgma_heatmap_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$upgma_heatmap_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$upgma_heatmap_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_heatmap_select]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_heatmap_select]), na.rm = TRUE)
-        }
-        scale_fill_gradient2(low = brewer.pal(3, input$upgma_heatmap_scale)[1],
-                             mid = brewer.pal(3, input$upgma_heatmap_scale)[2],
-                             high = brewer.pal(3, input$upgma_heatmap_scale)[3],
-                             midpoint = midpoint,
-                             name = input$upgma_heatmap_title)
-      } else {
-        if(input$upgma_heatmap_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_upgma[input$upgma_heatmap_select])) == "numeric") {
-            if(input$upgma_heatmap_scale == "magma") {
-              scale_fill_viridis(option = "A",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "inferno") {
-              scale_fill_viridis(option = "B",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "plasma") {
-              scale_fill_viridis(option = "C",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "viridis") {
-              scale_fill_viridis(option = "D",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "cividis") {
-              scale_fill_viridis(option = "E",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "rocket") {
-              scale_fill_viridis(option = "F",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "mako") {
-              scale_fill_viridis(option = "G",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "turbo") {
-              scale_fill_viridis(option = "H",
-                                 name = input$upgma_heatmap_title)
-            } 
-          } else {
-            if(input$upgma_heatmap_scale == "magma") {
-              scale_fill_viridis(discrete = TRUE, option = "A",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "inferno") {
-              scale_fill_viridis(discrete = TRUE, option = "B",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "plasma") {
-              scale_fill_viridis(discrete = TRUE, option = "C",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "viridis") {
-              scale_fill_viridis(discrete = TRUE, option = "D",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "cividis") {
-              scale_fill_viridis(discrete = TRUE, option = "E",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "rocket") {
-              scale_fill_viridis(discrete = TRUE, option = "F",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "mako") {
-              scale_fill_viridis(discrete = TRUE, option = "G",
-                                 name = input$upgma_heatmap_title)
-            } else if(input$upgma_heatmap_scale == "turbo") {
-              scale_fill_viridis(discrete = TRUE, option = "H",
-                                 name = input$upgma_heatmap_title)
-            } 
-          }
-        } else {
-          scale_fill_brewer(palette = input$upgma_heatmap_scale,
-                            name = input$upgma_heatmap_title)
-        }
-      }
-    }
-  })
-  
-  # Tippoint Scale
-  upgma_tippoint_scale <- reactive({
-    if(!is.null(input$upgma_tippoint_scale) & !is.null(input$upgma_tipcolor_mapping_div_mid)) {
-      if(input$upgma_tippoint_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$upgma_tipcolor_mapping_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$upgma_tipcolor_mapping_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_tipcolor_mapping]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_tipcolor_mapping]), na.rm = TRUE)
-        }
-        scale_color_gradient2(low = brewer.pal(3, input$upgma_tippoint_scale)[1],
-                              mid = brewer.pal(3, input$upgma_tippoint_scale)[2],
-                              high = brewer.pal(3, input$upgma_tippoint_scale)[3],
-                              midpoint = midpoint)
-      } else {
-        if(input$upgma_tippoint_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping])) == "numeric") {
-            if(input$upgma_tippoint_scale == "magma") {
-              scale_color_viridis(option = "A")
-            } else if(input$upgma_tippoint_scale == "inferno") {
-              scale_color_viridis(option = "B")
-            } else if(input$upgma_tippoint_scale == "plasma") {
-              scale_color_viridis(option = "C")
-            } else if(input$upgma_tippoint_scale == "viridis") {
-              scale_color_viridis(option = "D")
-            } else if(input$upgma_tippoint_scale == "cividis") {
-              scale_color_viridis(option = "E")
-            } else if(input$upgma_tippoint_scale == "rocket") {
-              scale_color_viridis(option = "F")
-            } else if(input$upgma_tippoint_scale == "mako") {
-              scale_color_viridis(option = "G")
-            } else if(input$upgma_tippoint_scale == "turbo") {
-              scale_color_viridis(option = "H")
-            } 
-          } else {
-            if(input$upgma_tippoint_scale == "magma") {
-              scale_color_viridis(discrete = TRUE, option = "A")
-            } else if(input$upgma_tippoint_scale == "inferno") {
-              scale_color_viridis(discrete = TRUE, option = "B")
-            } else if(input$upgma_tippoint_scale == "plasma") {
-              scale_color_viridis(discrete = TRUE, option = "C")
-            } else if(input$upgma_tippoint_scale == "viridis") {
-              scale_color_viridis(discrete = TRUE, option = "D")
-            } else if(input$upgma_tippoint_scale == "cividis") {
-              scale_color_viridis(discrete = TRUE, option = "E")
-            } else if(input$upgma_tippoint_scale == "rocket") {
-              scale_color_viridis(discrete = TRUE, option = "F")
-            } else if(input$upgma_tippoint_scale == "mako") {
-              scale_color_viridis(discrete = TRUE, option = "G")
-            } else if(input$upgma_tippoint_scale == "turbo") {
-              scale_color_viridis(discrete = TRUE, option = "H")
-            } 
-          }
-        } else {
-          scale_color_brewer(palette = input$upgma_tippoint_scale)
-        }
-      }
-    }
-  })
-  
-  # Tiplab Scale
-  upgma_tiplab_scale <- reactive({
-    if(!is.null(input$upgma_tiplab_scale) & !is.null(input$upgma_color_mapping_div_mid)) {
-      if(input$upgma_tiplab_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-        if(input$upgma_color_mapping_div_mid == "Zero") {
-          midpoint <- 0
-        } else if(input$upgma_color_mapping_div_mid == "Mean") {
-          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_color_mapping]), na.rm = TRUE)
-        } else {
-          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_color_mapping]), na.rm = TRUE)
-        }
-        scale_color_gradient2(low = brewer.pal(3, input$upgma_tiplab_scale)[1],
-                              mid = brewer.pal(3, input$upgma_tiplab_scale)[2],
-                              high = brewer.pal(3, input$upgma_tiplab_scale)[3],
-                              midpoint = midpoint)
-      } else {
-        if(input$upgma_tiplab_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-          if(class(unlist(Vis$meta_upgma[input$upgma_color_mapping])) == "numeric") {
-            if(input$upgma_tiplab_scale == "magma") {
-              scale_color_viridis(option = "A")
-            } else if(input$upgma_tiplab_scale == "inferno") {
-              scale_color_viridis(option = "B")
-            } else if(input$upgma_tiplab_scale == "plasma") {
-              scale_color_viridis(option = "C")
-            } else if(input$upgma_tiplab_scale == "viridis") {
-              scale_color_viridis(option = "D")
-            } else if(input$upgma_tiplab_scale == "cividis") {
-              scale_color_viridis(option = "E")
-            } else if(input$upgma_tiplab_scale == "rocket") {
-              scale_color_viridis(option = "F")
-            } else if(input$upgma_tiplab_scale == "mako") {
-              scale_color_viridis(option = "G")
-            } else if(input$upgma_tiplab_scale == "turbo") {
-              scale_color_viridis(option = "H")
-            } 
-          } else {
-            if(input$upgma_tiplab_scale == "magma") {
-              scale_color_viridis(discrete = TRUE, option = "A")
-            } else if(input$upgma_tiplab_scale == "inferno") {
-              scale_color_viridis(discrete = TRUE, option = "B")
-            } else if(input$upgma_tiplab_scale == "plasma") {
-              scale_color_viridis(discrete = TRUE, option = "C")
-            } else if(input$upgma_tiplab_scale == "viridis") {
-              scale_color_viridis(discrete = TRUE, option = "D")
-            } else if(input$upgma_tiplab_scale == "cividis") {
-              scale_color_viridis(discrete = TRUE, option = "E")
-            } else if(input$upgma_tiplab_scale == "rocket") {
-              scale_color_viridis(discrete = TRUE, option = "F")
-            } else if(input$upgma_tiplab_scale == "mako") {
-              scale_color_viridis(discrete = TRUE, option = "G")
-            } else if(input$upgma_tiplab_scale == "turbo") {
-              scale_color_viridis(discrete = TRUE, option = "H")
-            } 
-          }
-        } else {
-          scale_color_brewer(palette = input$upgma_tiplab_scale)
-        }
-      }
-    }
-  })
-  
-  # Clade Highlight
-  upgma_clades <- reactive({
-    if(!is.null(input$upgma_parentnode)) {
-      if(!length(input$upgma_parentnode) == 0) {
-        if(length(input$upgma_parentnode) == 1) {
-          fill <- input$upgma_clade_scale
-        } else if (length(input$upgma_parentnode) == 2) {
-          if(startsWith(input$upgma_clade_scale, "#")) {
-            fill <- brewer.pal(3, "Set1")[1:2]
-          } else {
-            fill <- brewer.pal(3, input$upgma_clade_scale)[1:2]
-          }
-        } else {
-          fill <- brewer.pal(length(input$upgma_parentnode), input$upgma_clade_scale)
-        }
-        geom_hilight(node = as.numeric(input$upgma_parentnode),
-                     fill = fill,
-                     type = input$upgma_clade_type,
-                     to.bottom = TRUE)
-      } else {NULL}
-    }
-  })
-  
-  # Legend Position
-  upgma_legend_pos <- reactive({
-    if(!is.null(input$upgma_legend_x) & !is.null(input$upgma_legend_y)) {
-      c(input$upgma_legend_x, input$upgma_legend_y)
-    } else {
-      c(0.1, 1)
-    }
-  })
-  
-  # Heatmap offset
-  upgma_heatmap_offset <- reactive({
-    if(is.null(input$upgma_heatmap_offset)) {
-      0
-    } else {input$upgma_heatmap_offset}
-  })
-  
-  # Tiles fill color gradient
-  upgma_gradient <- reactive({
-    if(!is.null(input$upgma_tiles_show_1) & 
-       !is.null(input$upgma_fruit_variable) & 
-       !is.null(input$upgma_tiles_scale_1) &
-       !is.null(input$upgma_tiles_mapping_div_mid_1)) {
-      if(input$upgma_tiles_show_1 == TRUE) {
-        if(input$upgma_tiles_scale_1 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$upgma_tiles_mapping_div_mid_1 == "Zero") {
-            midpoint <- 0
-          } else if(input$upgma_tiles_mapping_div_mid_1 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable]), na.rm = TRUE)
-          }
-          scale_fill_gradient2(low = brewer.pal(3, input$upgma_tiles_scale_1)[1],
-                               mid = brewer.pal(3, input$upgma_tiles_scale_1)[2],
-                               high = brewer.pal(3, input$upgma_tiles_scale_1)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$upgma_tiles_scale_1 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
-              if(input$upgma_tiles_scale_1 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$upgma_tiles_scale_1 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$upgma_tiles_scale_1 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$upgma_tiles_scale_1 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$upgma_tiles_scale_1 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$upgma_tiles_scale_1 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$upgma_tiles_scale_1 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$upgma_tiles_scale_1 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$upgma_tiles_scale_1 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$upgma_tiles_scale_1 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$upgma_tiles_scale_1 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$upgma_tiles_scale_1 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$upgma_tiles_scale_1 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$upgma_tiles_scale_1 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$upgma_tiles_scale_1 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$upgma_tiles_scale_1 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$upgma_tiles_scale_1)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_gradient2 <- reactive({
-    if(!is.null(input$upgma_tiles_show_2) & 
-       !is.null(input$upgma_fruit_variable_2) & 
-       !is.null(input$upgma_tiles_scale_2) &
-       !is.null(input$upgma_tiles_mapping_div_mid_2)) {
-      if(input$upgma_tiles_show_2 == TRUE) {
-        if(input$upgma_tiles_scale_2 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$upgma_tiles_mapping_div_mid_2 == "Zero") {
-            midpoint <- 0
-          } else if(input$upgma_tiles_mapping_div_mid_2 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_2]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_2]), na.rm = TRUE)
-          }
-          scale_fill_gradient2(low = brewer.pal(3, input$upgma_tiles_scale_2)[1],
-                               mid = brewer.pal(3, input$upgma_tiles_scale_2)[2],
-                               high = brewer.pal(3, input$upgma_tiles_scale_2)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$upgma_tiles_scale_2 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2])) == "numeric") {
-              if(input$upgma_tiles_scale_2 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$upgma_tiles_scale_2 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$upgma_tiles_scale_2 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$upgma_tiles_scale_2 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$upgma_tiles_scale_2 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$upgma_tiles_scale_2 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$upgma_tiles_scale_2 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$upgma_tiles_scale_2 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$upgma_tiles_scale_2 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$upgma_tiles_scale_2 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$upgma_tiles_scale_2 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$upgma_tiles_scale_2 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$upgma_tiles_scale_2 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$upgma_tiles_scale_2 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$upgma_tiles_scale_2 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$upgma_tiles_scale_2 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$upgma_tiles_scale_2)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_gradient3 <- reactive({
-    if(!is.null(input$upgma_tiles_show_3) & 
-       !is.null(input$upgma_fruit_variable_3) & 
-       !is.null(input$upgma_tiles_scale_3) &
-       !is.null(input$upgma_tiles_mapping_div_mid_3)) {
-      if(input$upgma_tiles_show_3 == TRUE) {
-        if(input$upgma_tiles_scale_3 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$upgma_tiles_mapping_div_mid_3 == "Zero") {
-            midpoint <- 0
-          } else if(input$upgma_tiles_mapping_div_mid_3 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_3]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_3]), na.rm = TRUE)
-          }
-          scale_fill_gradient3(low = brewer.pal(3, input$upgma_tiles_scale_3)[1],
-                               mid = brewer.pal(3, input$upgma_tiles_scale_3)[2],
-                               high = brewer.pal(3, input$upgma_tiles_scale_3)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$upgma_tiles_scale_3 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3])) == "numeric") {
-              if(input$upgma_tiles_scale_3 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$upgma_tiles_scale_3 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$upgma_tiles_scale_3 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$upgma_tiles_scale_3 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$upgma_tiles_scale_3 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$upgma_tiles_scale_3 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$upgma_tiles_scale_3 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$upgma_tiles_scale_3 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$upgma_tiles_scale_3 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$upgma_tiles_scale_3 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$upgma_tiles_scale_3 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$upgma_tiles_scale_3 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$upgma_tiles_scale_3 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$upgma_tiles_scale_3 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$upgma_tiles_scale_3 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$upgma_tiles_scale_3 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$upgma_tiles_scale_3)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_gradient4 <- reactive({
-    if(!is.null(input$upgma_tiles_show_4) & 
-       !is.null(input$upgma_fruit_variable_4) & 
-       !is.null(input$upgma_tiles_scale_4) &
-       !is.null(input$upgma_tiles_mapping_div_mid_4)) {
-      if(input$upgma_tiles_show_4 == TRUE) {
-        if(input$upgma_tiles_scale_4 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$upgma_tiles_mapping_div_mid_4 == "Zero") {
-            midpoint <- 0
-          } else if(input$upgma_tiles_mapping_div_mid_4 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_4]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_4]), na.rm = TRUE)
-          }
-          scale_fill_gradient4(low = brewer.pal(3, input$upgma_tiles_scale_4)[1],
-                               mid = brewer.pal(3, input$upgma_tiles_scale_4)[2],
-                               high = brewer.pal(3, input$upgma_tiles_scale_4)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$upgma_tiles_scale_4 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
-              if(input$upgma_tiles_scale_4 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$upgma_tiles_scale_4 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$upgma_tiles_scale_4 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$upgma_tiles_scale_4 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$upgma_tiles_scale_4 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$upgma_tiles_scale_4 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$upgma_tiles_scale_4 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$upgma_tiles_scale_4 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$upgma_tiles_scale_4 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$upgma_tiles_scale_4 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$upgma_tiles_scale_4 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$upgma_tiles_scale_4 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$upgma_tiles_scale_4 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$upgma_tiles_scale_4 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$upgma_tiles_scale_4 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$upgma_tiles_scale_4 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$upgma_tiles_scale_4)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_gradient5 <- reactive({
-    if(!is.null(input$upgma_tiles_show_5) & 
-       !is.null(input$upgma_fruit_variable_5) & 
-       !is.null(input$upgma_tiles_scale_5) &
-       !is.null(input$upgma_tiles_mapping_div_mid_5)) {
-      if(input$upgma_tiles_show_5 == TRUE) {
-        if(input$upgma_tiles_scale_5 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
-          if(input$upgma_tiles_mapping_div_mid_5 == "Zero") {
-            midpoint <- 0
-          } else if(input$upgma_tiles_mapping_div_mid_5 == "Mean") {
-            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_5]), na.rm = TRUE)
-          } else {
-            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_5]), na.rm = TRUE)
-          }
-          scale_fill_gradient5(low = brewer.pal(3, input$upgma_tiles_scale_5)[1],
-                               mid = brewer.pal(3, input$upgma_tiles_scale_5)[2],
-                               high = brewer.pal(3, input$upgma_tiles_scale_5)[3],
-                               midpoint = midpoint)
-        } else {
-          if(input$upgma_tiles_scale_5 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
-            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5])) == "numeric") {
-              if(input$upgma_tiles_scale_5 == "magma") {
-                scale_fill_viridis(option = "A")
-              } else if(input$upgma_tiles_scale_5 == "inferno") {
-                scale_fill_viridis(option = "B")
-              } else if(input$upgma_tiles_scale_5 == "plasma") {
-                scale_fill_viridis(option = "C")
-              } else if(input$upgma_tiles_scale_5 == "viridis") {
-                scale_fill_viridis(option = "D")
-              } else if(input$upgma_tiles_scale_5 == "cividis") {
-                scale_fill_viridis(option = "E")
-              } else if(input$upgma_tiles_scale_5 == "rocket") {
-                scale_fill_viridis(option = "F")
-              } else if(input$upgma_tiles_scale_5 == "mako") {
-                scale_fill_viridis(option = "G")
-              } else if(input$upgma_tiles_scale_5 == "turbo") {
-                scale_fill_viridis(option = "H")
-              } 
-            } else {
-              if(input$upgma_tiles_scale_5 == "magma") {
-                scale_fill_viridis(discrete = TRUE, option = "A")
-              } else if(input$upgma_tiles_scale_5 == "inferno") {
-                scale_fill_viridis(discrete = TRUE, option = "B")
-              } else if(input$upgma_tiles_scale_5 == "plasma") {
-                scale_fill_viridis(discrete = TRUE, option = "C")
-              } else if(input$upgma_tiles_scale_5 == "viridis") {
-                scale_fill_viridis(discrete = TRUE, option = "D")
-              } else if(input$upgma_tiles_scale_5 == "cividis") {
-                scale_fill_viridis(discrete = TRUE, option = "E")
-              } else if(input$upgma_tiles_scale_5 == "rocket") {
-                scale_fill_viridis(discrete = TRUE, option = "F")
-              } else if(input$upgma_tiles_scale_5 == "mako") {
-                scale_fill_viridis(discrete = TRUE, option = "G")
-              } else if(input$upgma_tiles_scale_5 == "turbo") {
-                scale_fill_viridis(discrete = TRUE, option = "H")
-              } 
-            }
-          } else {
-            scale_fill_brewer(palette = input$upgma_tiles_scale_5)
-          }
-        }
-      } else {NULL}
-    }
-  })
-  
-  # No label clip off for linear upgma tree
-  upgma_clip_label <- reactive({
-    if(!(input$upgma_layout == "circular" | input$upgma_layout == "inward")) {
-      coord_cartesian(clip = "off")
-    } else {NULL}
-  })
-  
-  # Geom Fruit
-  upgma_fruit <- reactive({
-    if((!is.null(input$upgma_tiles_show_1)) & 
-       (!is.null(input$upgma_fruit_variable)) & 
-       (!is.null(input$upgma_layout)) & 
-       (!is.null(input$upgma_fruit_offset_circ)) & 
-       (!is.null(input$upgma_fruit_width_circ)) & 
-       (!is.null(input$upgma_fruit_alpha))) {
-      if(input$upgma_tiles_show_1 == TRUE) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
-            offset = input$upgma_fruit_offset_circ,
-            width = input$upgma_fruit_width_circ,
-            alpha = input$upgma_fruit_alpha
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
-            offset = input$upgma_fruit_offset_circ,
-            width = input$upgma_fruit_width_circ,
-            alpha = input$upgma_fruit_alpha
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$upgma_tiles_show_1 == TRUE) {
-        if(!is.null(Vis$upgma_max_x)) {
-          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
-            offset = 0,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
-            offset = 0,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  # Geom Fruit
-  upgma_fruit2 <- reactive({
-    if((!is.null(input$upgma_tiles_show_2)) & 
-       (!is.null(input$upgma_fruit_variable_2)) & 
-       (!is.null(input$upgma_layout)) & 
-       (!is.null(input$upgma_fruit_offset_circ_2)) & 
-       (!is.null(input$upgma_fruit_width_circ_2)) & 
-       (!is.null(input$upgma_fruit_alpha_2))) {
-      if(input$upgma_tiles_show_2 == TRUE) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_2)),
-            offset = input$upgma_fruit_offset_circ_2,
-            width = input$upgma_fruit_width_circ_2,
-            alpha = input$upgma_fruit_alpha_2
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_2)),
-            offset = input$upgma_fruit_offset_circ_2,
-            width = input$upgma_fruit_width_circ_2,
-            alpha = input$upgma_fruit_alpha_2
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$upgma_tiles_show_2 == TRUE) {
-        if(!is.null(Vis$upgma_max_x)) {
-          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_2)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_2)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_fruit3 <- reactive({
-    if((!is.null(input$upgma_tiles_show_3)) & 
-       (!is.null(input$upgma_fruit_variable_3)) & 
-       (!is.null(input$upgma_layout)) & 
-       (!is.null(input$upgma_fruit_offset_circ_3)) & 
-       (!is.null(input$upgma_fruit_width_circ_3)) & 
-       (!is.null(input$upgma_fruit_alpha_3))) {
-      if(input$upgma_tiles_show_3 == TRUE) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_3)),
-            offset = input$upgma_fruit_offset_circ_3,
-            width = input$upgma_fruit_width_circ_3,
-            alpha = input$upgma_fruit_alpha_3
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_3)),
-            offset = input$upgma_fruit_offset_circ_3,
-            width = input$upgma_fruit_width_circ_3,
-            alpha = input$upgma_fruit_alpha_3
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$upgma_tiles_show_3 == TRUE) {
-        if(!is.null(Vis$upgma_max_x)) {
-          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_3)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_3)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  upgma_fruit4 <- reactive({
-    if((!is.null(input$upgma_tiles_show_4)) & 
-       (!is.null(input$upgma_fruit_variable_4)) & 
-       (!is.null(input$upgma_layout)) & 
-       (!is.null(input$upgma_fruit_offset_circ_4)) & 
-       (!is.null(input$upgma_fruit_width_circ_4)) & 
-       (!is.null(input$upgma_fruit_alpha_4))) {
-      if(input$upgma_tiles_show_4 == TRUE) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_4)),
-            offset = input$upgma_fruit_offset_circ_4,
-            width = input$upgma_fruit_width_circ_4,
-            alpha = input$upgma_fruit_alpha_4
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_4)),
-            offset = input$upgma_fruit_offset_circ_4,
-            width = input$upgma_fruit_width_circ_4,
-            alpha = input$upgma_fruit_alpha_4
-          )
-        }
-      } else {
-        if(input$upgma_tiles_show_4 == TRUE) {
-          if(!is.null(Vis$upgma_max_x)) {
-            if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-              width <- 1
-            } else {
-              width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-            }
-          } else {
-            width <- 2
-          }
-          if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-            geom_fruit(
-              geom = geom_tile,
-              mapping = aes(fill= !!sym(input$upgma_fruit_variable_4)),
-              offset = 0.15,
-              width = width * 3,
-              alpha = 1
-            )
-          } else {
-            geom_fruit(
-              geom = geom_tile,
-              mapping = aes(fill= !!sym(input$upgma_fruit_variable_4)),
-              offset = 0.05,
-              width = width,
-              alpha = 1
-            )
-          }
-        } else {NULL}
-      }
-    }
-  })
-  
-  upgma_fruit5 <- reactive({
-    if((!is.null(input$upgma_tiles_show_5)) & 
-       (!is.null(input$upgma_fruit_variable_5)) & 
-       (!is.null(input$upgma_layout)) & 
-       (!is.null(input$upgma_fruit_offset_circ_5)) & 
-       (!is.null(input$upgma_fruit_width_circ_5)) & 
-       (!is.null(input$upgma_fruit_alpha_5))) {
-      if(input$upgma_tiles_show_5 == TRUE) {
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_5)),
-            offset = input$upgma_fruit_offset_circ_5,
-            width = input$upgma_fruit_width_circ_5,
-            alpha = input$upgma_fruit_alpha_5
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill = !!sym(input$upgma_fruit_variable_5)),
-            offset = input$upgma_fruit_offset_circ_5,
-            width = input$upgma_fruit_width_circ_5,
-            alpha = input$upgma_fruit_alpha_5
-          )
-        }
-      } else {NULL}
-    } else {
-      if(input$upgma_tiles_show_5 == TRUE) {
-        if(!is.null(Vis$upgma_max_x)) {
-          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
-            width <- 1
-          } else {
-            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
-          }
-        } else {
-          width <- 2
-        }
-        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_5)),
-            offset = 0.15,
-            width = width * 3,
-            alpha = 1
-          )
-        } else {
-          geom_fruit(
-            geom = geom_tile,
-            mapping = aes(fill= !!sym(input$upgma_fruit_variable_5)),
-            offset = 0.05,
-            width = width,
-            alpha = 1
-          )
-        }
-      } else {NULL}
-    }
-  })
-  
-  # Xlim
-  upgma_limit <- reactive({
-    if(input$upgma_layout == "circular") {
-      xlim(input$upgma_xlim, NA)
-    } else {NULL}
-  })
-  
-  # Treescale
-  upgma_treescale <- reactive({
-    if(!input$upgma_layout == "circular") {
-      if(input$upgma_treescale_show == TRUE) {
-        geom_treescale(x = upgma_treescale_x(),
-                       y = upgma_treescale_y(),
-                       width = upgma_treescale_width(),
-                       color = input$upgma_color,
-                       fontsize = 4)
-      } else {NULL}
-    } else {NULL}
-  }) 
-  
-  # Treescale Y Position
-  upgma_treescale_y <- reactive({
-    if(is.null(input$upgma_treescale_y)) {
-      0
-    } else {input$upgma_treescale_y}
-  })
-  
-  # Treescale X Position
-  upgma_treescale_x <- reactive({
-    if(is.null(input$upgma_treescale_x)) {
-      round(ceiling(Vis$upgma_max_x) * 0.2, 0)
-    } else {input$upgma_treescale_x}
-  })
-  
-  # Treescale width
-  upgma_treescale_width <- reactive({
-    if(!is.null(input$upgma_treescale_width)) {
-      input$upgma_treescale_width
-    } else {
-      round(ceiling(Vis$upgma_max_x) * 0.1, 0)
-    }
-  })
-  
-  # Label branches
-  upgma_label_branch <- reactive({
-    if(!input$upgma_layout == "circular" | !input$upgma_layout == "inward") {
-      if(input$upgma_show_branch_label == TRUE) {
-        geom_label(
-          aes(
-            x=!!sym("branch"), 
-            label= !!sym(input$upgma_branch_label)),
-          fill = input$upgma_branch_label_color,
-          size = upgma_branch_size(),
-          label.r = unit(input$upgma_branch_labelradius, "lines"),
-          nudge_x = input$upgma_branch_x,
-          nudge_y = input$upgma_branch_y,
-          fontface = input$upgma_branchlab_fontface,
-          alpha = input$upgma_branchlab_alpha
-        )
-      } else {NULL}
-    } else {NULL}
-  })
-  
-  # Branch label size
-  upgma_branch_size <- reactive({
-    if(!is.null(input$upgma_branch_size)) {
-      input$upgma_branch_size
-    } else {
-      Vis$branch_size_upgma
-    }
-  })
-  
-  # Rootedge
-  upgma_rootedge <- reactive({
-    if(input$upgma_rootedge_show == TRUE) {
-      if(is.null(input$upgma_rootedge_length)) {
-        geom_rootedge(rootedge = round(ceiling(Vis$upgma_max_x) * 0.05, 0),
-                      linetype = input$upgma_rootedge_line)
-      } else {
-        geom_rootedge(rootedge = input$upgma_rootedge_length,
-                      linetype = input$upgma_rootedge_line)
-      }
-    } else {NULL}
-  })
-  
-  # Tippoints
-  upgma_tippoint <- reactive({
-    if(input$upgma_tippoint_show == TRUE | input$upgma_tipcolor_mapping_show == TRUE | input$upgma_tipshape_mapping_show == TRUE) {
-      if(input$upgma_tipcolor_mapping_show == TRUE & input$upgma_tipshape_mapping_show == FALSE) {
-        geom_tippoint(
-          aes(color = !!sym(input$upgma_tipcolor_mapping)),
-          alpha = input$upgma_tippoint_alpha,
-          shape = input$upgma_tippoint_shape,
-          size = upgma_tippoint_size()
-        )
-      } else if (input$upgma_tipcolor_mapping_show == FALSE & input$upgma_tipshape_mapping_show == TRUE) {
-        geom_tippoint(
-          aes(shape = !!sym(input$upgma_tipshape_mapping)),
-          alpha = input$upgma_tippoint_alpha,
-          color = input$upgma_tippoint_color,
-          size = upgma_tippoint_size()
-        )
-      } else if (input$upgma_tipcolor_mapping_show == TRUE & input$upgma_tipshape_mapping_show == TRUE) {
-        geom_tippoint(
-          aes(shape = !!sym(input$upgma_tipshape_mapping),
-              color = !!sym(input$upgma_tipcolor_mapping)),
-          alpha = input$upgma_tippoint_alpha,
-          size = upgma_tippoint_size()
-        )
-      } else {
-        geom_tippoint(
-          alpha = input$upgma_tippoint_alpha,
-          colour = input$upgma_tippoint_color,
-          fill = input$upgma_tippoint_color,
-          shape = input$upgma_tippoint_shape,
-          size = upgma_tippoint_size()
-        )
-      } 
-    } else {NULL}
-  })
-  
-  # Nodepoints
-  upgma_nodepoint <- reactive({
-    if(input$upgma_nodepoint_show == TRUE) {
-      geom_nodepoint(
-        alpha = input$upgma_nodepoint_alpha,
-        color = input$upgma_nodepoint_color,
-        shape = input$upgma_nodepoint_shape,
-        size = upgma_nodepoint_size()
-      )
-    } else {NULL}
-  })
-  
-  # Nodepoint size
-  upgma_nodepoint_size <- reactive({
-    if(!is.null(input$upgma_nodepoint_size)) {
-      input$upgma_nodepoint_size
-    } else {
-      Vis$nodepointsize_upgma
-    }
-  })
-  
-  # upgma circular or not
-  upgma_tiplab <- reactive({
-    if(input$upgma_tiplab_show == TRUE) {
-      if(input$upgma_layout == "circular") {
-        if(input$upgma_mapping_show == TRUE) {
-          geom_tiplab(
-            upgma_mapping_tiplab(), 
-            geom = "text",
-            size = upgma_tiplab_size(),
-            alpha = input$upgma_tiplab_alpha,
-            fontface = input$upgma_tiplab_fontface,
-            align = as.logical(input$upgma_align),
-            hjust = as.numeric(input$upgma_tiplab_position),
-            check.overlap = input$upgma_tiplab_overlap
-          )
-        } else {
-          geom_tiplab(
-            upgma_mapping_tiplab(),
-            color = input$upgma_tiplab_color,
-            geom = "text",
-            size = upgma_tiplab_size(),
-            alpha = input$upgma_tiplab_alpha,
-            fontface = input$upgma_tiplab_fontface,
-            align = as.logical(input$upgma_align),
-            hjust = as.numeric(input$upgma_tiplab_position),
-            check.overlap = input$upgma_tiplab_overlap
-          )
-        }
-      } else if (input$upgma_layout == "inward") {
-        if(input$upgma_mapping_show == TRUE) {
-          geom_tiplab(
-            upgma_mapping_tiplab(), 
-            geom = "text",
-            size = upgma_tiplab_size(),
-            alpha = input$upgma_tiplab_alpha,
-            fontface = input$upgma_tiplab_fontface,
-            align = as.logical(input$upgma_align),
-            hjust = as.numeric(input$upgma_tiplab_position_inw),
-            check.overlap = input$upgma_tiplab_overlap
-          )
-        } else {
-          geom_tiplab(
-            upgma_mapping_tiplab(),
-            color = input$upgma_tiplab_color,
-            geom = "text",
-            size = upgma_tiplab_size(),
-            alpha = input$upgma_tiplab_alpha,
-            fontface = input$upgma_tiplab_fontface,
-            align = as.logical(input$upgma_align),
-            hjust = as.numeric(input$upgma_tiplab_position_inw),
-            check.overlap = input$upgma_tiplab_overlap
-          )
-        }
-      } else {
-        if(input$upgma_mapping_show == TRUE) {
-          if(input$upgma_geom == TRUE) {
-            geom_tiplab(
-              upgma_mapping_tiplab(), 
-              geom = upgma_geom(),
-              angle = input$upgma_tiplab_angle,
-              size = upgma_tiplab_size(),
-              alpha = input$upgma_tiplab_alpha,
-              fontface = input$upgma_tiplab_fontface,
-              align = as.logical(input$upgma_align),
-              nudge_x = input$upgma_tiplab_nudge_x,
-              check.overlap = input$upgma_tiplab_overlap,
-              label.padding = unit(upgma_tiplab_padding(), "lines"),
-              label.r = unit(input$upgma_tiplab_labelradius, "lines"), 
-              fill = input$upgma_tiplab_fill
-            )
-          } else {
-            geom_tiplab(
-              upgma_mapping_tiplab(), 
-              geom = upgma_geom(),
-              angle = input$upgma_tiplab_angle,
-              size = upgma_tiplab_size(),
-              alpha = input$upgma_tiplab_alpha,
-              fontface = input$upgma_tiplab_fontface,
-              align = as.logical(input$upgma_align),
-              nudge_x = input$upgma_tiplab_nudge_x,
-              check.overlap = input$upgma_tiplab_overlap
-            )
-          }
-        } else {
-          if(input$upgma_geom == TRUE) {
-            geom_tiplab(
-              upgma_mapping_tiplab(), 
-              geom = upgma_geom(),
-              color = input$upgma_tiplab_color,
-              angle = input$upgma_tiplab_angle,
-              size = upgma_tiplab_size(),
-              alpha = input$upgma_tiplab_alpha,
-              fontface = input$upgma_tiplab_fontface,
-              align = as.logical(input$upgma_align),
-              nudge_x = input$upgma_tiplab_nudge_x,
-              check.overlap = input$upgma_tiplab_overlap,
-              label.padding = unit(upgma_tiplab_padding(), "lines"),
-              label.r = unit(input$upgma_tiplab_labelradius, "lines"), 
-              fill = input$upgma_tiplab_fill
-            )
-          } else {
-            geom_tiplab(
-              upgma_mapping_tiplab(), 
-              geom = upgma_geom(),
-              color = input$upgma_tiplab_color,
-              angle = input$upgma_tiplab_angle,
-              size = upgma_tiplab_size(),
-              alpha = input$upgma_tiplab_alpha,
-              fontface = input$upgma_tiplab_fontface,
-              align = as.logical(input$upgma_align),
-              nudge_x = input$upgma_tiplab_nudge_x,
-              check.overlap = input$upgma_tiplab_overlap
-            )
-          }
-        }
-      }
-    } else {NULL}
-  })
-  
-  # Tip panel size
-  upgma_tiplab_padding <- reactive({
-    if(!is.null(input$upgma_tiplab_padding)) {
-      input$upgma_tiplab_padding
-    } else {
-      Vis$tiplab_padding_upgma
-    }
-  })
-  
-  # Tiplab size
-  upgma_tiplab_size <- reactive({
-    if(!is.null(input$upgma_tiplab_size)) {
-      input$upgma_tiplab_size
-    } else {
-      Vis$labelsize_upgma
-    }
-  })
-  
-  # Tippoint size
-  upgma_tippoint_size <- reactive({
-    if(!is.null(input$upgma_tippoint_size)) {
-      input$upgma_tippoint_size
-    } else {
-      Vis$tippointsize_upgma
-    }
-  })
-  
-  # Show Label Panels?
-  upgma_geom <- reactive({
-    if(input$upgma_geom == TRUE) {
-      "label"
-    } else {"text"}
-  })
-  
-  # upgma Tiplab color
-  upgma_mapping_tiplab <- reactive({
-    if(input$upgma_mapping_show == TRUE) {
-      if(!is.null(input$upgma_tiplab)) {
-        aes(label = !!sym(input$upgma_tiplab),
-            color = !!sym(input$upgma_color_mapping))
-      } else {
-        aes(label = !!sym("Assembly Name"),
-            color = !!sym(input$upgma_color_mapping))
-      }
-    } else {
-      if(!is.null(input$upgma_tiplab)) {
-        aes(label = !!sym(input$upgma_tiplab))
-      } else {
-        aes(label = !!sym("Assembly Name"))
-      }
-    }
-  })
-  
-  # upgma Tree Layout
-  layout_upgma <- reactive({
-    if(input$upgma_layout == "inward") {
-      "circular"
-    } else {input$upgma_layout}
-  })
-  
-  # upgma inward circular
-  upgma_inward <- reactive({
-    if (input$upgma_layout == "inward") {
-      layout_inward_circular(xlim = input$upgma_inward_xlim)
-    } else {
-      NULL
-    }
-  })
-  
-  ### Save MST Plot ----
-  output$save_plot_html <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save MST;", paste0("MST_", Sys.Date(), ".html")))
-      paste0("MST_", Sys.Date(), ".html")
-    },
-    content = function(file) {
-      mst_tree() %>% visSave(file = file, background = mst_background_color())
-    }
-  )
-  
-  ### Save NJ Plot ----
-  
-  # Define download handler to save the plot
-  
-  output$download_nj <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save NJ;", paste0("NJ_", Sys.Date(), ".", input$filetype_nj)))
-      paste0("NJ_", Sys.Date(), ".", input$filetype_nj)
-    },
-    content = function(file) {
-      if (input$filetype_nj == "png") {
-        png(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale))
-        print(nj_tree())
-        dev.off()
-      } else if (input$filetype_nj == "jpeg") {
-        jpeg(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale), quality = 100)
-        print(nj_tree())
-        dev.off()
-      } else if (input$filetype_nj == "svg") {
-        plot <- print(nj_tree())
-        ggsave(file=file, plot=plot, device = svg(width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio))/96,
-                                                  height = as.numeric(input$nj_scale)/96))
-      } else if (input$filetype_nj == "bmp") {
-        bmp(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale))
-        print(nj_tree())
-        dev.off()
-      }
-    }
-  )
-  
-  ### Save UPGMA Plot ----
-  
-  # Define download handler to save the plot
-  
-  output$download_upgma <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save UPGMA;", paste0("UPGMA_", Sys.Date(), ".", input$filetype_upgma)))
-      paste0("UPGMA_", Sys.Date(), ".", input$filetype_upgma)
-    },
-    content = function(file) {
-      if (input$filetype_upgma == "png") {
-        png(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale))
-        print(upgma_tree())
-        dev.off()
-      } else if (input$filetype_upgma == "jpeg") {
-        jpeg(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale), quality = 100)
-        print(upgma_tree())
-        dev.off()
-      } else if (input$filetype_upgma == "svg") {
-        plot <- print(upgma_tree())
-        ggsave(file=file, plot=plot, device = svg(width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio))/96,
-                                                  height = as.numeric(input$upgma_scale)/96))
-      } else if (input$filetype_upgma == "bmp") {
-        bmp(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale))
-        print(upgma_tree())
-        dev.off()
-      }
-    }
-  )
-  
-  ### Reactive Events ----
-  
-  # MST cluster reset button
-  observeEvent(input$mst_cluster_reset, {
-    if(!is.null(DB$schemeinfo))
-    updateNumericInput(session, "mst_cluster_threshold", value = as.numeric(DB$schemeinfo[7, 2]))
-  })
-  
-  # Shut off "Align Labels" control for UPGMA trees
-  shinyjs::disable('upgma_align')
-  shinyjs::disable('upgma_tiplab_linesize')
-  shinyjs::disable('upgma_tiplab_linetype')
-  
-  # Conditional disabling of control elemenmts
-  observe({
-    
-    # Tiles for inward layout
-    if(input$nj_layout == "inward") {
-      shinyjs::disable('nj_tiles_show') 
-      shinyjs::disable('nj_tiles_show_2')
-      shinyjs::disable('nj_tiles_show_3') 
-      shinyjs::disable('nj_tiles_show_4')
-      shinyjs::disable('nj_tiles_show_5') 
-      shinyjs::disable('nj_fruit_variable')
-      shinyjs::disable('nj_fruit_variable_2')
-      shinyjs::disable('nj_fruit_variable_3')
-      shinyjs::disable('nj_fruit_variable_4')
-      shinyjs::disable('nj_fruit_variable_5')
-      shinyjs::disable('nj_fruit_width')
-      shinyjs::disable('nj_fruit_width_2')
-      shinyjs::disable('nj_fruit_width_3')
-      shinyjs::disable('nj_fruit_width_4')
-      shinyjs::disable('nj_fruit_width_5')
-      shinyjs::disable('nj_fruit_offset')
-      shinyjs::disable('nj_fruit_offset_2')
-      shinyjs::disable('nj_fruit_offset_3')
-      shinyjs::disable('nj_fruit_offset_4')
-      shinyjs::disable('nj_fruit_offset_5')
-    } else {
-      shinyjs::enable('nj_tiles_show') 
-      shinyjs::enable('nj_tiles_show_2')
-      shinyjs::enable('nj_tiles_show_3') 
-      shinyjs::enable('nj_tiles_show_4')
-      shinyjs::enable('nj_tiles_show_5') 
-      shinyjs::enable('nj_fruit_variable')
-      shinyjs::enable('nj_fruit_variable_2')
-      shinyjs::enable('nj_fruit_variable_3')
-      shinyjs::enable('nj_fruit_variable_4')
-      shinyjs::enable('nj_fruit_variable_5')
-      shinyjs::enable('nj_fruit_width')
-      shinyjs::enable('nj_fruit_width_2')
-      shinyjs::enable('nj_fruit_width_3')
-      shinyjs::enable('nj_fruit_width_4')
-      shinyjs::enable('nj_fruit_width_5')
-      shinyjs::enable('nj_fruit_offset')
-      shinyjs::enable('nj_fruit_offset_2')
-      shinyjs::enable('nj_fruit_offset_3')
-      shinyjs::enable('nj_fruit_offset_4')
-      shinyjs::enable('nj_fruit_offset_5')
-    }
-    
-    if(input$upgma_layout == "inward") {
-      shinyjs::disable('upgma_tiles_show') 
-      shinyjs::disable('upgma_tiles_show_2')
-      shinyjs::disable('upgma_tiles_show_3') 
-      shinyjs::disable('upgma_tiles_show_4')
-      shinyjs::disable('upgma_tiles_show_5') 
-      shinyjs::disable('upgma_fruit_variable')
-      shinyjs::disable('upgma_fruit_variable_2')
-      shinyjs::disable('upgma_fruit_variable_3')
-      shinyjs::disable('upgma_fruit_variable_4')
-      shinyjs::disable('upgma_fruit_variable_5')
-      shinyjs::disable('upgma_fruit_width')
-      shinyjs::disable('upgma_fruit_width_2')
-      shinyjs::disable('upgma_fruit_width_3')
-      shinyjs::disable('upgma_fruit_width_4')
-      shinyjs::disable('upgma_fruit_width_5')
-      shinyjs::disable('upgma_fruit_offset')
-      shinyjs::disable('upgma_fruit_offset_2')
-      shinyjs::disable('upgma_fruit_offset_3')
-      shinyjs::disable('upgma_fruit_offset_4')
-      shinyjs::disable('upgma_fruit_offset_5')
-    } else {
-      shinyjs::enable('upgma_tiles_show') 
-      shinyjs::enable('upgma_tiles_show_2')
-      shinyjs::enable('upgma_tiles_show_3') 
-      shinyjs::enable('upgma_tiles_show_4')
-      shinyjs::enable('upgma_tiles_show_5') 
-      shinyjs::enable('upgma_fruit_variable')
-      shinyjs::enable('upgma_fruit_variable_2')
-      shinyjs::enable('upgma_fruit_variable_3')
-      shinyjs::enable('upgma_fruit_variable_4')
-      shinyjs::enable('upgma_fruit_variable_5')
-      shinyjs::enable('upgma_fruit_width')
-      shinyjs::enable('upgma_fruit_width_2')
-      shinyjs::enable('upgma_fruit_width_3')
-      shinyjs::enable('upgma_fruit_width_4')
-      shinyjs::enable('upgma_fruit_width_5')
-      shinyjs::enable('upgma_fruit_offset')
-      shinyjs::enable('upgma_fruit_offset_2')
-      shinyjs::enable('upgma_fruit_offset_3')
-      shinyjs::enable('upgma_fruit_offset_4')
-      shinyjs::enable('upgma_fruit_offset_5')
-    }
-    
-    # Shut off branch labels for NJ and UPGMA plots for circular layout
-    if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-      shinyjs::disable('nj_show_branch_label')
-    } else {
-      shinyjs::enable('nj_show_branch_label')
-    }
-    
-    if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-      shinyjs::disable('upgma_show_branch_label')
-    } else {
-      shinyjs::enable('upgma_show_branch_label')
-    }
-  })
-  
-  #### Generate Plot ----
-  
-  hamming_nj <- reactive({
-    if(anyNA(DB$allelic_profile)) {
-      if(input$na_handling == "omit") {
-        allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
-        
-        allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
-        
-        compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
-        
-      } else if(input$na_handling == "ignore_na"){
-        compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
-        
-      } else {
-        compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
-      } 
-      
-    } else {compute.distMatrix(DB$allelic_profile_true, hamming.dist)}
-  })
-  
-  hamming_mst <- reactive({
-    if(anyNA(DB$allelic_profile)) {
-      if(input$na_handling == "omit") {
-        allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
-        
-        allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
-        
-        dist <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
-        
-      } else if (input$na_handling == "ignore_na") {
-        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
-      } else {
-        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
-      }
-    } else {
-      dist <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
-    }
-    
-    # Find indices of pairs with a distance of 0
-    zero_distance_pairs <- as.data.frame(which(as.matrix(dist) == 0, arr.ind = TRUE))
-    
-    zero_distance_pairs <- zero_distance_pairs[zero_distance_pairs$row != zero_distance_pairs$col, ]
-    
-    if(nrow(zero_distance_pairs) > 0) {
-      
-      # Sort each row so that x <= y
-      df_sorted <- t(apply(zero_distance_pairs, 1, function(row) sort(row)))
-      
-      # Remove duplicate rows
-      df_unique <- as.data.frame(unique(df_sorted))
-      
-      colnames(df_unique) <- c("col", "row")
-      
-      # get metadata in df
-      vector_col <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        vector_col[count] <- Vis$meta_mst$`Assembly Name`[i]
-        count <- count + 1
-      }
-      
-      vector_row <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        vector_row[count] <- Vis$meta_mst$`Assembly Name`[i]
-        count <- count + 1
-      }
-      
-      col_id <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_id[count] <- Vis$meta_mst$`Assembly ID`[i]
-        count <- count + 1
-      }
-      
-      row_id <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_id[count] <- Vis$meta_mst$`Assembly ID`[i]
-        count <- count + 1
-      }
-      
-      col_index <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_index[count] <- Vis$meta_mst$Index[i]
-        count <- count + 1
-      }
-      
-      row_index <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_index[count] <- Vis$meta_mst$Index[i]
-        count <- count + 1
-      }
-      
-      col_date <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_date[count] <- Vis$meta_mst$`Isolation Date`[i]
-        count <- count + 1
-      }
-      
-      row_date <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_date[count] <- Vis$meta_mst$`Isolation Date`[i]
-        count <- count + 1
-      }
-      
-      col_host <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_host[count] <- Vis$meta_mst$Host[i]
-        count <- count + 1
-      }
-      
-      row_host <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_host[count] <- Vis$meta_mst$Host[i]
-        count <- count + 1
-      }
-      
-      col_country <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_country[count] <- Vis$meta_mst$Country[i]
-        count <- count + 1
-      }
-      
-      row_country <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_country[count] <- Vis$meta_mst$Country[i]
-        count <- count + 1
-      }
-      
-      col_city <- character(0)
-      count <- 1
-      for (i in df_unique$col) {
-        col_city[count] <- Vis$meta_mst$City[i]
-        count <- count + 1
-      }
-      
-      row_city <- character(0)
-      count <- 1
-      for (i in df_unique$row) {
-        row_city[count] <- Vis$meta_mst$City[i]
-        count <- count + 1
-      }
-      
-      df_unique <- cbind(df_unique, col_name = vector_col, row_name = vector_row, 
-                         col_index = col_index, row_index = row_index, col_id = col_id,
-                         row_id = row_id, col_date = col_date, row_date = row_date,
-                         col_host = col_host, row_host = row_host, col_country = col_country,
-                         row_country = row_country, col_city = col_city, row_city = row_city)
-      
-      # Add groups
-      grouped_df <- df_unique %>%
-        group_by(col) %>%
-        mutate(group_id = cur_group_id())
-      
-      # Merge groups
-      name <- character(0)
-      index <- character(0)
-      id <- character(0)
-      count <- 1
-      for (i in grouped_df$group_id) {
-        name[count] <- paste(unique(append(grouped_df$col_name[which(grouped_df$group_id == i)], 
-                                           grouped_df$row_name[which(grouped_df$group_id == i)])), 
-                             collapse = "\n")
-        
-        id[count] <- paste(unique(append(grouped_df$col_id[which(grouped_df$group_id == i)], 
-                                         grouped_df$row_id[which(grouped_df$group_id == i)])), 
-                           collapse = "\n")
-        
-        index[count] <- paste(unique(append(grouped_df$col_index[which(grouped_df$group_id == i)], 
-                                            grouped_df$row_index[which(grouped_df$group_id == i)])), 
-                              collapse = "\n")
-        
-        count <- count + 1
-      }
-      
-      merged_names <- cbind(grouped_df, "Index" = index, "Assembly Name" = name, "Assembly ID" = id)
-      
-      # remove duplicate groups
-      
-      final <- merged_names[!duplicated(merged_names$group_id), ]
-      
-      final_cleaned <- final[!(final$col_name %in% final$row_name),]
-      
-      final_cleaned <- select(final_cleaned, 3, 17:20)
-      
-      # adapt metadata
-      Date_merged <- character(0)
-      for(j in 1:length(final_cleaned$Index)) {
-        Date <- character(0)
-        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
-          Date <- append(Date, Vis$meta_mst$`Isolation Date`[which(Vis$meta_mst$Index == i)])
-        }
-        Date_merged <- append(Date_merged, paste(Date, collapse = "\n"))
-      }
-      
-      Host_merged <- character(0)
-      for(j in 1:length(final_cleaned$Index)) {
-        Host <- character(0)
-        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
-          Host <- append(Host, Vis$meta_mst$Host[which(Vis$meta_mst$Index == i)])
-        }
-        Host_merged <- append(Host_merged, paste(Host, collapse = "\n"))
-      }
-      
-      Country_merged <- character(0)
-      for(j in 1:length(final_cleaned$Index)) {
-        Country <- character(0)
-        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
-          Country <- append(Country, Vis$meta_mst$Country[which(Vis$meta_mst$Index == i)])
-        }
-        Country_merged <- append(Country_merged, paste(Country, collapse = "\n"))
-      }
-      
-      City_merged <- character(0)
-      for(j in 1:length(final_cleaned$Index)) {
-        City <- character(0)
-        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
-          City <- append(City, Vis$meta_mst$City[which(Vis$meta_mst$Index == i)])
-        }
-        City_merged <- append(City_merged, paste(City, collapse = "\n"))
-      }
-      
-      final_meta <- cbind(final_cleaned, "Isolation Date" = Date_merged, 
-                          "Host" = Host_merged, "Country" = Country_merged, "City" = City_merged)
-      
-      
-      # Merging with original data frame / allelic profile
-      
-      allelic_profile_true <- DB$allelic_profile_true
-      meta_true <- Vis$meta_mst
-      
-      rownames(allelic_profile_true) <- Vis$meta_mst$`Assembly Name`
-      rownames(meta_true) <- Vis$meta_mst$`Assembly Name`
-      
-      omit <- unique(append(df_unique$col_name, df_unique$row_name)) %in% final_cleaned$col_name
-      
-      omit_id <- unique(append(df_unique$col_name, df_unique$row_name))[!omit]
-      
-      remove <- !(rownames(allelic_profile_true) %in% omit_id)
-      
-      allelic_profile_clean <- allelic_profile_true[remove, ]
-      
-      meta_clean <- meta_true[remove, ]
-      
-      # substitute meta assembly names with group names
-      
-      count <- 1
-      for(i in which(rownames(meta_clean) %in% final_meta$col_name)) {
-        meta_clean$Index[i] <- final_meta$Index[count]
-        meta_clean$`Assembly Name`[i] <- final_meta$`Assembly Name`[count]
-        meta_clean$`Assembly ID`[i] <- final_meta$`Assembly ID`[count]
-        meta_clean$`Isolation Date`[i] <- final_meta$`Isolation Date`[count]
-        meta_clean$Host[i] <- final_meta$Host[count]
-        meta_clean$Country[i] <- final_meta$Country[count]
-        meta_clean$City[i] <- final_meta$City[count]
-        count <- count + 1
-      }
-      
-      # Metadata completion
-      # get group size
-      
-      size_vector <- numeric(0)
-      for(i in 1:nrow(meta_clean)) {
-        if (str_count(meta_clean$`Assembly Name`[i], "\n") == 0) {
-          size_vector[i] <- 1
-        } else {
-          size_vector[i] <- str_count(meta_clean$`Assembly Name`[i], "\n") +1
-        }
-      }
-      
-      meta_clean <- mutate(meta_clean, size = size_vector)
-      
-      # get font size dependent on group size
-      
-      font_size <- numeric(nrow(meta_clean))
-      
-      for (i in 1:length(font_size)) {
-        if(meta_clean$size[i] < 3) {
-          font_size[i] <- 12
-        } else {
-          font_size[i] <- 11
-        }
-      }
-      
-      # get v-align dependent on group size
-      valign <- numeric(nrow(meta_clean))
-      
-      for (i in 1:length(valign)) {
-        if(meta_clean$size[i] == 1) {
-          valign[i] <- -30
-        } else if(meta_clean$size[i] == 2) {
-          valign[i] <- -38
-        } else if(meta_clean$size[i] == 3) {
-          valign[i] <- -46
-        } else if(meta_clean$size[i] == 4) {
-          valign[i] <- -54
-        } else if(meta_clean$size[i] == 5) {
-          valign[i] <- -62
-        } else if(meta_clean$size[i] > 5) {
-          valign[i] <- -70
-        }
-      }
-      
-      Vis$unique_meta <- meta_clean %>%
-        cbind(font_size = font_size, valign = valign)
-      
-      # final dist calculation
-      
-      if(anyNA(DB$allelic_profile)){
-        if(input$na_handling == "omit") {
-          allelic_profile_clean_noNA_names <- allelic_profile_clean[, colSums(is.na(allelic_profile_clean)) == 0]
-          compute.distMatrix(allelic_profile_clean_noNA_names, hamming.dist)
-        } else if (input$na_handling == "ignore_na") {
-          compute.distMatrix(allelic_profile_clean, hamming.distIgnore)
-        } else {
-          compute.distMatrix(allelic_profile_clean, hamming.distCategory)
-        }
-      } else {compute.distMatrix(allelic_profile_clean, hamming.dist)}
-      
-      
-    } else {
-      font_size <- rep(12, nrow(Vis$meta_mst))
-      valign <- rep(-30, nrow(Vis$meta_mst))
-      size <- rep(1, nrow(Vis$meta_mst))
-      Vis$unique_meta <- Vis$meta_mst %>%
-        cbind(size , font_size, valign)
-      
-      dist
-    }
-    
-  })
-  
-  observeEvent(input$create_tree, {
-    log_print("Input create_tree")
-    
-    if(is.null(DB$data)) {
-      log_print("Missing data")
-      
-      show_toast(
-        title = "Missing data",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if(nrow(DB$allelic_profile_true) < 3) {
-      log_print("Min. of 3 entries required for visualization")
-      
-      show_toast(
-        title = "Min. of 3 entries required for visualization",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      
-      if(any(duplicated(DB$meta$`Assembly Name`)) | any(duplicated(DB$meta$`Assembly ID`))) {
-        log_print("Duplicated assemblies")
-        
-        dup_name <- which(duplicated(DB$meta_true$`Assembly Name`))
-        dup_id <- which(duplicated(DB$meta_true$`Assembly ID`))
-        
-        showModal(
-          modalDialog(
-            if((length(dup_name) + length(dup_id)) == 1) {
-              if(length(dup_name) == 1) {
-                HTML(paste0("Entry #", dup_name,
-                            " contains a duplicated assembly name:", "<br><br>",
-                            DB$meta_true$`Assembly Name`[dup_name]))
-              } else {
-                HTML(paste0("Entry #", dup_id,
-                            " contains a duplicated assembly ID:", "<br><br>",
-                            DB$meta_true$`Assembly ID`[dup_id]))
-              }
-            } else {
-              if(length(dup_name) == 0) {
-                HTML(c("Entries contain duplicated IDs <br><br>",
-                       paste0(unique(DB$meta_true$`Assembly ID`[dup_id]), "<br>")))
-              } else if(length(dup_id) == 0) {
-                HTML(c("Entries contain duplicated names<br><br>",
-                       paste0(unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>")))
-              } else {
-                HTML(c("Entries contain duplicated names and IDs <br><br>",
-                       paste0("Name: ", unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>"),
-                       paste0("ID: ", unique(DB$meta_true$`Assembly ID`[dup_id]), "<br>")))
-              }
-            },
-            title = "Duplicate entries",
-            fade = TRUE,
-            easyClose = TRUE,
-            footer = tagList(
-              modalButton("Cancel"),
-              actionButton("change_entries", "Go to Entry Table", class = "btn btn-default")
-            )
-          )
-        )
-      } else {
-        
-        set.seed(1)
-        
-        if (input$tree_algo == "Neighbour-Joining") {
-          
-          log_print("Rendering NJ tree")
-          
-          output$nj_field <- renderUI({
-            addSpinner(
-              plotOutput("tree_nj", width = paste0(as.character(as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), "px"), height = paste0(as.character(input$nj_scale), "px")),
-              spin = "dots",
-              color = "#ffffff"
-            )
-          })
-          
-          Vis$meta_nj <- select(DB$meta_true, -2)
-          
-          if(length(unique(gsub(" ", "_", colnames(Vis$meta_nj)))) < length(gsub(" ", "_", colnames(Vis$meta_nj)))) {
-            show_toast(
-              title = "Conflicting Custom Variable Names",
-              type = "warning",
-              position = "bottom-end",
-              timer = 6000
-            )
-          } else {
-            
-            # Create phylogenetic tree data
-            Vis$nj <- ape::nj(hamming_nj())
-            
-            # Create phylogenetic tree meta data
-            Vis$meta_nj <- mutate(Vis$meta_nj, taxa = Index) %>%
-              relocate(taxa)
-            
-            # Get number of included entries calculate start values for tree 
-            if(!is.null(input$nj_layout)) {
-              if(input$nj_layout == "circular" | input$nj_layout == "inward") {
-                if(sum(DB$data$Include) < 21) {
-                  Vis$labelsize_nj <- 5.5
-                  Vis$tippointsize_nj <- 5.5
-                  Vis$nodepointsize_nj <- 4
-                  Vis$tiplab_padding_nj <- 0.25
-                  Vis$branch_size_nj <- 4.5
-                } else if (between(sum(DB$data$Include), 21, 40)) {
-                  Vis$labelsize_nj <- 5
-                  Vis$tippointsize_nj <- 5
-                  Vis$nodepointsize_nj <- 3.5
-                  Vis$tiplab_padding_nj <- 0.2
-                  Vis$branch_size_nj <- 4
-                } else if (between(sum(DB$data$Include), 41, 60)) {
-                  Vis$labelsize_nj <- 4.5
-                  Vis$tippointsize_nj <- 4.5
-                  Vis$nodepointsize_nj <- 3
-                  Vis$tiplab_padding_nj <- 0.15
-                  Vis$branch_size_nj <- 3.5
-                } else if (between(sum(DB$data$Include), 61, 80)) {
-                  Vis$labelsize_nj <- 4
-                  Vis$tippointsize_nj <- 4
-                  Vis$nodepointsize_nj <- 2.5
-                  Vis$tiplab_padding_nj <- 0.1
-                  Vis$branch_size_nj <- 3
-                } else if (between(sum(DB$data$Include), 81, 100)) {
-                  Vis$labelsize_nj <- 3.5
-                  Vis$tippointsize_nj <- 3.5
-                  Vis$nodepointsize_nj <- 2
-                  Vis$tiplab_padding_nj <- 0.1
-                  Vis$branch_size_nj <- 2.5
-                } else {
-                  Vis$labelsize_nj <- 3
-                  Vis$tippointsize_nj <- 3
-                  Vis$nodepointsize_nj <- 1.5
-                  Vis$tiplab_padding_nj <- 0.05
-                  Vis$branch_size_nj <- 2
-                }
-              } else {
-                if(sum(DB$data$Include) < 21) {
-                  Vis$labelsize_nj <- 5
-                  Vis$tippointsize_nj <- 5
-                  Vis$nodepointsize_nj <- 4
-                  Vis$tiplab_padding_nj <- 0.25
-                  Vis$branch_size_nj <- 4.5
-                } else if (between(sum(DB$data$Include), 21, 40)) {
-                  Vis$labelsize_nj <- 4.5
-                  Vis$tippointsize_nj <- 4.5
-                  Vis$nodepointsize_nj <- 3.5
-                  Vis$tiplab_padding_nj <- 0.2
-                  Vis$branch_size_nj <- 4
-                } else if (between(sum(DB$data$Include), 41, 60)) {
-                  Vis$labelsize_nj <- 4
-                  Vis$tippointsize_nj <- 4
-                  Vis$nodepointsize_nj <- 3
-                  Vis$tiplab_padding_nj <- 0.15
-                  Vis$branch_size_nj <- 3.5
-                } else if (between(sum(DB$data$Include), 61, 80)) {
-                  Vis$labelsize_nj <- 3.5
-                  Vis$tippointsize_nj <- 3.5
-                  Vis$nodepointsize_nj <- 2.5
-                  Vis$tiplab_padding_nj <- 0.1
-                  Vis$branch_size_nj <- 3
-                } else if (between(sum(DB$data$Include), 81, 100)) {
-                  Vis$labelsize_nj <- 3
-                  Vis$tippointsize_nj <- 3
-                  Vis$nodepointsize_nj <- 2
-                  Vis$tiplab_padding_nj <- 0.1
-                  Vis$branch_size_nj <- 2.5
-                } else {
-                  Vis$labelsize_nj <- 2.5
-                  Vis$tippointsize_nj <- 2.5
-                  Vis$nodepointsize_nj <- 1.5
-                  Vis$tiplab_padding_nj <- 0.05
-                  Vis$branch_size_nj <- 2
-                }
-              }
-            } else {
-              Vis$labelsize_nj <- 4
-              Vis$tippointsize_nj <- 4
-              Vis$nodepointsize_nj <- 2.5
-              Vis$tiplab_padding_nj <- 0.2
-              Vis$branch_size_nj <- 3.5
-            }
-            
-            Vis$nj_tree <- ggtree(Vis$nj)
-            
-            # Get upper and lower end of x range
-            Vis$nj_max_x <- max(Vis$nj_tree$data$x)
-            Vis$nj_min_x <- min(Vis$nj_tree$data$x)
-            
-            # Get parent node numbers
-            Vis$nj_parentnodes <- Vis$nj_tree$data$parent
-            
-            # Update visualization control inputs
-            if(!is.null(input$nj_tiplab_size)) {
-              updateNumericInput(session, "nj_tiplab_size", value = Vis$labelsize_nj)
-            }
-            if(!is.null(input$nj_tippoint_size)) {
-              updateSliderInput(session, "nj_tippoint_size", value = Vis$tippointsize_nj)
-            }
-            if(!is.null(input$nj_nodepoint_size)) {
-              updateSliderInput(session, "nj_nodepoint_size", value = Vis$nodepointsize_nj)
-            }
-            if(!is.null(input$nj_tiplab_padding)) {
-              updateSliderInput(session, "nj_tiplab_padding", value = Vis$tiplab_padding_nj)
-            }
-            if(!is.null(input$nj_branch_size)) {
-              updateNumericInput(session, "nj_branch_size", value = Vis$branch_size_nj)
-            }
-            if(!is.null(input$nj_treescale_width)) {
-              updateNumericInput(session, "nj_treescale_width", value = round(ceiling(Vis$nj_max_x) * 0.1, 0))
-            }
-            if(!is.null(input$nj_rootedge_length)) {
-              updateSliderInput(session, "nj_rootedge_length", value = round(ceiling(Vis$nj_max_x) * 0.05, 0))
-            }
-            
-            output$tree_nj <- renderPlot({
-              nj_tree()
-            })
-            
-            Vis$nj_true <- TRUE
-          }
-        } else if (input$tree_algo == "UPGMA") {
-          
-          log_print("Rendering UPGMA tree")
-          
-          output$upgma_field <- renderUI({
-            addSpinner(
-              plotOutput("tree_upgma", width = paste0(as.character(as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), "px"), height = paste0(as.character(input$upgma_scale), "px")),
-              spin = "dots",
-              color = "#ffffff"
-            )
-          })
-          
-          Vis$meta_upgma <- select(DB$meta_true, -2)
-          
-          if(length(unique(gsub(" ", "_", colnames(Vis$meta_upgma)))) < length(gsub(" ", "_", colnames(Vis$meta_upgma)))) {
-            show_toast(
-              title = "Conflicting Custom Variable Names",
-              type = "warning",
-              position = "bottom-end",
-              timer = 6000
-            )
-          } else {
-            
-            # Create phylogenetic tree data
-            Vis$upgma <- phangorn::upgma(hamming_nj())
-            
-            # Create phylogenetic tree meta data
-            Vis$meta_upgma <- mutate(Vis$meta_upgma, taxa = Index) %>%
-              relocate(taxa)
-            
-            # Get number of included entries calculate start values for tree 
-            if(!is.null(input$upgma_layout)) {
-              if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
-                if(sum(DB$data$Include) < 21) {
-                  Vis$labelsize_upgma <- 5.5
-                  Vis$tippointsize_upgma <- 5.5
-                  Vis$nodepointsize_upgma <- 4
-                  Vis$tiplab_padding_upgma <- 0.25
-                  Vis$branch_size_upgma <- 4.5
-                } else if (between(sum(DB$data$Include), 21, 40)) {
-                  Vis$labelsize_upgma <- 5
-                  Vis$tippointsize_upgma <- 5
-                  Vis$nodepointsize_upgma <- 3.5
-                  Vis$tiplab_padding_upgma <- 0.2
-                  Vis$branch_size_upgma <- 4
-                } else if (between(sum(DB$data$Include), 41, 60)) {
-                  Vis$labelsize_upgma <- 4.5
-                  Vis$tippointsize_upgma <- 4.5
-                  Vis$nodepointsize_upgma <- 3
-                  Vis$tiplab_padding_upgma <- 0.15
-                  Vis$branch_size_upgma <- 3.5
-                } else if (between(sum(DB$data$Include), 61, 80)) {
-                  Vis$labelsize_upgma <- 4
-                  Vis$tippointsize_upgma <- 4
-                  Vis$nodepointsize_upgma <- 2.5
-                  Vis$tiplab_padding_upgma <- 0.1
-                  Vis$branch_size_upgma <- 3
-                } else if (between(sum(DB$data$Include), 81, 100)) {
-                  Vis$labelsize_upgma <- 3.5
-                  Vis$tippointsize_upgma <- 3.5
-                  Vis$nodepointsize_upgma <- 2
-                  Vis$tiplab_padding_upgma <- 0.1
-                  Vis$branch_size_upgma <- 2.5
-                } else {
-                  Vis$labelsize_upgma <- 3
-                  Vis$tippointsize_upgma <- 3
-                  Vis$nodepointsize_upgma <- 1.5
-                  Vis$tiplab_padding_upgma <- 0.05
-                  Vis$branch_size_upgma <- 2
-                }
-              } else {
-                if(sum(DB$data$Include) < 21) {
-                  Vis$labelsize_upgma <- 5
-                  Vis$tippointsize_upgma <- 5
-                  Vis$nodepointsize_upgma <- 4
-                  Vis$tiplab_padding_upgma <- 0.25
-                  Vis$branch_size_upgma <- 4.5
-                } else if (between(sum(DB$data$Include), 21, 40)) {
-                  Vis$labelsize_upgma <- 4.5
-                  Vis$tippointsize_upgma <- 4.5
-                  Vis$nodepointsize_upgma <- 3.5
-                  Vis$tiplab_padding_upgma <- 0.2
-                  Vis$branch_size_upgma <- 4
-                } else if (between(sum(DB$data$Include), 41, 60)) {
-                  Vis$labelsize_upgma <- 4
-                  Vis$tippointsize_upgma <- 4
-                  Vis$nodepointsize_upgma <- 3
-                  Vis$tiplab_padding_upgma <- 0.15
-                  Vis$branch_size_upgma <- 3.5
-                } else if (between(sum(DB$data$Include), 61, 80)) {
-                  Vis$labelsize_upgma <- 3.5
-                  Vis$tippointsize_upgma <- 3.5
-                  Vis$nodepointsize_upgma <- 2.5
-                  Vis$tiplab_padding_upgma <- 0.1
-                  Vis$branch_size_upgma <- 3
-                } else if (between(sum(DB$data$Include), 81, 100)) {
-                  Vis$labelsize_upgma <- 3
-                  Vis$tippointsize_upgma <- 3
-                  Vis$nodepointsize_upgma <- 2
-                  Vis$tiplab_padding_upgma <- 0.1
-                  Vis$branch_size_upgma <- 2.5
-                } else {
-                  Vis$labelsize_upgma <- 2.5
-                  Vis$tippointsize_upgma <- 2.5
-                  Vis$nodepointsize_upgma <- 1.5
-                  Vis$tiplab_padding_upgma <- 0.05
-                  Vis$branch_size_upgma <- 2
-                }
-              }
-            } else {
-              Vis$labelsize_upgma <- 4
-              Vis$tippointsize_upgma <- 4
-              Vis$nodepointsize_upgma <- 2.5
-              Vis$tiplab_padding_upgma <- 0.2
-              Vis$branch_size_upgma <- 3.5
-            }
-            
-            Vis$upgma_tree <- ggtree(Vis$upgma)
-            
-            # Get upper and lower end of x range
-            Vis$upgma_max_x <- max(Vis$upgma_tree$data$x)
-            Vis$upgma_min_x <- min(Vis$upgma_tree$data$x)
-            
-            # Get parent node numbers
-            Vis$upgma_parentnodes <- Vis$upgma_tree$data$parent
-            
-            # Update visualization control inputs
-            if(!is.null(input$upgma_tiplab_size)) {
-              updateNumericInput(session, "upgma_tiplab_size", value = Vis$labelsize_upgma)
-            }
-            if(!is.null(input$upgma_tippoint_size)) {
-              updateSliderInput(session, "upgma_tippoint_size", value = Vis$tippointsize_upgma)
-            }
-            if(!is.null(input$upgma_nodepoint_size)) {
-              updateSliderInput(session, "upgma_nodepoint_size", value = Vis$nodepointsize_upgma)
-            }
-            if(!is.null(input$upgma_tiplab_padding)) {
-              updateSliderInput(session, "upgma_tiplab_padding", value = Vis$tiplab_padding_upgma)
-            }
-            if(!is.null(input$upgma_branch_size)) {
-              updateNumericInput(session, "upgma_branch_size", value = Vis$branch_size_upgma)
-            }
-            if(!is.null(input$upgma_treescale_width)) {
-              updateNumericInput(session, "upgma_treescale_width", value = round(ceiling(Vis$upgma_max_x) * 0.1, 0))
-            }
-            if(!is.null(input$upgma_rootedge_length)) {
-              updateSliderInput(session, "upgma_rootedge_length", value = round(ceiling(Vis$upgma_max_x) * 0.05, 0))
-            }
-            
-            output$tree_upgma <- renderPlot({
-              upgma_tree()
-            })
-            
-            Vis$upgma_true <- TRUE
-          }
-        } else {
-          
-          log_print("Rendering MST graph")
-          
-          output$mst_field <- renderUI({
-            if(input$mst_background_transparent == TRUE) {
-              visNetworkOutput("tree_mst", width = paste0(as.character(as.numeric(input$mst_scale) * as.numeric(input$mst_ratio)), "px"), height = paste0(as.character(input$mst_scale), "px"))
-            } else {
-              addSpinner(
-                visNetworkOutput("tree_mst", width = paste0(as.character(as.numeric(input$mst_scale) * as.numeric(input$mst_ratio)), "px"), height = paste0(as.character(input$mst_scale), "px")),
-                spin = "dots",
-                color = "#ffffff"
-              )
-            }
-          })
-          
-          if(nrow(DB$meta_true) > 100) {
-            
-            log_print("Over 100 isolates in MST graph")
-            
-            show_toast(
-              title = "Computation might take a while",
-              type = "warning",
-              position = "bottom-end",
-              timer = 10000
-            )
-          }
-          
-          meta_mst <- DB$meta_true
-          Vis$meta_mst <- meta_mst
-          
-          # prepare igraph object
-          Vis$ggraph_1 <- hamming_mst() |>
-            as.matrix() |>
-            graph.adjacency(weighted = TRUE) |>
-            igraph::mst() 
-          
-          output$tree_mst <- renderVisNetwork({
-            mst_tree()
-          })
-          
-          Vis$mst_true <- TRUE
-        }
-      }
-    }
-  })
-  
-  # _______________________ ####
-  
-  ## Report ----
-  
-  observe({
-    if(!is.null(DB$data)) {
-      if(!is.null(input$tree_algo)) {
-        if(input$tree_algo == "Minimum-Spanning") {
-          shinyjs::disable("rep_plot_report")
-          updateCheckboxInput(session, "rep_plot_report", value = FALSE)
-        } else {
-          shinyjs::enable("rep_plot_report")
-        }
-      }
-    }
-  })
-  
-  ### Report creation UI ----
-  
-  observeEvent(input$create_rep, {
-    
-    if((input$tree_algo == "Minimum-Spanning" & isTRUE(Vis$mst_true)) |
-       (input$tree_algo == "UPGMA" & isTRUE(Vis$upgma_true)) |
-       (input$tree_algo == "Neighbour-Joining" & isTRUE(Vis$nj_true))) {
-      # Get currently selected missing value handling option
-      if(input$na_handling == "ignore_na") {
-        na_handling <- "Ignore missing values for pairwise comparison"
-      } else if(input$na_handling == "omit") {
-        na_handling <- "Omit loci with missing values for all assemblies"
-      } else if(input$na_handling == "category") {
-        na_handling <- "Treat missing values as allele variant"
-      }
-      
-      extra_var <- character()
-      if(input$tree_algo == "Minimum-Spanning") {
-        shinyjs::runjs("mstReport();")
-        if(isTRUE(input$mst_color_var)) {
-          extra_var <- c(extra_var, input$mst_col_var)
-        }
-      } else if(input$tree_algo == "Neighbour-Joining") {
-        if(isTRUE(input$nj_mapping_show)) {
-          extra_var <- c(extra_var, input$nj_color_mapping)
-        }
-        if(isTRUE(input$nj_tipcolor_mapping_show)) {
-          extra_var <- c(extra_var, input$nj_tipcolor_mapping)
-        }
-        if(isTRUE(input$nj_tipshape_mapping_show)) {
-          extra_var <- c(extra_var, input$nj_tipshape_mapping)
-        }
-        if(isTRUE(input$nj_tiles_show_1)) {
-          extra_var <- c(extra_var, input$nj_fruit_variable)
-        }
-        if(isTRUE(input$nj_tiles_show_2)) {
-          extra_var <- c(extra_var, input$nj_fruit_variable_2)
-        }
-        if(isTRUE(input$nj_tiles_show_3)) {
-          extra_var <- c(extra_var, input$nj_fruit_variable_3)
-        }
-        if(isTRUE(input$nj_tiles_show_4)) {
-          extra_var <- c(extra_var, input$nj_fruit_variable_4)
-        }
-        if(isTRUE(input$nj_tiles_show_5)) {
-          extra_var <- c(extra_var, input$nj_fruit_variable_5)
-        }
-        if(isTRUE(input$nj_heatmap_show)) {
-          extra_var <- c(extra_var, input$nj_heatmap_select)
-        }
-      } else if(input$tree_algo == "UPGMA") {
-        if(isTRUE(input$UPGMA_mapping_show)) {
-          extra_var <- c(extra_var, input$UPGMA_color_mapping)
-        }
-        if(isTRUE(input$UPGMA_tipcolor_mapping_show)) {
-          extra_var <- c(extra_var, input$UPGMA_tipcolor_mapping)
-        }
-        if(isTRUE(input$UPGMA_tipshape_mapping_show)) {
-          extra_var <- c(extra_var, input$UPGMA_tipshape_mapping)
-        }
-        if(isTRUE(input$UPGMA_tiles_show_1)) {
-          extra_var <- c(extra_var, input$UPGMA_fruit_variable)
-        }
-        if(isTRUE(input$UPGMA_tiles_show_2)) {
-          extra_var <- c(extra_var, input$UPGMA_fruit_variable_2)
-        }
-        if(isTRUE(input$UPGMA_tiles_show_3)) {
-          extra_var <- c(extra_var, input$UPGMA_fruit_variable_3)
-        }
-        if(isTRUE(input$UPGMA_tiles_show_4)) {
-          extra_var <- c(extra_var, input$UPGMA_fruit_variable_4)
-        }
-        if(isTRUE(input$UPGMA_tiles_show_5)) {
-          extra_var <- c(extra_var, input$UPGMA_fruit_variable_5)
-        }
-        if(isTRUE(input$UPGMA_heatmap_show)) {
-          extra_var <- c(extra_var, input$UPGMA_heatmap_select)
-        }
-      }
-      
-      showModal(
-        modalDialog(
-          fluidRow(
-            column(
-              width = 12,
-              fluidRow(
-                column(
-                  width = 4,
-                  align = "left",
-                  HTML(
-                    paste(
-                      tags$span(style='color:black; font-size: 15px; font-weight: 900', 'General')
-                    )
-                  )
-                ),
-                column(
-                  width = 3,
-                  align = "left",
-                  checkboxInput(
-                    "rep_general",
-                    label = "",
-                    value = TRUE
-                  )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 12,
-                  align = "left",
-                  fluidRow(
-                    column(
-                      width = 3,
-                      checkboxInput(
-                        "rep_date_general", 
-                        label = h5("Date", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 7,
-                      dateInput(
-                        "mst_date_general_select",
-                        "",
-                        max = Sys.Date()
-                      )
-                    )
-                  ),
-                  fluidRow(
-                    column(
-                      width = 3,
-                      checkboxInput(
-                        "rep_operator_general", 
-                        label = h5("Operator", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 8,
-                      textInput(
-                        "mst_operator_general_select",
-                        ""
-                      ) 
-                    )
-                  ),
-                  fluidRow(
-                    column(
-                      width = 3,
-                      checkboxInput(
-                        "rep_institute_general", 
-                        label = h5("Institute", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 8,
-                      textInput(
-                        "mst_institute_general_select",
-                        ""
-                      ) 
-                    )
-                  ),
-                  fluidRow(
-                    column(
-                      width = 3,
-                      checkboxInput(
-                        "rep_comm_general", 
-                        label = h5("Comment", style = "color:black;")
-                      )
-                    ),
-                    column(
-                      width = 8,
-                      textAreaInput(
-                        inputId = "mst_comm_general_select",
-                        label = "",
-                        width = "100%",
-                        height = "60px",
-                        cols = NULL,
-                        rows = NULL,
-                        placeholder = NULL,
-                        resize = "vertical"
-                      ) 
-                    )
-                  )
-                )
-              ),
-              hr(),
-              fluidRow(
-                column(
-                  width = 4,
-                  align = "left",
-                  HTML(
-                    paste(
-                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Isolate Table')
-                    )
-                  )
-                ),
-                column(
-                  width = 3,
-                  align = "left",
-                  checkboxInput(
-                    "rep_entrytable",
-                    label = "",
-                    value = TRUE
-                  )
-                ),
-                column(
-                  width = 4,
-                  align = "left",
-                  HTML(
-                    paste(
-                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Include Plot')
-                    )
-                  )
-                ),
-                column(
-                  width = 1,
-                  align = "left",
-                  checkboxInput(
-                    "rep_plot_report",
-                    label = "",
-                    value = TRUE
-                  )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 6,
-                  align = "left",
-                  div(
-                    class = "rep_tab_sel",
-                    pickerInput("select_rep_tab",
-                                label = "",
-                                choices = names(DB$meta)[-2],
-                                selected = c("Assembly Name", "Scheme", "Isolation Date",
-                                             "Host", "Country", "City", extra_var),
-                                options = list(
-                                  size = 10,
-                                  `actions-box` = TRUE,
-                                  style = "background-color: white; border-radius: 5px;"
-                                ),
-                                multiple = TRUE)
-                  )
-                )
-              ),
-              hr(),
-              fluidRow(
-                column(
-                  width = 4,
-                  align = "left",
-                  HTML(
-                    paste(
-                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Analysis Parameter')
-                    )
-                  )
-                ),
-                column(
-                  width = 3,
-                  align = "left",
-                  checkboxInput(
-                    "rep_analysis",
-                    label = "",
-                    value = TRUE
-                  )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 6,
-                  align = "left",
-                  fluidRow(
-                    column(
-                      width = 4,
-                      checkboxInput(
-                        "rep_cgmlst_analysis",
-                        label = h5("Scheme", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 8,
-                      align = "right",
-                      HTML(
-                        paste(
-                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', DB$scheme)
-                        )
-                      )
-                    )
-                  ),
-                  fluidRow(
-                    column(
-                      width = 4,
-                      checkboxInput(
-                        "rep_tree_analysis",
-                        label = h5("Tree", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 8,
-                      align = "right",
-                      HTML(
-                        paste(
-                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', input$tree_algo)
-                        )
-                      )
-                    )
-                  )
-                ),
-                column(
-                  width = 6,
-                  align = "left",
-                  fluidRow(
-                    column(2),
-                    column(
-                      width = 4,
-                      checkboxInput(
-                        "rep_distance",
-                        label = h5("Distance", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 5,
-                      align = "right",
-                      HTML(
-                        paste(
-                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', 'Hamming')
-                        )
-                      )
-                    )
-                  ),
-                  fluidRow(
-                    column(2),
-                    column(
-                      width = 4,
-                      checkboxInput(
-                        "rep_version",
-                        label = h5("Version", style = "color:black;"),
-                        value = TRUE
-                      )
-                    ),
-                    column(
-                      width = 5,
-                      align = "right",
-                      HTML(
-                        paste(
-                          tags$span(style='color:black; position: relative; top: 17px; font-style: italic', phylotraceVersion)
-                        )
-                      )
-                    )
-                  )
-                )
-              ),
-              fluidRow(
-                column(
-                  width = 3,
-                  align = "left",
-                  checkboxInput(
-                    "rep_missval",
-                    label = h5("NA handling", style = "color:black;"),
-                    value = TRUE
-                  )
-                ),
-                column(
-                  width = 7,
-                  align = "right",
-                  HTML(
-                    paste(
-                      tags$span(style='color: black; position: relative; top: 17px; font-style: italic; right: 35px;', na_handling)
-                    )
-                  )
-                )
-              )
-            )
-          ),
-          title = "cgMLST Report Generation",
-          easyClose = TRUE,
-          footer = tagList(
-            modalButton("Cancel"),
-            downloadBttn(
-              "download_report",
-              style = "simple",
-              label = "Save",
-              size = "sm",
-              icon = icon("download")
-            )
-          )
-        )
-      )
-    } else {
-      show_toast(
-        title = "No tree created",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    }
-  })
-  
-  observe({
-    if(!is.null(input$rep_general)) {
-      if(isFALSE(input$rep_general)) {
-        shinyjs::disable('rep_date_general') 
-        shinyjs::disable('rep_operator_general') 
-        shinyjs::disable('rep_institute_general') 
-        shinyjs::disable('rep_comm_general') 
-        shinyjs::disable('mst_date_general_select') 
-        shinyjs::disable('mst_operator_general_select') 
-        shinyjs::disable('mst_institute_general_select') 
-        shinyjs::disable('mst_comm_general_select') 
-      } else {
-        shinyjs::enable('rep_date_general') 
-        shinyjs::enable('rep_operator_general') 
-        shinyjs::enable('rep_institute_general') 
-        shinyjs::enable('rep_comm_general')
-        shinyjs::enable('mst_date_general_select') 
-        shinyjs::enable('mst_operator_general_select') 
-        shinyjs::enable('mst_institute_general_select') 
-        shinyjs::enable('mst_comm_general_select') 
-      }
-    }
-    
-    if(!is.null(input$rep_analysis)) {
-      if(isFALSE(input$rep_analysis)) {
-        shinyjs::disable('rep_cgmlst_analysis') 
-        shinyjs::disable('rep_tree_analysis') 
-        shinyjs::disable('rep_distance') 
-        shinyjs::disable('rep_missval') 
-        shinyjs::disable('rep_version') 
-      } else {
-        shinyjs::enable('rep_cgmlst_analysis') 
-        shinyjs::enable('rep_tree_analysis') 
-        shinyjs::enable('rep_distance') 
-        shinyjs::enable('rep_missval') 
-        shinyjs::enable('rep_version') 
-      }
-    }
-    
-    if(length(input$select_rep_tab) > 0) {
-      updateCheckboxInput(session, "rep_entrytable", value = TRUE)
-    } else {
-      updateCheckboxInput(session, "rep_entrytable", value = FALSE)
-    }
-  })
-  
-  ### Save Report ----
-  
-  #### Get Report elements ----
-  
-  observe({
-    if(!is.null(DB$data)){
-      if(!is.null(input$tree_algo)) {
-        req(c(input$rep_entrytable, input$rep_general,
-              input$rep_date_general, input$rep_operator_general,
-              input$rep_institute_general, input$rep_comm_general,
-              input$rep_analysis, input$rep_cgmlst_analysis,
-              input$rep_tree_analysis, input$rep_distance,
-              input$rep_missval, input$rep_version,
-              input$rep_plot_report, input$select_rep_tab))
-        Report$report_df <- data.frame(Element = c("entry_table", "general_show",
-                                                   "general_date", "operator",
-                                                   "institute", "comment",
-                                                   "analysis_show", "scheme",
-                                                   "tree", "distance", "na_handling", "version",
-                                                   "plot"),
-                                       Include = c(input$rep_entrytable, input$rep_general,
-                                                   input$rep_date_general, input$rep_operator_general,
-                                                   input$rep_institute_general, input$rep_comm_general,
-                                                   input$rep_analysis, input$rep_cgmlst_analysis,
-                                                   input$rep_tree_analysis, input$rep_distance,
-                                                   input$rep_missval, input$rep_version,
-                                                   input$rep_plot_report))
-      }
-    }
-  })
-  
-  #### Get Report values ----
-  
-  observeEvent(input$create_tree, {
-    if(input$tree_algo == "Minimum-Spanning") {
-      Report$report_list_mst <- list(entry_table = DB$meta_true,
-                                     scheme = DB$schemeinfo, 
-                                     tree = input$tree_algo,
-                                     na_handling = if(anyNA(DB$allelic_profile_true)){input$na_handling} else {NULL},
-                                     distance = "Hamming Distances",
-                                     version = c(phylotraceVersion, "2.5.1"),
-                                     plot = "MST")
-    } else if(input$tree_algo == "Neighbour-Joining") {
-      Report$report_list_nj <- list(entry_table = DB$meta_true,
-                                    scheme = DB$schemeinfo, 
-                                    tree = input$tree_algo,
-                                    na_handling = input$na_handling,
-                                    distance = "Hamming Distances",
-                                    version = c(phylotraceVersion, "2.5.1"),
-                                    plot = "NJ")
-    } else {
-      Report$report_list_upgma <- list(entry_table = DB$meta_true,
-                                       scheme = DB$schemeinfo, 
-                                       tree = input$tree_algo,
-                                       na_handling = input$na_handling,
-                                       distance = "Hamming Distances",
-                                       version = c(phylotraceVersion, "2.5.1"),
-                                       plot = "UPGMA")
-    }
-  })
-  
-  # Save plot for Report
-  plot.report <- reactive({
-    if(input$tree_algo == "Neighbour-Joining") {
-      jpeg(paste0(getwd(), "/Report/NJ.jpeg"), width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale), quality = 100)
-      print(nj_tree())
-      dev.off()
-    } else if(input$tree_algo == "UPGMA") {
-      jpeg(paste0(getwd(), "/Report/UPGMA.jpeg"), width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale), quality = 100)
-      print(upgma_tree())
-      dev.off()
-    } else if (input$tree_algo == "Minimum-Spanning") {
-      shinyjs::runjs("mstReport();")
-      decoded_data <- base64enc::base64decode(input$canvas_data)
-      writeBin(decoded_data, paste0(getwd(), "/Report/MST.jpg"))
-    }
-  })
-  
-  #### Event Save Report ----
-  output$download_report <- downloadHandler(
-    filename = function() {
-      if(input$tree_algo == "Minimum-Spanning") {
-        paste0("MST_Report_", Sys.Date(), ".html")
-      } else if(input$tree_algo == "Neighbour-Joining") {
-        paste0("NJ_Report_", Sys.Date(), ".html")
-      } else {paste0("UPGMA_Report_", Sys.Date(), ".html")}
-    },
-    content = function(file) {
-      if(input$tree_algo == "Minimum-Spanning") {
-        plot.report()
-        
-        report <- c(Report$report_list_mst, 
-                    "general_date" = as.character(input$mst_date_general_select),
-                    "operator" = input$mst_operator_general_select,
-                    "institute" = input$mst_institute_general_select,
-                    "comment" = input$mst_comm_general_select,
-                    "report_df" = Report$report_df)
-        
-        report[["table_columns"]] <- input$select_rep_tab
-        
-        # Save data to an RDS file if any elements were selected
-        if (!is.null(report)) {
-          
-          log_print("Creating MST report")
-          
-          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
-          
-          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
-          
-          file.copy(paste0(getwd(), "/Report/Report.html"), file)
-        } else {
-          log_print("Creating MST report failed (report is null)")
-        }
-      } else if(input$tree_algo == "Neighbour-Joining") {
-        plot.report()
-        report <- c(Report$report_list_nj, 
-                    "general_date" = as.character(input$mst_date_general_select),
-                    "operator" = input$mst_operator_general_select,
-                    "institute" = input$mst_institute_general_select,
-                    "comment" = input$mst_comm_general_select,
-                    "report_df" = Report$report_df)
-        
-        report[["table_columns"]] <- input$select_rep_tab
-        
-        # Save data to an RDS file if any elements were selected
-        if (!is.null(report)) {
-          log_print("Creating NJ report")
-          
-          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
-          
-          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
-          
-          file.copy(paste0(getwd(), "/Report/Report.html"), file)
-        } else {
-          log_print("Creating NJ report failed (report is null)")
-        }
-        
-      } else {
-        plot.report()
-        report <- c(Report$report_list_upgma, 
-                    "general_date" = as.character(input$mst_date_general_select),
-                    "operator" = input$mst_operator_general_select,
-                    "institute" = input$mst_institute_general_select,
-                    "comment" = input$mst_comm_general_select,
-                    "report_df" = Report$report_df)
-        
-        report[["table_columns"]] <- input$select_rep_tab
-        
-        # Save data to an RDS file if any elements were selected
-        if (!is.null(report)) {
-          log_print("Creating UPGMA report")
-          
-          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
-          
-          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
-          
-          file.copy(paste0(getwd(), "/Report/Report.html"), file)
-        } else {
-          log_print("Creating UPGMA report failed (report is null)")
-        }
-        
-      }
-      removeModal()
-    }
-  )
-  
-  
-  # _______________________ ####
-  
-  ## Gene Screening  ----
-  
-  ### Render UI Elements ----
-  
-  # Rendering results table
-  output$gs_results_table <- renderUI({
-    req(DB$data)
-    if(!is.null(Screening$selected_isolate)) {
-      if(length(Screening$selected_isolate) > 0) {
-        fluidRow(
-          div(class = "loci_table",
-              DT::dataTableOutput("gs_profile_table")),
-          br(),
-          HTML(
-            paste0("<span style='color: white; font-size: 12px'>", 
-                   '<strong>RSL</strong> = <em>Reference Sequence Length</em>&nbsp&nbsp|&nbsp&nbsp',
-                   '<strong>%CRS</strong> = <em>% Coverage of Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
-                   '<strong>%IRS</strong> = <em>% Identity to Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
-                   '<strong>ACS</strong> = <em>Accession of Closest Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
-                   '<strong>NCS</strong> = <em>Name of Closest Sequence</em>')
-            
-          )
-        )
-      } else {
-        fluidRow(
-          br(), br(),
-          p(
-            HTML(
-              paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
-                     'Select entry from the table to display resistance profile')
-              
-            )
-          )
-        )
-      }
-    } else {
-      fluidRow(
-        br(), br(),
-        p(
-          HTML(
-            paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
-                   'Select entry from the table to display resistance profile')
-            
-          )
-        )
-      )
-    }
-  })
-  
-  # Gene screening download button
-  output$gs_download <- renderUI({
-    req(DB$data)
-    if(!is.null(Screening$selected_isolate)) {
-      if(length(Screening$selected_isolate) > 0) {
-        fluidRow(
-          downloadBttn(
-            "download_resistance_profile",
-            style = "simple",
-            label = "Profile Table",
-            size = "sm",
-            icon = icon("download"),
-            color = "primary"
-          ),
-          bsTooltip("download_resistance_profile_bttn", 
-                    HTML(paste0("Save resistance profile table for</br>",
-                                Screening$selected_isolate)), 
-                    placement = "bottom", trigger = "hover")
-        )
-      } else {NULL}
-    } else {NULL}
-  })
-  
-  # Conditionally render table selectiom interface
-  output$gs_table_selection <- renderUI({
-    req(DB$data, input$gs_view)
-    if(input$gs_view == "Table") {
-      fluidRow(
-        column(1),
-        column(
-          width = 10,
-          div(class = "loci_table",
-              dataTableOutput("gs_isolate_table"))
-        )
-      )
-    } else {NULL}
-  })
-  
-  # Resistance profile table output display
-  output$gs_profile_display <- renderUI({
-    req(DB$data)
-    if(!is.null(DB$meta_gs) & !is.null(input$gs_view)) {
-      if(input$gs_view == "Table") {
-        column(
-          width = 10,
-          hr(), 
-          fluidRow(
-            column(
-              width = 4,
-              p(
-                HTML(
-                  paste0("<span style='color: white; font-size: 18px'>", 
-                         "Gene Screening Results</br>",
-                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
-                         "Comprising genes for resistance, virulence, stress, etc.")
-                )
-              )
-            ),
-            column(
-              width = 4,
-              uiOutput("gs_download")
-            )
-          ),
-          br(),
-          uiOutput("gs_results_table")
-        )
-      } else {
-        column(
-          width = 10,
-          fluidRow(
-            column(
-              width = 4,
-              p(
-                HTML(
-                  paste0("<span style='color: white; font-size: 18px'>", 
-                         "Gene Screening Results</br>",
-                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
-                         "Comprising genes for resistance, virulence, stress, etc.")
-                )
-              )
-            ),
-            column(
-              width = 4,
-              div(
-                class = "gs-picker",
-                pickerInput(
-                  "gs_profile_select",
-                  "",
-                  choices = list(
-                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
-                    },
-                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
-                    },
-                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
-                    }
-                  ),
-                  choicesOpt = list(
-                    disabled = c(
-                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
-                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
-                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
-                    )
-                  ),
-                  options = list(
-                    `live-search` = TRUE,
-                    size = 10,
-                    style = "background-color: white; border-radius: 5px;"
-                  )
-                )
-              )
-            ),
-            column(
-              width = 3,
-              uiOutput("gs_download")
-            )
-          ),
-          br(),
-          uiOutput("gs_results_table")
-        )
-      }
-    } else {NULL}
-  })
-  
-  # Screening sidebar
-  output$screening_sidebar <- renderUI({
-    req(DB$data)
-    if(!is.null(DB$meta_gs)) {
-      column(
-        width = 12,
-        align = "center",
-        br(), br(),
-        p(
-          HTML(
-            paste(
-              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Toggle View')
-            )
-          )
-        ),
-        radioGroupButtons(
-          inputId = "gs_view",
-          choices = c("Picker", "Table"),
-          selected = "Picker",
-          checkIcon = list(
-            yes = icon("square-check"),
-            no = icon("square")
-          )
-        ),
-        br()
-      )
-    } else {NULL}
-  })
-  
-  # Resistance profile table
-  observe({
-    req(DB$meta_gs, Screening$selected_isolate, DB$database, DB$scheme, DB$data)
-    
-    if(length(Screening$selected_isolate) > 0 & any(Screening$selected_isolate %in% DB$data$`Assembly ID`)) {
-      iso_select <- Screening$selected_isolate
-      iso_path <- file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
-                            iso_select, "resProfile.tsv")
-      
-      res_profile <- read.delim(iso_path)
-      
-      colnames(res_profile) <- c(
-        "Protein Identifier",	"Contig ID", "Start", "Stop", "Strand", "Gene Symbol", 
-        "Sequence Name", "Scope", "Element Type",  "Element Subtype", "Class", 
-        "Subclass", "Method", "Target Length", "RSL",	"%CRS", "%IRS", 
-        "Alignment Length", "ACS", "Name of Closest Sequence", "HMM ID", "HMM Description")
-      
-      Screening$res_profile <- res_profile %>%
-        relocate(c("Gene Symbol", "Sequence Name", "Element Subtype", "Class", 
-                   "Subclass", "Scope", "Contig ID", "Target Length", "Alignment Length",
-                   "Start", "Stop", "Strand"))
-      
-      # Generate gene profile table
-      output$gs_profile_table <- DT::renderDataTable(
-        Screening$res_profile,
-        selection = "single",
-        rownames= FALSE,
-        options = list(pageLength = 10, scrollX = TRUE,
-                       autoWidth = TRUE,
-                       columnDefs = list(list(width = '400px', targets = c("Sequence Name",
-                                                                           "Name of Closest Sequence"))),
-                       columnDefs = list(list(width = 'auto', targets = "_all")),
-                       columnDefs = list(list(searchable = TRUE,
-                                              targets = "_all")),
-                       initComplete = DT::JS(
-                         "function(settings, json) {",
-                         "$('th:first-child').css({'border-top-left-radius': '5px'});",
-                         "$('th:last-child').css({'border-top-right-radius': '5px'});",
-                         # "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                         # "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                         "}"
-                       ),
-                       drawCallback = DT::JS(
-                         "function(settings) {",
-                         # "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                         # "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                         "}"
-                       ))
-      )
-    } else {
-      output$gs_profile_table <- NULL
-    }
-  })
-
-  #Resistance profile selection table
-  observe({
-    req(DB$meta, DB$data)
-    output$gs_isolate_table <- renderDataTable(
-      select(DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ], -c(3, 4, 10, 11, 12)),
-      selection = "single",
-      rownames= FALSE,
-      options = list(pageLength = 10,
-                     columnDefs = list(list(searchable = TRUE,
-                                            targets = "_all")),
-                     initComplete = DT::JS(
-                       "function(settings, json) {",
-                       "$('th:first-child').css({'border-top-left-radius': '5px'});",
-                       "$('th:last-child').css({'border-top-right-radius': '5px'});",
-                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                       "}"
-                     ),
-                     drawCallback = DT::JS(
-                       "function(settings) {",
-                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                       "}"
-                     ))
-    )
-  })
-  
-  observe({
-    req(input$screening_res_sel, DB$database, DB$scheme, DB$data)
-    if(!is.null(Screening$status_df) &
-       !is.null(input$screening_res_sel) & 
-       !is.null(Screening$status_df$status) & 
-       !is.null(Screening$status_df$isolate)) {
-      if(length(input$screening_res_sel) > 0) {
-        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
-          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
-            results <- read.delim(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
-                                            input$screening_res_sel, "resProfile.tsv"))
-            
-            output$screening_table <- renderDataTable(
-              select(results, c(6, 7, 8, 9, 11)),
-              selection = "single",
-              options = list(pageLength = 10,
-                             columnDefs = list(list(searchable = TRUE,
-                                                    targets = "_all")),
-                             initComplete = DT::JS(
-                               "function(settings, json) {",
-                               "$('th:first-child').css({'border-top-left-radius': '5px'});",
-                               "$('th:last-child').css({'border-top-right-radius': '5px'});",
-                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                               "}"
-                             ),
-                             drawCallback = DT::JS(
-                               "function(settings) {",
-                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
-                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
-                               "}"
-                             )))
-          } else {output$screening_table <- NULL}
-        }
-      } else {
-        output$screening_table <- NULL
-      }
-    } else {
-      output$screening_table <- NULL
-    }
-      
-  })
-  
-  # Availablity feedback
-  output$gene_screening_info <- renderUI({
-    req(DB$data)
-    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
-      p(
-        HTML(
-          paste(
-            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
-          )
-        )
-      )
-    } else {
-      p(
-        HTML(
-          paste(
-            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
-          )
-        )
-      )
-    }
-  })
-  
-  output$gene_resistance_info <- renderUI({
-    req(DB$data)
-    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
-      p(
-        HTML(
-          paste(
-            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
-          )
-        )
-      )
-    } else {
-      p(
-        HTML(
-          paste(
-            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
-            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
-                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
-          )
-        )
-      )
-    }
-  })
-  
-  # Screening Interface
-  
-  output$screening_interface <- renderUI({
-    req(DB$data)
-    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
-      column(
-        width = 12,
-        fluidRow(
-          column(1),
-          column(
-            width = 3,
-            align = "center",
-            br(), br(),
-            p(
-              HTML(
-                paste(
-                  tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Isolates for Screening')
-                )
-              )
-            ),
-            if(Screening$picker_status) {
-              div(
-                class = "screening_div",
-                pickerInput(
-                  "screening_select",
-                  "",
-                  choices = list(
-                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
-                    },
-                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
-                    },
-                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
-                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
-                    } else {
-                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
-                    }
-                  ),
-                  choicesOpt = list(
-                    disabled = c(
-                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
-                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
-                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
-                    )
-                  ),
-                  options = list(
-                    `live-search` = TRUE,
-                    `actions-box` = TRUE,
-                    size = 10,
-                    style = "background-color: white; border-radius: 5px;"
-                  ),
-                  multiple = TRUE
-                )
-              )
-            } else {
-              div(
-                class = "screening_div",
-                pickerInput(
-                  "screening_select",
-                  "",
-                  choices = Screening$picker_choices,
-                  selected = Screening$picker_selected,
-                  options = list(
-                    `live-search` = TRUE,
-                    `actions-box` = TRUE,
-                    size = 10,
-                    style = "background-color: white; border-radius: 5px;"
-                  ),
-                  multiple = TRUE
-                ) 
-              )
-            },
-            br(), br(),
-            uiOutput("genome_path_gs")
-          ),
-          column(
-            width = 3,
-            uiOutput("screening_start")
-          ),
-          column(
-            width = 3,
-            align = "center",
-            br(), br(),
-            uiOutput("screening_result_sel")
-          ),
-          column(1)
-        ),
-        fluidRow(
-          column(1),
-          column(
-            width = 10,
-            br(), br(), 
-            uiOutput("screening_result"),
-            br(), br(), br(), br()
-          )
-        )
-      )
-    }
-  })
-  
-  ### Screening Events ----
-  
-  observe({
-    req(DB$data, input$gs_view)
-    if(input$gs_view == "Table") {
-      meta_gs <- DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ]
-      Screening$selected_isolate <- meta_gs$`Assembly ID`[input$gs_isolate_table_rows_selected]
-    } else if(input$gs_view == "Picker") {
-      Screening$selected_isolate <- input$gs_profile_select
-    }
-  })
-  
-  output$download_resistance_profile <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save resistance profile table ", Screening$selected_isolate, "_Profile.csv"))
-      
-      paste0(format(Sys.Date()), "_", Screening$selected_isolate, "_Profile.csv")
-    },
-    content = function(file) {
-      write.table(
-        Screening$res_profile,
-        file, 
-        sep = ";",
-        row.names = FALSE, 
-        quote = FALSE
-      ) 
-    }
-  )
-  
-  # Reset screening 
-  observeEvent(input$screening_reset_bttn, {
-    log_print("Reset gene screening")
-    
-    # reset status file
-    sapply(Screening$status_df$isolate, remove.screening.status)
-    
-    # set feedback variables
-    Screening$status <- "idle"
-    Screening$status_df <- NULL
-    Screening$choices <- NULL
-    Screening$picker_status <- TRUE
-    Screening$first_result <- NULL
-    
-    # change reactive UI
-    output$screening_table <- NULL
-    output$screening_result <- NULL
-    output$screening_fail <- NULL
-    
-    updatePickerInput(session, "screening_select", selected = character(0))
-    
-    # disable isolate picker
-    shinyjs::runjs("$('#screening_select').prop('disabled', false);")
-    shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
-  })
-  
-  # Cancel screening
-  observeEvent(input$screening_cancel, {
-    showModal(
-      modalDialog(
-        paste0(
-          "Gene screening is still pending. Stopping this process will cancel the screening."
-        ),
-        title = "Reset Multi Typing",
-        fade = TRUE,
-        easyClose = TRUE,
-        footer = tagList(
-          modalButton("Cancel"),
-          actionButton("conf_screening_cancel", "Stop", class = "btn btn-danger")
-        )
-      )
-    )
-  })
-  
-  observeEvent(input$conf_screening_cancel, {
-    log_print("Cancelled gene screening")
-    removeModal()
-    
-    show_toast(
-      title = "Gene Screening Terminated",
-      type = "warning",
-      position = "bottom-end",
-      timer = 6000
-    )
-    
-    # terminate screening
-    system(paste("kill $(pgrep -f 'execute/screening.sh')"), wait = FALSE)
-    system(paste("killall -TERM tblastn"), wait = FALSE)
-    
-    # reset status file
-    sapply(Screening$status_df$isolate, remove.screening.status)
-    
-    # set feedback variables
-    Screening$status <- "idle"
-    Screening$status_df <- NULL
-    Screening$choices <- NULL
-    Screening$picker_status <- TRUE
-    Screening$first_result <- NULL
-    
-    # change reactive UI
-    output$screening_table <- NULL
-    output$screening_result <- NULL
-    
-    updatePickerInput(session, "screening_select", selected = character(0))
-    
-    # disable isolate picker
-    shinyjs::runjs("$('#screening_select').prop('disabled', false);")
-    shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
-  })
-  
-  # Get selected assembly
-  observe({
-    req(DB$data, Screening$status)
-    if (length(input$screening_select) < 1) {
-      output$genome_path_gs <- renderUI(HTML(
-        paste("<span style='color: white; font-style:italic'>", length(input$screening_select), " isolate(s) queried for screening")
-      ))
-      
-      output$screening_start <- NULL
-      
-    } else if (length(input$screening_select) > 0) {
-      
-      output$screening_start <- renderUI({
-        
-        fluidRow(
-          column(
-            width = 12,
-            br(), br(), 
-            if(length(input$screening_select) < 1) {
-              column(
-                width = 12,
-                align = "center",
-                p(
-                  HTML(paste(
-                    '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-                    paste("<span style='color: white; font-style:italic'>", 
-                          "&nbsp Select Isolate(s) for Screening")))
-                )
-              )
-            } else if(Screening$status == "finished") {
-              column(
-                width = 12,
-                align = "center",
-                p(
-                  HTML(paste(
-                    '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:white"></i>',
-                    paste("<span style='color: white; font-style:italic'>", 
-                          "&nbsp Reset to Perform Screening Again")))
-                ),
-                actionButton(
-                  "screening_reset_bttn",
-                  "Reset",
-                  icon = icon("arrows-rotate")
-                ),
-                if(!is.null(Screening$status_df)) {
-                  p(
-                    HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
-                               sum(Screening$status_df$status != "unfinished"), "/",
-                               nrow(Screening$status_df), " Isolate(s) screened"))
-                  )
-                }
-              )
-            } else if(Screening$status == "idle") {
-              column(
-                width = 12,
-                align = "center",
-                p(
-                  HTML(paste(
-                    '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
-                    paste("<span style='color: white;'>",
-                          "&nbsp Screening Ready")))
-                ),
-                actionButton(
-                  inputId = "screening_start_button",
-                  label = "Start",
-                  icon = icon("circle-play")
-                )
-              )
-            } else if(Screening$status == "started") {
-              column(
-                width = 12,
-                align = "center",
-                p(
-                  HTML(paste(
-                    '<i class="fa-solid fa-clock" style="font-size:15px;color:white"></i>',
-                    paste("<span style='color: white;'>",
-                          "&nbsp Running Screening ...")))
-                ),
-                fluidRow(
-                  column(3),
-                  column(
-                    width = 3,
-                    actionButton(
-                      inputId = "screening_cancel",
-                      label = "Terminate",
-                      icon = icon("ban")
-                    )
-                  ),
-                  column(
-                    width = 3,
-                    HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:22px;color:white;margin-top:27px;position:relative;left:20px"></i>'))
-                  )
-                ),
-                if(!is.null(Screening$status_df)) {
-                  p(
-                    HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
-                               sum(Screening$status_df$status != "unfinished"), "/",
-                               nrow(Screening$status_df), " isolate(s) screened"))
-                  )
-                }
-              )
-            }
-          )
-        )
-      })
-    } else {NULL}
-  })
-  
-  #### Running Screening ----
-  
-  observeEvent(input$screening_start_button, {
-    
-    if(tail(readLogFile(), 1) != "0") {
-      show_toast(
-        title = "Pending Multi Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
-      show_toast(
-        title = "Pending Single Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      
-      log_print("Started gene screening")
-      
-      Screening$status <- "started"
-      Screening$picker_choices <- list(
-        Unscreened = if (sum(DB$data$Screened == "No") == 1) {
-          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
-        } else {
-          DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
-        },
-        Screened =  if (sum(DB$data$Screened == "Yes") == 1) {
-          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
-        } else {
-          DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
-        },
-        `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
-          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
-        } else {
-          DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
-        }
-      )
-      Screening$picker_selected <- input$screening_select
-      Screening$picker_status <- FALSE
-      
-      show_toast(
-        title = "Gene screening started",
-        type = "success",
-        position = "bottom-end",
-        timer = 6000
-      )
-      
-      Screening$meta_df <- data.frame(wd = getwd(),
-                                 selected = paste(
-                                   file.path(DB$database, gsub(" ", "_", DB$scheme),
-                                             "Isolates", input$screening_select,
-                                             paste0(input$screening_select, ".zip")), 
-                                   collapse = " "),
-                                 species = gsub(" ", "_", DB$scheme))
-      
-      Screening$status_df <- data.frame(isolate = basename(gsub(".zip", "", str_split_1(Screening$meta_df$selected, " "))), 
-                                        status = "unfinished")
-      
-       # Reset screening status
-      sapply(Screening$status_df$isolate, remove.screening.status)
-      
-      saveRDS(Screening$meta_df, paste0(getwd(), "/execute/screening_meta.rds"))
-      
-      # Disable pickerInput
-      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').prop('disabled', true);"))
-      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').selectpicker('refresh');"))
-    
-      # System execution screening.sh
-      system(paste("bash", paste0(getwd(), "/execute/screening.sh")), wait = FALSE)
-    }
-  })
-  
-  observe({
-    req(DB$data, Screening$status, input$screening_res_sel, Screening$status_df)
-    if(!is.null(Screening$status_df) &
-       !is.null(Screening$status_df$status) & 
-       !is.null(Screening$status_df$isolate) &
-       !is.null(input$screening_res_sel)) {
-      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
-        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
-          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
-            output$screening_result <- renderUI(
-              column(
-                width = 12,
-                hr(), br(),
-                dataTableOutput("screening_table") 
-              )
-            )
-          } else {
-            output$screening_result <- renderUI(
-              column(
-                width = 12,
-                hr(), br(),
-                verbatimTextOutput("screening_fail")
-              )
-            )
-          }
-        }
-      } else {
-        output$screening_result <- NULL
-      }
-    } else {
-      output$screening_result <- NULL
-    }
-  })
-  
-  observe({
-    req(DB$data, Screening$status, input$screening_res_sel)
-    if(!is.null(Screening$status_df) &
-       !is.null(Screening$status_df$status) & 
-       !is.null(Screening$status_df$isolate) &
-       !is.null(input$screening_res_sel)) {
-      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
-        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
-          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "fail") {
-            output$screening_fail <- renderPrint({
-              cat(paste(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
-                                            "Isolates", input$screening_res_sel, "status.txt")),"\n"))
-            })
-          }
-        }
-      } else {
-        output$screening_fail <- NULL
-      }
-    } else {
-      output$screening_fail <- NULL
-    }
-  })
-  
-  observe({
-    req(DB$data)
-    if(!is.null(Screening$status)) {
-      if(Screening$status != "idle") {
-        
-        # start status screening for user feedback
-        check_screening()
-        
-        if(isTRUE(Screening$first_result)) {
-          output$screening_result_sel <- renderUI(
-            column(
-              width = 12,
-              align = "center",
-              selectInput(
-                "screening_res_sel",
-                label = h5("Select Result", style = "color:white; margin-bottom: 28px; margin-top: -10px;"),
-                choices = ""
-              ),
-              if(!is.null(Screening$status_df)) {
-                p(HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
-                             if(sum(Screening$status_df$status == "success") == 1) {
-                               "1 success &nbsp / &nbsp"
-                             } else {
-                               paste0(sum(Screening$status_df$status == "success"), " successes &nbsp / &nbsp")
-                             },
-                             if(sum(Screening$status_df$status == "fail") == 1) {
-                               "1 failure"
-                             } else {
-                               paste0(sum(Screening$status_df$status == "fail"), " failures")
-                             })))
-              }
-            )
-          )
-          
-          Screening$first_result <- FALSE
-        }
-      } else if(Screening$status == "idle") {
-        output$screening_result_sel <- NULL
-      }
-    }
-  }) 
-    
-  check_screening <- reactive({
-    invalidateLater(500, session)
-    
-    req(Screening$status_df)
-    
-    if(Screening$status == "started") {
-      
-      Screening$status_df$status <- sapply(Screening$status_df$isolate, check_status)
-      
-      if(any("unfinished" != Screening$status_df$status) &
-         !identical(Screening$choices, Screening$status_df$isolate[which(Screening$status_df$status != "unfinished")])) {
-        
-        status_df <- Screening$status_df[which(Screening$status_df$status != "unfinished"),]
-        
-        Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
-                                                                 Screening$status_df$status == "fail")]
-        
-        if(sum(Screening$status_df$status != "unfinished") > 0) {
-          if(is.null(Screening$first_result)) {
-            Screening$first_result <- TRUE
-          }
-        }
-        
-        if(tail(status_df$status, 1) == "success") {
-          
-          # Changing "Screened" metadata variable in database
-          Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
-          
-          Database[["Typing"]]$Screened[which(Database[["Typing"]]["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
-
-          saveRDS(Database, file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
-
-          DB$data$Screened[which(DB$data["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
-          
-          DB$meta_gs <- select(DB$data, c(1, 3:13))
-          DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
-          DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
-          
-          show_toast(
-            title = paste("Successful screening of", tail(Screening$choices, 1)),
-            type = "success",
-            position = "bottom-end",
-            timer = 6000)
-          
-          updateSelectInput(session = session,
-                            inputId = "screening_res_sel",
-                            choices = Screening$choices,
-                            selected = tail(Screening$choices, 1))
-          
-        } else if(tail(status_df$status, 1) == "fail") {
-          
-          show_toast(
-            title = paste("Failed screening of", tail(status_df$isolate, 1)),
-            type = "error",
-            position = "bottom-end",
-            timer = 6000)
-          
-          updateSelectInput(session = session,
-                            inputId = "screening_res_sel",
-                            choices = Screening$choices,
-                            selected = tail(Screening$choices, 1))
-        }
-        
-        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
-          Screening$status <- "finished"
-        }
-      } else {
-        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
-          Screening$status <- "finished"
-        }
-      }
-      
-      if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
-        Screening$status <- "finished"
-      }
-    }
-  }) 
-  
-  
-  # _______________________ ####
-  
-  ## Typing  ----
-  
-  # Render Single/Multi Switch
-  
-  readLogFile <- reactive({
-    invalidateLater(5000, session)
-    readLines(paste0(getwd(), "/logs/script_log.txt"))
-  })
-  
-  # Render sidebar dependent on data presence
-  # No sidebar
-  output$typing_sidebar <- renderUI({
-    if(!is.null(DB$exist)) {
-      if(DB$exist) {
-        NULL
-      } else {
-        column(
-          width = 12,
-          align = "center",
-          br(), br(),
-          p(
-            HTML(
-              paste(
-                tags$span(style='color: white; font-size: 18px; margin-bottom: 0px', 'Typing Mode')
-              )
-            )
-          ),
-          radioGroupButtons(
-            inputId = "typing_mode",
-            choices = c("Single", "Multi"),
-            selected = "Single",
-            checkIcon = list(
-              yes = icon("square-check"),
-              no = icon("square")
-            )
-          ),
-          br()
-        )
-      }
-    }
-    
-  })
-  
-  # No db typing message
-  output$typing_no_db <- renderUI({
-    if(!is.null(DB$exist)) {
-      if(DB$exist) {
-        column(
-          width = 4,
-          align = "left",
-          br(),
-          br(),
-          br(),
-          br(),
-          p(
-            HTML(
-              paste0(
-                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 50px', 'To initiate allelic typing, a cgMLST scheme must be downloaded first.'
-                )
-              )
-            )
-          )
-        )
-      } else {NULL}
-    } else {NULL}
-  })
-  
-  ### Single Typing ----
-  
-  #### Render UI Elements ----
-  
-  # Render single typing naming issues
-  output$single_select_issues <- renderUI({
-    req(input$assembly_id)
-    
-    if(nchar(trimws(input$assembly_id)) < 1) {
-      ass_id <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
-    } else {
-      ass_id <- trimws(input$assembly_id)
-    }
-    
-    if(ass_id %in% unlist(DB$data["Assembly ID"])) {
-      HTML(paste(
-        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-        paste("<span style='color: white; font-style:italic'>", 
-              "&nbsp Assembly ID already present in database.")))
-    } else if (ass_id == "") {
-      HTML(paste(
-        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-        paste("<span style='color: white; font-style:italic'>", 
-              "&nbsp Empty Assembly ID.")))
-    } else if (grepl("[()/\\:*?\"<>|]", ass_id)) {
-      HTML(paste(
-        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-        paste("<span style='color: white; font-style:italic'>", 
-              "&nbsp Invalid Assembly ID. Avoid special characters.")))
-    } else if(grepl(" ", ass_id)) {
-      HTML(paste(
-        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-        paste("<span style='color: white; font-style:italic'>", 
-              "&nbsp Invalid Assembly ID. Avoid empty spaces.")))
-    } else {HTML(paste(
-      '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
-      paste("<span style='color: white; font-style:italic'>",
-            "&nbsp Assembly ID compatible with local database.")))}
-  })
-  
-  # Render Typing Results if finished
-  observe({
-    if(Typing$progress_format_end == 999999) {
-      if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
-        if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
-          output$typing_result_table <- renderRHandsontable({
-            Typing$typing_result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
-            Typing$typing_result_table <- mutate_all(Typing$typing_result_table, as.character)
-            if(nrow(Typing$typing_result_table) > 0) {
-              if(nrow(Typing$typing_result_table) > 15) {
-                rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
-                              stretchH = "all", height = 500, readOnly = TRUE,
-                              contextMenu = FALSE) %>%
-                  hot_cols(columnSorting = TRUE) %>%
-                  hot_rows(rowHeights = 25) %>%
-                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter",
-                          cellWidths = list(100, 160, NULL)) %>%
-                  hot_col("Value", renderer=htmlwidgets::JS(
-                    "function(instance, td, row, col, prop, value, cellProperties) {
-                      if (value.length > 8) {
-                        value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                      }
-                      td.innerHTML = value;
-                      td.style.textAlign = 'center';
-                      return td;
-                     }"
-                  ))
-              } else {
-                rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
-                              stretchH = "all", readOnly = TRUE,
-                              contextMenu = FALSE,) %>%
-                  hot_cols(columnSorting = TRUE) %>%
-                  hot_rows(rowHeights = 25) %>%
-                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter",
-                          cellWidths = list(100, 160, NULL)) %>%
-                  hot_col("Value", renderer=htmlwidgets::JS(
-                    "function(instance, td, row, col, prop, value, cellProperties) {
-                      if (value.length > 8) {
-                        value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                      }
-                      td.innerHTML = value;
-                      td.style.textAlign = 'center';
-                      return td;
-                     }"
-                  ))
-              }
-            }
-          })
-          
-          output$single_typing_results <- renderUI({
-            result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
-            number_events <- nrow(result_table)
-            
-            n_new <- length(grep("New Variant", result_table$Event))
-            
-            n_missing <- number_events - n_new
-            
-            # Show results table only if successful typing 
-            if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
-              if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
-                if(number_events > 0) {
-                  column(
-                    width = 12,
-                    HTML(paste("<span style='color: white;'>", 
-                               length(Typing$scheme_loci_f) - number_events,
-                               "loci were assigned a variant from local scheme.")),
-                    br(), 
-                    HTML(paste("<span style='color: white;'>", 
-                               n_missing,
-                               if(n_missing == 1) " locus not assigned (<i>NA</i>)." else " loci not assigned (<i>NA</i>).")),
-                    br(),
-                    HTML(paste("<span style='color: white;'>", 
-                               n_new,
-                               if(n_new == 1) " locus with new variant."  else " loci with new variants.")),
-                    br(), br(),
-                    rHandsontableOutput("typing_result_table")
-                  )
-                } else {
-                  column(
-                    width = 12,
-                    HTML(paste("<span style='color: white;'>", 
-                               length(Typing$scheme_loci_f),
-                               "successfully assigned from local scheme."))
-                  )
-                }
-              }
-            }
-          })
-          
-        } else {
-          
-          output$single_typing_results <- NULL
-          
-        }
-      } else {
-        output$single_typing_results <- NULL
-      }
-    }
-    
-  })
-  
-  # Render Initiate Typing UI
-  output$initiate_typing_ui <- renderUI({
-    column(
-      width = 4,
-      align = "center",
-      br(),
-      br(),
-      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-      br(),
-      br(),
-      p(
-        HTML(
-          paste(
-            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File (FASTA)')
-          )
-        )
-      ),
-      fluidRow(
-        column(1),
-        column(
-          width = 11,
-          align = "center",
-          shinyFilesButton(
-            "genome_file",
-            "Browse" ,
-            icon = icon("file"),
-            title = "Select the assembly in .fasta/.fna/.fa format:",
-            multiple = FALSE,
-            buttonType = "default",
-            class = NULL,
-            root = path_home()
-          ),
-          br(),
-          br(),
-          uiOutput("genome_path"),
-          br()
-        )
-      )
-    )
-  })
-  
-  # Render Declare Metadata UI
-  
-  observe({
-    if (nrow(Typing$single_path) < 1) {
-      output$genome_path <- renderUI(HTML(
-        paste("<span style='color: white; margin-left:-30px'>", "No file selected.")
-      ))
-      
-      # dont show subsequent metadata declaration and typing start UI
-      output$metadata_single_box <- NULL
-      output$start_typing_ui <- NULL
-      
-    } else if (nrow(Typing$single_path) > 0) {
-      
-      if (str_detect(str_sub(Typing$single_path$name, start = -6), ".fasta") | 
-          str_detect(str_sub(Typing$single_path$name, start = -6), ".fna") | 
-          str_detect(str_sub(Typing$single_path$name, start = -6), ".fa")) {
-        
-        # Render selected assembly path
-        output$genome_path <- renderUI({
-          HTML(
-            paste(
-              "<span style='color: white; margin-left:-30px; font-weight: bolder'>",
-              as.character(Typing$single_path$name)
-            )
-          )
-        })
-        
-        # Render metadata declaration box
-        output$metadata_single_box <- renderUI({
-          
-          # Render placeholder 
-          updateTextInput(session, "assembly_id", value = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
-          updateTextInput(session, "assembly_name", value = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
-          
-          column(
-            width = 3,
-            align = "center",
-            br(), br(),
-            h3(p("Declare Metadata"), style = "color:white; margin-left:-40px"),
-            br(), br(),
-            div(
-              class = "multi_meta_box",
-              box(
-                solidHeader = TRUE,
-                status = "primary",
-                width = "90%",
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput("assembly_id",
-                                value = "",
-                                label = "",
-                                width = "80%")
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 12,
-                    uiOutput("single_select_issues")
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput("assembly_name",
-                                label = "",
-                                width = "80%")
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      dateInput("append_isodate",
-                                label = "",
-                                width = "80%",
-                                max = Sys.Date())
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput("append_host",
-                                label = "",
-                                width = "80%")
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table_country",
-                      pickerInput(
-                        "append_country",
-                        label = "",
-                        choices = list("Common" = sel_countries,
-                                       "All Countries" = country_names),
-                        options = list(
-                          `live-search` = TRUE,
-                          `actions-box` = TRUE,
-                          size = 10,
-                          style = "background-color: white; border-radius: 5px;"
-                        ),
-                        width = "90%"
-                      )
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput(
-                        "append_city",
-                        label = "",
-                        width = "80%"
-                      )
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 12,
-                    align = "center",
-                    br(), br(),
-                    actionButton(
-                      inputId = "conf_meta_single",
-                      label = "Confirm"
-                    ),
-                    br()
-                  )
-                ),
-                br()
-              )
-            )
-          )
-        })
-      } else {
-        show_toast(
-          title = "Wrong file type (only fasta/fna/fa)",
-          type = "error",
-          position = "bottom-end",
-          timer = 6000
-        )
-      }
-    }
-  })
-  
-  # Get genome datapath
-  
-  observe({
-    # Get selected Genome in Single Mode
-    shinyFileChoose(input,
-                    "genome_file",
-                    roots = c(Home = path_home(), Root = "/"),
-                    defaultRoot = "Home",
-                    session = session,
-                    filetypes = c('', 'fasta', 'fna', 'fa'))
-    Typing$single_path <- parseFilePaths(roots = c(Home = path_home(), Root = "/"), input$genome_file)
-    
-  })
-  
-  #### Run blat ----
-  
-  observeEvent(input$typing_start, {
-    
-    log_print("Input typing_start")
-    
-    if(tail(readLogFile(), 1) != "0") {
-      show_toast(
-        title = "Pending Multi Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if (Screening$status == "started") {
-      show_toast(
-        title = "Pending Gene Screening",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      
-      if(!is.null(DB$data)) {
-        if(sum(apply(DB$data, 1, anyNA)) >= 1) {
-          DB$no_na_switch <- TRUE
-        } else {
-          DB$no_na_switch <- FALSE
-        }
-      }
-      
-      # Activate entry detection
-      DB$check_new_entries <- TRUE
-      
-      Typing$single_end <- FALSE
-      
-      Typing$progress_format_start <- 0
-      Typing$progress_format_end <- 0
-      
-      # Remove Initiate Typing UI 
-      output$initiate_typing_ui <- NULL
-      output$metadata_single_box <- NULL
-      output$start_typing_ui <- NULL
-      
-      # status feedback
-      Typing$status <- "Processing"
-      
-      # Locate folder containing cgMLST scheme
-      search_string <- paste0(gsub(" ", "_", DB$scheme), "_alleles")
-      
-      scheme_folders <- dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme)))
-      
-      if (any(grepl(search_string, scheme_folders))) {
-        
-        # reset results file 
-        if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
-          unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
-        }
-        
-        # blat initiate index
-        scheme_select <- as.character(scheme_folders[which(grepl(search_string, scheme_folders))])
-        
-        show_toast(
-          title = "Typing Initiated",
-          type = "success",
-          position = "bottom-end",
-          timer = 6000
-        )
-        
-        log_print("Initiated single typing")
-        
-        ### Run blat Typing
-        
-        single_typing_df <- data.frame(
-          db_path = DB$database,
-          wd = getwd(),
-          save = input$save_assembly_st,
-          scheme = paste0(gsub(" ", "_", DB$scheme)),
-          genome = Typing$single_path$datapath,
-          alleles = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", search_string)
-        )
-        
-        saveRDS(single_typing_df, "execute/single_typing_df.rds")
-        
-        # Execute single typing script
-        system(paste("bash", paste0(getwd(), "/execute/single_typing.sh")), 
-               wait = FALSE)
-        
-        scheme_loci <- list.files(path = scheme_select, full.names = TRUE)
-        
-        # Filter the files that have FASTA extensions
-        Typing$scheme_loci_f <-
-          scheme_loci[grep("\\.(fasta|fa|fna)$", scheme_loci, ignore.case = TRUE)]
-        
-        output$single_typing_progress <- renderUI({
-          fluidRow(
-            br(), br(), 
-            column(width = 1),
-            column(
-              width = 3,
-              h3(p("Pending Single Typing ..."), style = "color:white")
-            ),
-            br(), br(), br(), 
-            fluidRow(
-              column(width = 1),
-              column(
-                width = 4,
-                br(), br(), br(),
-                fluidRow(
-                  column(
-                    width = 12,
-                    uiOutput("reset_single_typing"),
-                    HTML(
-                      paste(
-                        "<span style='color: white; font-weight: bolder'>",
-                        as.character(Typing$single_path$name)
-                      )
-                    ),
-                    br(), br(),
-                    progressBar(
-                      "progress_bar",
-                      value = 0,
-                      display_pct = TRUE,
-                      title = ""
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 12,
-                    uiOutput("typing_formatting"),
-                    uiOutput("typing_fin")
-                  )
-                )
-              ),
-              column(1),
-              column(
-                width = 5,
-                br(), br(), br(),
-                uiOutput("single_typing_results")
-              )
-            )
-          )
-        })
-      } else {
-        log_print("Folder containing cgMLST alleles not in working directory")
-        
-        show_alert(
-          title = "Error",
-          text = paste0(
-            "Folder containing cgMLST alleles not in working directory.",
-            "\n",
-            "Download cgMLST Scheme for selected Organism first."
-          ),
-          type = "error"
-        )
-      }
-    }
-  })
-  
-  # Function to update Progress Bar
-  update <- reactive({
-    invalidateLater(3000, session)
-    
-    # write progress in process tracker
-    cat(
-      c(length(list.files(paste0(getwd(), "/execute/blat_single/results"))),
-        readLines(paste0(getwd(), "/logs/progress.txt"))[-1]), 
-      file = paste0(getwd(), "/logs/progress.txt"),
-      sep = "\n"
-    )
-    
-    progress <- readLines(paste0(getwd(), "/logs/progress.txt"))
-    
-    # if typing with blat is finished -> "attaching" phase started
-    if(!is.na(progress[1])) {
-      if(!is.na(progress[2])) {
-        if(progress[2] == "888888") {
-          Typing$progress_format_start <- progress[2]
-          Typing$pending_format <- progress[2]
-          Typing$status <- "Attaching"
-        }
-      }
-      # "attaching" phase completed
-      if(!is.na(progress[3])) {
-        if(progress[3] == "999999") {
-          Typing$progress_format_end <- progress[3]
-          Typing$entry_added <- progress[3]
-          Typing$status <- "Finalized"
-        }
-      }
-      Typing$progress <- as.numeric(progress[1])
-      floor((Typing$progress / length(Typing$scheme_loci_f)) * 100)
-    } else {
-      floor((Typing$progress / length(Typing$scheme_loci_f)) * 100)
-    }
-  })
-  
-  # Observe Typing Progress
-  observe({
-    
-    if(readLogFile()[1] == "0") {
-      # Update Progress Bar
-      updateProgressBar(
-        session = session,
-        id = "progress_bar",
-        value = update(),
-        total = 100,
-        title = paste0(as.character(Typing$progress), "/", length(Typing$scheme_loci_f), " loci screened")
-      )
-    }
-    
-    if (Typing$progress_format_start == 888888) {
-      output$typing_formatting <- renderUI({
-        column(
-          width = 12,
-          align = "center",
-          br(),
-          fluidRow(
-            column(
-              width = 6,
-              HTML(paste("<span style='color: white;'>", "Transforming data ..."))
-            ),
-            column(
-              width = 3,
-              align = "left",
-              HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px;color:white"></i>'))
-            )
-          )
-        )
-      })
-    } else {
-      output$typing_formatting <- NULL
-    }
-    
-    # Render when finalized  
-    if (Typing$progress_format_end == 999999) {
-      
-      output$typing_formatting <- NULL
-      
-      output$typing_fin <- renderUI({
-        fluidRow(
-          column(
-            width = 12,
-            align = "center",
-            br(), br(),
-            if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
-              if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
-                req(Typing$scheme_loci_f, Typing$typing_result_table)
-                if(sum(Typing$typing_result_table$Event != "New Variant") >  (0.5 * length(Typing$scheme_loci_f))){
-                  HTML(
-                    paste("<span style='color: white;'>", 
-                          sub(".*Successful", "Finished", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
-                          paste("<span style='color: orange;'>", "Warning: Isolate contains large number of failed allele assignments."),
-                          paste("<span style='color: white;'>", "Reset to start another typing process."),
-                          sep = '<br/>\n'))                    
-                } else {
-                  HTML(paste("<span style='color: white;'>", 
-                             sub(".*Successful", "Successful", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
-                             "Reset to start another typing process.", sep = '<br/>'))
-                }
-              } else {
-                HTML(paste("<span style='color: white;'>", 
-                           sub(".*typing", "Typing", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
-                           "Reset to start another typing process.", sep = '<br/>'))
-              }
-            },
-            br(), br(),
-            actionButton(
-              "reset_single_typing",
-              "Reset",
-              icon = icon("arrows-rotate")
-            )
-          )
-        )
-      })
-    } else {
-      output$typing_fin <- NULL
-      output$single_typing_results <- NULL
-    }
-    
-  })
-  
-  #### Declare Metadata  ----
-  
-  observeEvent(input$conf_meta_single, {
-    
-    if(nchar(trimws(input$assembly_id)) < 1) {
-      ass_id <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
-    } else {
-      ass_id <- trimws(input$assembly_id)
-    }
-    
-    if(nchar(trimws(input$assembly_name)) < 1) {
-      ass_name <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
-    } else {
-      ass_name <- trimws(input$assembly_name)
-    }
-    
-    if(ass_id %in% unlist(DB$data["Assembly ID"])) {
-      show_toast(
-        title = "Assembly ID already present",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (isFALSE(Typing$reload)) {
-      show_toast(
-        title = "Reload Database first",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if (ass_id == "") {
-    show_toast(
-      title = "Empty Assembly ID",
-      type = "error",
-      position = "bottom-end",
-      timer = 3000
-      )
-    } else if (grepl("[()/\\:*?\"<>|]", ass_id)) {
-      show_toast(
-        title = "Invalid Assembly ID. No special characters allowed: ()/\\:*?\"<>|",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if(grepl(" ", ass_id)) {
-      show_toast(
-        title = "Empty spaces in Assembly ID not allowed",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if(Screening$status == "started") {
-      show_toast(
-        title = "Pending Single Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      
-      log_print("Single typing metadata confirmed")
-      
-      meta_info <- data.frame(assembly_id = ass_id,
-                              assembly_name = ass_name,
-                              cgmlst_typing = DB$scheme,
-                              append_isodate = input$append_isodate,
-                              append_host = trimws(input$append_host),
-                              append_country = trimws(input$append_country),
-                              append_city = trimws(input$append_city),
-                              append_analysisdate = Sys.Date(),
-                              db_directory = getwd()) 
-      
-      saveRDS(meta_info, paste0(
-        getwd(),
-        "/execute/meta_info_single.rds"
-      ))
-      
-      show_toast(
-        title = "Metadata declared",
-        type = "success",
-        position = "bottom-end",
-        timer = 3000
-      )
-      
-      # Render Start Typing UI
-      output$start_typing_ui <- renderUI({
-        div(
-          class = "multi_start_col",
-          column(
-            width = 3,
-            align = "center",
-            br(),
-            br(),
-            h3(p("Start Typing"), style = "color:white"),
-            br(),
-            br(),
-            HTML(
-              paste(
-                "<span style='color: white;'>",
-                "Typing by <strong>",
-                DB$scheme,
-                "</strong> scheme."
-              )
-            ),
-            br(), br(), br(), br(),
-            div(
-              class = "save-assembly",
-              materialSwitch(
-                "save_assembly_st",
-                h5(p("Save Assemblies in Local Database"), style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
-                value = TRUE,
-                right = TRUE)
-            ),
-            HTML(
-              paste(
-                "<span style='color: orange;'>",
-                "Isolates with unsaved assembly files can NOT be applied to screening for resistance genes."
-              )
-            ),
-            br(), br(), br(), br(),
-            actionButton(
-              inputId = "typing_start",
-              label = "Start",
-              icon = icon("circle-play")
-            )
-          )
-        )
-      })
-    }
-  })
-  
-  ####  Events Single Typing ----
-  
-  observeEvent(input$reset_single_typing, {
-    log_print("Reset single typing")
-    
-    Typing$status <- "Inactive"
-    
-    Typing$progress <- 0
-    
-    Typing$progress_format <- 900000
-    
-    output$single_typing_progress <- NULL
-    
-    output$typing_fin <- NULL
-    
-    output$single_typing_results <- NULL
-    
-    output$typing_formatting <- NULL
-    
-    Typing$single_path <- data.frame()
-    
-    # reset results file 
-    if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
-      unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
-      # Resetting single typing progress logfile bar 
-      con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
-      
-      cat("0\n", file = con)   
-      
-      close(con)
-    }
-    
-    output$initiate_typing_ui <- renderUI({
-      column(
-        width = 4,
-        align = "center",
-        br(),
-        br(),
-        h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-        br(),
-        br(),
-        p(
-          HTML(
-            paste(
-              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File (FASTA)')
-            )
-          )
-        ),
-        fluidRow(
-          column(1),
-          column(
-            width = 11,
-            align = "center",
-            shinyFilesButton(
-              "genome_file",
-              "Browse" ,
-              icon = icon("file"),
-              title = "Select the assembly in .fasta/.fna/.fa format:",
-              multiple = FALSE,
-              buttonType = "default",
-              class = NULL,
-              root = path_home()
-            ),
-            br(),
-            br(),
-            uiOutput("genome_path"),
-            br()
-          )
-        )
-      )
-    })
-  })
-  
-  # Notification for finalized Single typing
-  Typing$single_end <- TRUE
-  Typing$progress_format_end <- 0
-  
-  observe({
-    if(Typing$single_end == FALSE) {
-      if (Typing$progress_format_end == 999999) {
-        show_toast(
-          title = "Single Typing finalized",
-          type = "success",
-          position = "bottom-end",
-          timer = 8000
-        )
-        Typing$single_end <- TRUE
-      }
-    }
-  })
-  
-  ### Multi Typing ----
-  
-  #### Render Multi Typing UI Elements ----
-  output$initiate_multi_typing_ui <- renderUI({
-    column(
-      width = 4,
-      align = "center",
-      br(),
-      br(),
-      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-      br(), br(),
-      p(
-        HTML(
-          paste(
-            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
-          )
-        )
-      ),
-      fluidRow(
-        column(1),
-        column(
-          width = 11,
-          align = "center",
-          shinyDirButton(
-            "genome_file_multi",
-            "Browse",
-            icon = icon("folder-open"),
-            title = "Select the folder containing the genome assemblies (FASTA)",
-            buttonType = "default",
-            root = path_home()
-          ),
-          br(),
-          br(),
-          uiOutput("multi_select_info"),
-          br()
-        )
-      ),
-      uiOutput("multi_select_tab_ctrls"),
-      br(),
-      fluidRow(
-        column(1),
-        column(
-          width = 11,
-          align = "left",
-          rHandsontableOutput("multi_select_table")
-        )
-      )
-    )
-  })
-  
-  # Render selection info
-  output$multi_select_info <- renderUI({
-    
-    if(!is.null(Typing$multi_path)) {
-      if(length(Typing$multi_path) < 1) {
-        HTML(paste("<span style='color: white; margin-left:-30px'>", 
-                   "No files selected."))
-      } else {
-        HTML(paste("<span style='color: white; margin-left:-30px'>",
-                   sum(hot_to_r(input$multi_select_table)$Include == TRUE),
-                   " files selected."))
-      }
-    }
-  })
-  
-  # Render multi selection table issues
-  output$multi_select_issues <- renderUI({
-    req(Typing$multi_sel_table, input$multi_select_table)
-    if(any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
-       any(duplicated(hot_to_r(input$multi_select_table)$Files))){
-      HTML(
-        paste(
-          paste("<span style='color: orange;'>",
-                "Some name(s) are already present in local database.<br/>"),
-          paste("<span style='color: #ff7334;'>",
-                "Duplicated name(s). <br/>")
-        )
-      )
-    } else if (any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
-               !any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
-      HTML(
-        paste("<span style='color: #e0b300;'>",
-              "Some name(s) are already present in local database.<br/>")
-      )
-    } else if (!any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
-               any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
-      HTML(
-        paste("<span style='color: #ff7334;'>",
-              "Duplicated name(s). <br/>")
-      )
-    }
-  })
-  
-  output$multi_select_issue_info <- renderUI({
-    req(Typing$multi_sel_table, input$multi_select_table)
-    
-    multi_select_table <- hot_to_r(input$multi_select_table)
-    
-    if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
-       any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)])) |
-       any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
-      
-      if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)])))  {
-        
-        if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
-           any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
-          HTML(paste(
-            paste(
-              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-              paste("<span style='color: white; font-style:italic'>",
-                  "&nbspRename highlighted isolates or deselect them.</br>")),
-            paste(
-              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-              paste("<span style='color: white; font-style:italic'>",
-                  "&nbspFilename(s) contain(s) empty spaces."))
-          ))
-        } else {
-          HTML(paste(
-            '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-            paste("<span style='color: white; font-style:italic'>",
-                     "&nbspFilename(s) contain(s) empty spaces.")))
-        }
-      } else {
-        HTML(paste(
-          '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
-          paste("<span style='color: white; font-style:italic'>", 
-                   "&nbspRename highlighted isolates or deselect them.")))
-      }
-    } else {
-      HTML(paste(
-        '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
-        paste("<span style='color: white; font-style:italic'>",
-              "&nbspFiles ready for allelic typing.")))
-    }
-  })
-  
-  # Render Metadata Select Box after Folder selection
-  observe({
-    if(!is.null(Typing$multi_sel_table)) {
-      if (nrow(Typing$multi_sel_table) > 0) {
-        
-        output$multi_select_tab_ctrls <- renderUI(
-          fluidRow(
-            column(1),
-            column(
-              width = 2,
-              align = "left",
-              actionButton(
-                "sel_all_mt",
-                "All",
-                icon = icon("check")
-              )
-            ),
-            column(
-              width = 2,
-              align = "left",
-              actionButton(
-                "desel_all_mt",
-                "None",
-                icon = icon("xmark")
-              )
-            ),
-            column(2),
-            column(
-              width = 5,
-              align = "right",
-              br(),
-              uiOutput("multi_select_issues")
-            )
-          )
-        )
-        
-        output$metadata_multi_box <- renderUI({
-          column(
-            width = 3,
-            align = "center",
-            br(),
-            br(),
-            h3(p("Declare Metadata"), style = "color:white;margin-left:-40px"),
-            br(), br(),
-            div(
-              class = "multi_meta_box",
-              box(
-                solidHeader = TRUE,
-                status = "primary",
-                width = "90%",
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      dateInput("append_isodate_multi",
-                                label = "",
-                                width = "80%",
-                                max = Sys.Date())
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput("append_host_multi",
-                                label = "",
-                                width = "80%")
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table_country",
-                      pickerInput(
-                        "append_country_multi",
-                        label = "",
-                        choices = list("Common" = sel_countries,
-                                       "All Countries" = country_names),
-                        options = list(
-                          `live-search` = TRUE,
-                          `actions-box` = TRUE,
-                          size = 10,
-                          style = "background-color: white; border-radius: 5px;"
-                        ),
-                        width = "90%"
-                      )
-                    )  
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    div(
-                      class = "append_table",
-                      textInput("append_city_multi",
-                                label = "",
-                                width = "80%")
-                    )
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 5,
-                    align = "left",
-                    h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
-                  ),
-                  column(
-                    width = 7,
-                    align = "left",
-                    h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
-                  )
-                ),
-                fluidRow(
-                  column(
-                    width = 12,
-                    align = "center",
-                    br(), br(),
-                    actionButton(
-                      inputId = "conf_meta_multi",
-                      label = "Confirm"
-                    ),
-                    br(), br(),
-                    uiOutput("multi_select_issue_info")
-                  )
-                )
-              )    
-            )
-          )
-        }) 
-      } else {
-        output$metadata_multi_box <- NULL
-      }
-    }
-  })
-  
-  # Check if ongoing Multi Typing - Render accordingly
-  observe({
-    # Get selected Genome in Multi Mode
-    shinyDirChoose(input,
-                   "genome_file_multi",
-                   roots = c(Home = path_home(), Root = "/"),
-                   defaultRoot = "Home",
-                   session = session,
-                   filetypes = c('', 'fasta', 'fna', 'fa'))
-    
-    Typing$multi_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)
-    
-    files_selected <- list.files(as.character(Typing$multi_path))
-    Typing$files_filtered <- files_selected[which(!endsWith(files_selected, ".gz") &
-                                                    grepl("\\.fasta|\\.fna|\\.fa", files_selected))]
-    
-    Typing$multi_sel_table <- data.frame(
-      Include = rep(TRUE, length(Typing$files_filtered)),
-      Files = gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", 
-                   Typing$files_filtered),
-      Type = sub(".*(\\.fasta|\\.fasta\\.gz|\\.fna|\\.fna\\.gz|\\.fa|\\.fa\\.gz)$",
-                 "\\1", Typing$files_filtered, perl = F))
-    
-    if(nrow(Typing$multi_sel_table) > 0) {
-      output$multi_select_tab_ctrls <- renderUI(
-        fluidRow(
-          column(1),
-          column(
-            width = 2,
-            align = "left",
-            actionButton(
-              "sel_all_mt",
-              "All",
-              icon = icon("check")
-            )
-          ),
-          column(
-            width = 2,
-            align = "left",
-            actionButton(
-              "desel_all_mt",
-              "None",
-              icon = icon("xmark")
-            )
-          ),
-          column(2),
-          column(
-            width = 5,
-            align = "right",
-            br(),
-            uiOutput("multi_select_issues")
-          )
-        )
-      )
-    } else {
-      output$multi_select_tab_ctrls <- NULL
-    }
-    
-    if(between(nrow(Typing$multi_sel_table), 1, 15)) {
-      output$multi_select_table <- renderRHandsontable({
-        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
-                             stretchH = "all", contextMenu = FALSE
-        ) %>%
-          hot_cols(columnSorting = FALSE) %>%
-          hot_rows(rowHeights = 25) %>%
-          hot_col(2, readOnly = FALSE,
-                  valign = "htBottom") %>%
-          hot_col(3, readOnly = TRUE) %>%
-          hot_col(1,
-                  halign = "htCenter",
-                  valign = "htTop", 
-                  colWidths = 60)
-        
-        htmlwidgets::onRender(rht, sprintf(
-          "function(el, x) {
-        var hot = this.hot;
-        
-        var columnData = hot.getDataAtCol(1); // Change column index if needed
-        var duplicates = {};
-          
-        var highlightInvalidAndDuplicates = function(invalidValues) {
-          
-          var columnData = hot.getDataAtCol(1); // Change column index if needed
-          var duplicates = {};
-
-          // Find all duplicate values
-          for (var i = 0; i < columnData.length; i++) {
-            var value = columnData[i];
-            if (value !== null && value !== undefined) {
-              if (duplicates[value]) {
-                duplicates[value].push(i);
-              } else {
-                duplicates[value] = [i];
-              }
-            }
-          }
-
-          // Reset all cell backgrounds in the column
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            if (cell) {
-              cell.style.background = 'white';
-            }
-          }
-
-          // Highlight duplicates and invalid values
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            var value = columnData[i];
-            if (cell) {
-              if (invalidValues.includes(value)) {
-                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
-              } else if (duplicates[value] && duplicates[value].length > 1) {
-                cell.style.background = '#FF7334'; // Highlight color for duplicates
-              }
-            }
-          }
-        };
-
-        var changefn = function(changes, source) {
-          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
-            highlightInvalidAndDuplicates(%s);
-          }
-        };
-
-        hot.addHook('afterChange', changefn);
-        hot.addHook('afterLoadData', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-        hot.addHook('afterRender', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-
-        highlightInvalidAndDuplicates(%s); // Initial highlight on load
-        
-        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
-          var colData = hot.getDataAtCol(0);
-          for (var i = 0; i < colData.length; i++) {
-            hot.setDataAtCell(i, 0, message.value);
-          }
-          hot.render(); // Re-render the table
-        });
-      }", 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id())))
-      })
-      
-    } else if(nrow(Typing$multi_sel_table) > 15) {
-      output$multi_select_table <- renderRHandsontable({
-        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
-                             stretchH = "all", height = 500,
-                             contextMenu = FALSE
-        ) %>%
-          hot_cols(columnSorting = FALSE) %>%
-          hot_rows(rowHeights = 25) %>%
-          hot_col(2,
-                  readOnly = FALSE,
-                  valign = "htBottom") %>%
-          hot_col(3, readOnly = TRUE) %>%
-          hot_col(1,
-                  halign = "htCenter",
-                  valign = "htTop", 
-                  colWidths = 60)
-        
-        htmlwidgets::onRender(rht, sprintf(
-          "function(el, x) {
-        var hot = this.hot;
-        
-        var columnData = hot.getDataAtCol(1); // Change column index if needed
-        var duplicates = {};
-          
-        var highlightInvalidAndDuplicates = function(invalidValues) {
-          
-          var columnData = hot.getDataAtCol(1); // Change column index if needed
-          var duplicates = {};
-
-          // Find all duplicate values
-          for (var i = 0; i < columnData.length; i++) {
-            var value = columnData[i];
-            if (value !== null && value !== undefined) {
-              if (duplicates[value]) {
-                duplicates[value].push(i);
-              } else {
-                duplicates[value] = [i];
-              }
-            }
-          }
-
-          // Reset all cell backgrounds in the column
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            if (cell) {
-              cell.style.background = 'white';
-            }
-          }
-
-          // Highlight duplicates and invalid values
-          for (var i = 0; i < columnData.length; i++) {
-            var cell = hot.getCell(i, 1); // Change column index if needed
-            var value = columnData[i];
-            if (cell) {
-              if (invalidValues.includes(value)) {
-                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
-              } else if (duplicates[value] && duplicates[value].length > 1) {
-                cell.style.background = '#FF7334'; // Highlight color for duplicates
-              }
-            }
-          }
-        };
-
-        var changefn = function(changes, source) {
-          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
-            highlightInvalidAndDuplicates(%s);
-          }
-        };
-
-        hot.addHook('afterChange', changefn);
-        hot.addHook('afterLoadData', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-        hot.addHook('afterRender', function() {
-          highlightInvalidAndDuplicates(%s);
-        });
-
-        highlightInvalidAndDuplicates(%s); // Initial highlight on load
-        
-        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
-          var colData = hot.getDataAtCol(0);
-          for (var i = 0; i < colData.length; i++) {
-            hot.setDataAtCell(i, 0, message.value);
-          }
-          hot.render(); // Re-render the table
-        });
-      }", 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id()), 
-          jsonlite::toJSON(dupl_mult_id())))
-        
-      })
-      
-    } else {
-      output$multi_select_table <- NULL
-    } 
-  })
-  
-  observeEvent(input$conf_meta_multi, {
-    
-    multi_select_table <- hot_to_r(input$multi_select_table)[hot_to_r(input$multi_select_table)$Include == TRUE,]
-    
-    if(any(unlist(gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", multi_select_table$Files)) %in% unlist(DB$data["Assembly ID"]))) {
-      show_toast(
-        title = "Assembly ID(s) already present",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (any(duplicated(multi_select_table$Files))) {
-      show_toast(
-        title = "Duplicated filename(s)",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (any(multi_select_table$Files == "")) {
-      show_toast(
-        title = "Empty filename(s)",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (any(grepl("[()/\\:*?\"<>|]", multi_select_table$Files))) {
-      show_toast(
-        title = "Invalid filename(s). No special characters allowed: ()/\\:*?\"<>|",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (!any(multi_select_table$Include == TRUE)) {
-      show_toast(
-        title = "No files selected",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
-      show_toast(
-        title = "Empty spaces in filename(s) not allowed",
-        type = "error",
-        position = "bottom-end",
-        timer = 3000
-      )
-    } else if (isFALSE(Typing$reload)) {
-      show_toast(
-        title = "Reload Database first",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if(Screening$status == "started") {
-      show_toast(
-        title = "Pending Single Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      
-      log_print("Multi typing metadata confirmed")
-      
-      meta_info <- data.frame(cgmlst_typing = DB$scheme,
-                              append_isodate = trimws(input$append_isodate_multi),
-                              append_host = trimws(input$append_host_multi),
-                              append_country = trimws(input$append_country_multi),
-                              append_city = trimws(input$append_city_multi),
-                              append_analysisdate = Sys.Date(),
-                              db_directory = getwd())
-      
-      saveRDS(meta_info, paste0(getwd(), "/execute/meta_info.rds"))
-      
-      show_toast(
-        title = "Metadata declared",
-        type = "success",
-        position = "bottom-end",
-        timer = 3000
-      )
-      
-      output$start_multi_typing_ui <- renderUI({
-        div(
-          class = "multi_start_col",
-          column(
-            width = 3,
-            align = "center",
-            br(),
-            br(),
-            h3(p("Start Typing"), style = "color:white"),
-            br(),
-            br(),
-            HTML(
-              paste(
-                "<span style='color: white;'>",
-                "Typing by <strong>",
-                DB$scheme,
-                "</strong> scheme."
-              )
-            ),
-            br(), br(), br(), br(),
-            div(
-              class = "save-assembly",
-              materialSwitch(
-                "save_assembly_mt",
-                h5(p("Save Assemblies in Local Database"), style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
-                value = TRUE,
-                right = TRUE)
-            ),
-            HTML(
-              paste(
-                "<span style='color: orange;font-style:italic'>",
-                "Isolates with unsaved assembly files can NOT be applied to screening for resistance genes."
-              )
-            ),
-            br(), br(), br(), br(),
-            actionButton(
-              "start_typ_multi",
-              "Start",
-              icon = icon("circle-play")
-            )
-          )
-        )
-      })
-    }
-  })
-  
-  #### Events Multi Typing ----
-  
-  observeEvent(input$sel_all_mt, {
-    session$sendCustomMessage(type = "setColumnValue", message = list(value = TRUE))
-  })
-  
-  observeEvent(input$desel_all_mt, {
-    session$sendCustomMessage(type = "setColumnValue", message = list(value = FALSE))
-  })
-  
-  # Print Log
-  output$print_log <- downloadHandler(
-    filename = function() {
-      log_print(paste0("Save multi typing log ", paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")))
-      paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")
-    },
-    content = function(file) {
-      writeLines(readLines(paste0(getwd(), "/logs/script_log.txt")), file)
-    }
-  )
-  
-  # Reset Multi Typing
-  observeEvent(input$reset_multi, {
-    if(!grepl("Multi Typing", tail(readLines(paste0(getwd(),"/logs/script_log.txt")), n = 1))) {
-      showModal(
-        modalDialog(
-          paste0(
-            "A Multi Typing process is still pending. Stopping this process will cancel the processing."
-          ),
-          title = "Reset Multi Typing",
-          fade = TRUE,
-          easyClose = TRUE,
-          footer = tagList(
-            modalButton("Cancel"),
-            actionButton("conf_multi_kill", "Stop", class = "btn btn-danger")
-          )
-        )
-      )
-    } else {
-      
-      log_print("Reset multi typing")
-      
-      # Reset multi typing result list
-      saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
-      multi_help <- FALSE
-      Typing$result_list <- NULL
-      
-      # Null logfile
-      writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
-      
-      # Reset User Feedback variable
-      Typing$pending_format <- 0
-      Typing$multi_started <- FALSE
-      
-      output$initiate_multi_typing_ui <- renderUI({
-        column(
-          width = 4,
-          align = "center",
-          br(),
-          br(),
-          h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-          br(), br(),
-          p(
-            HTML(
-              paste(
-                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
-              )
-            )
-          ),
-          fluidRow(
-            column(1),
-            column(
-              width = 11,
-              align = "center",
-              shinyDirButton(
-                "genome_file_multi",
-                "Browse",
-                icon = icon("folder-open"),
-                title = "Select the folder containing the genome assemblies (FASTA)",
-                buttonType = "default",
-                root = path_home()
-              ),
-              br(),
-              br(),
-              uiOutput("multi_select_info"),
-              br()
-            )
-          ),
-          uiOutput("multi_select_tab_ctrls"),
-          br(),
-          fluidRow(
-            column(1),
-            column(
-              width = 11,
-              align = "left",
-              rHandsontableOutput("multi_select_table")
-            )
-          )
-        )
-      })
-      
-      output$pending_typing <- NULL
-      output$multi_typing_results <- NULL
-    }
-  })
-  
-  # Confirm Reset after 
-  observeEvent(input$conf_multi_kill, {
-    removeModal()
-    
-    log_print("Kill multi typing")
-    
-    # Kill multi typing and reset logfile  
-    system(paste("bash", paste0(getwd(), "/execute/kill_multi.sh")), 
-           wait = TRUE)
-    
-    show_toast(
-      title = "Execution cancelled",
-      type = "warning",
-      position = "bottom-end",
-      timer = 6000
-    )
-    
-    # Kill multi typing and reset logfile  
-    writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
-    
-    #Reset multi typing result list
-    saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
-    multi_help <- FALSE
-    Typing$result_list <- NULL
-    
-    # Reset User Feedback variable
-    Typing$pending_format <- 0
-    output$pending_typing <- NULL
-    output$multi_typing_results <- NULL
-    Typing$failures <- 0
-    Typing$successes <- 0
-    Typing$multi_started <- FALSE
-    
-    output$initiate_multi_typing_ui <- renderUI({
-      column(
-        width = 4,
-        align = "center",
-        br(),
-        br(),
-        h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
-        br(), br(),
-        p(
-          HTML(
-            paste(
-              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
-            )
-          )
-        ),
-        fluidRow(
-          column(1),
-          column(
-            width = 11,
-            align = "center",
-            shinyDirButton(
-              "genome_file_multi",
-              "Browse",
-              icon = icon("folder-open"),
-              title = "Select the folder containing the genome assemblies (FASTA)",
-              buttonType = "default",
-              root = path_home()
-            ),
-            br(),
-            br(),
-            uiOutput("multi_select_info"),
-            br()
-          )
-        ),
-        uiOutput("multi_select_tab_ctrls"),
-        br(),
-        fluidRow(
-          column(1),
-          column(
-            width = 11,
-            align = "left",
-            rHandsontableOutput("multi_select_table")
-          )
-        )
-      )
-    })
-    
-  })
-  
-  observeEvent(input$start_typ_multi, {
-    log_print("Initiate multi typing")
-    
-    if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
-      show_toast(
-        title = "Pending Single Typing",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else if (Screening$status == "started") {
-      show_toast(
-        title = "Pending Gene Screening",
-        type = "warning",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      removeModal()
-      
-      show_toast(
-        title = "Multi Typing started",
-        type = "success",
-        position = "bottom-end",
-        timer = 10000
-      )
-      
-      Typing$new_table <- NULL
-      
-      # Remove Allelic Typing Controls
-      output$initiate_multi_typing_ui <- NULL
-      output$metadata_multi_box <- NULL
-      output$start_multi_typing_ui <- NULL
-      
-      # Activate entry detection
-      DB$check_new_entries <- TRUE
-      
-      # Initiate Feedback variables
-      Typing$multi_started <- TRUE
-      Typing$pending <- TRUE
-      Typing$failures <- 0
-      Typing$successes <- 0
-      
-      # get selected file table
-      multi_select_table <- hot_to_r(input$multi_select_table)
-      
-      filenames <- paste(multi_select_table$Files[which(multi_select_table$Include == TRUE)], collapse = " ")
-      
-      files <- Typing$multi_sel_table$Files[which(multi_select_table$Include == TRUE)]
-      type <- Typing$multi_sel_table$Type[which(multi_select_table$Include == TRUE)]
-      genome_names <- paste(paste0(gsub(" ", "~", files), type), collapse = " ")
-      
-      # Start Multi Typing Script
-      multi_typing_df <- data.frame(
-        db_path = DB$database,
-        wd = getwd(),
-        save = input$save_assembly_mt,
-        scheme = paste0(gsub(" ", "_", DB$scheme)),
-        genome_folder = as.character(parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)),
-        filenames = paste0(filenames, collapse= " "),
-        genome_names = genome_names,
-        alleles = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")
-      )
-      
-      saveRDS(multi_typing_df, "execute/multi_typing_df.rds")
-      
-      # Execute multi blat script  
-      system(paste("bash", paste0(getwd(), "/execute/multi_typing.sh")), wait = FALSE)
-    }
-  })
-  
-  
-  #### User Feedback ----
-  
-  observe({
-    if(file.exists(paste0(getwd(), "/logs/script_log.txt"))) {
-      if(Typing$multi_started == TRUE) {
-        check_multi_status()
-      } else {
-        Typing$status <- "Inactive"
-      }
-    }
-  })
-  
-  check_multi_status <- reactive({
-    
-    invalidateLater(3000, session)
-    
-    log <- readLines(paste0(getwd(), "/logs/script_log.txt"))
-    
-    # Determine if Single or Multi Typing
-    if(str_detect(log[1], "Multi")) {
-      Typing$pending_mode <- "Multi"
-    } else {
-      Typing$pending_mode <- "Single"
-    }
-    
-    # Check typing status
-    if(str_detect(tail(log, 1), "Attaching")) {
-      Typing$status <- "Attaching"
-    } else if(str_detect(tail(log, 1), "Successful")) {
-      Typing$multi_help <- TRUE
-      Typing$status <- "Successful"
-      show_toast(
-        title = paste0("Successful", sub(".*Successful", "", tail(log, 1))),
-        type = "success",
-        position = "bottom-end",
-        timer = 8000
-      )
-    } else if(str_detect(tail(log, 1), "failed")) {
-      Typing$status <- "Failed"
-      show_toast(
-        title = sub(".* - ", "", tail(log, 1)),
-        type = "error",
-        position = "bottom-end",
-        timer = 8000
-      )
-    } else if(str_detect(tail(log, 1), "Processing")) {
-      Typing$status <- "Processing"
-      
-      if(any(str_detect(tail(log, 2), "Successful"))) {
-        
-        if(!identical(Typing$last_success, tail(log, 2)[1])) {
-          Typing$multi_help <- TRUE
-          show_toast(
-            title = paste0("Successful", sub(".*Successful", "", tail(log, 2)[1])),
-            type = "success",
-            position = "bottom-end",
-            timer = 8000
-          )
-          
-          Typing$last_success <- tail(log, 2)[1]
-        }
-      } else if(any(str_detect(tail(log, 2), "failed"))) {
-        
-        if(!identical(Typing$last_failure, tail(log, 2)[1])) {
-          
-          show_toast(
-            title = sub(".* - ", "", tail(log, 2)[1]),
-            type = "error",
-            position = "bottom-end",
-            timer = 8000
-          )
-          
-          Typing$last_failure <- tail(log, 2)[1]
-        }
-      }
-    } else if(str_detect(tail(log, 1), "finalized")) {
-      Typing$multi_help <- TRUE
-      Typing$status <- "Finalized"
-      
-      if(Typing$pending == TRUE) {
-        show_toast(
-          title = "Typing finalized",
-          type = "success",
-          position = "bottom-end",
-          timer = 8000
-        )
-        
-        Typing$pending <- FALSE
-      }
-    }
-  })
-  
-  ##### Render Multi Typing UI Feedback ----
-  
-  observe({
-    if(!is.null(input$multi_results_picker)) {
-      Typing$multi_table_length <- nrow(Typing$result_list[[input$multi_results_picker]])
-    } else {
-      Typing$multi_table_length <- NULL
-    }
-  })
-  
-  observe({
-    if(!is.null(Typing$result_list)) {
-      if(length(Typing$result_list) > 0) {
-        if(is.null(Typing$multi_table_length)) {
-          output$multi_typing_result_table <- renderRHandsontable({
-            rhandsontable(Typing$result_list[[input$multi_results_picker]], 
-                          rowHeaders = NULL, stretchH = "all",
-                          readOnly = TRUE, contextMenu = FALSE) %>%
-              hot_rows(rowHeights = 25) %>%
-              hot_col(1:3, valign = "htMiddle", halign = "htCenter",
-                      cellWidths = list(100, 160, NULL)) %>%
-              hot_col("Value", renderer=htmlwidgets::JS(
-                "function(instance, td, row, col, prop, value, cellProperties) {
-                  if (value.length > 8) {
-                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                  }
-                  td.innerHTML = value;
-                  td.style.textAlign = 'center';
-                  return td;
-                 }"
-              ))
-            })
-          
-        } else {
-          if(Typing$multi_table_length > 15) {
-            output$multi_typing_result_table <- renderRHandsontable({
-              rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
-                            stretchH = "all", height = 500,
-                            readOnly = TRUE, contextMenu = FALSE) %>%
-                hot_rows(rowHeights = 25) %>%
-                hot_col(1:3, valign = "htMiddle", halign = "htCenter",
-                        cellWidths = list(100, 160, NULL)) %>%
-                hot_col("Value", renderer=htmlwidgets::JS(
-                  "function(instance, td, row, col, prop, value, cellProperties) {
-                  if (value.length > 8) {
-                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                  }
-                  td.innerHTML = value;
-                  td.style.textAlign = 'center';
-                  return td;
-                 }"
-                ))
-              })
-          } else {
-            output$multi_typing_result_table <- renderRHandsontable({
-              rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
-                            stretchH = "all", readOnly = TRUE,
-                            contextMenu = FALSE) %>%
-                hot_rows(rowHeights = 25) %>%
-                hot_col(1:3, valign = "htMiddle", halign = "htCenter",
-                        cellWidths = list(100, 160, NULL)) %>%
-                hot_col("Value", renderer=htmlwidgets::JS(
-                  "function(instance, td, row, col, prop, value, cellProperties) {
-                  if (value.length > 8) {
-                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
-                  }
-                  td.innerHTML = value;
-                  td.style.textAlign = 'center';
-                  return td;
-                 }"
-                ))
-              })
-          }
-        }
-      } else {
-        output$multi_typing_result_table <- NULL
-      }
-    } else {
-      output$multi_typing_result_table <- NULL
-    }
-  })
-  
-  observe({
-    if(!is.null(Typing$multi_result_status)) {
-      if(Typing$multi_result_status == "start" | Typing$multi_result_status == "finalized"){
-        
-        if(Typing$multi_help == TRUE) {
-          Typing$result_list <- readRDS(paste0(getwd(), "/execute/event_list.rds"))
-          Typing$multi_help <- FALSE
-        }
-      } 
-    }
-  })
-  
-  
-  observe({
-    #Render multi typing result feedback table
-    
-    if(!is.null(Typing$result_list)) {
-      if(length(Typing$result_list) > 0) {
-        output$multi_typing_results <- renderUI({
-          column(
-            width = 12,
-            fluidRow(
-              column(1),
-              column(
-                width = 9,
-                br(), br(),
-                br(), br(),
-                br(), 
-                div(
-                  class = "mult_res_sel",
-                  selectInput(
-                    "multi_results_picker",
-                    label = h5("Select Typing Results", style = "color:white"),
-                    choices = names(Typing$result_list),
-                    selected = names(Typing$result_list)[length(names(Typing$result_list))],
-                  )
-                ),
-                br(), br()
-              )
-            ),
-            rHandsontableOutput("multi_typing_result_table")
-          )
-        })
-      }
-    }
-  })
-  
-  observe({
-    
-    # Render log content
-    output$logText <- renderPrint({
-      cat(rev(paste0(tail(readLogFile(), 50), "\n")))
-    })
-    
-    output$logTextFull <- renderPrint({
-      cat(rev(paste0(readLines(paste0(getwd(), "/logs/script_log.txt")), "\n")))
-    })
-    
-    # Render Pending UI
-    if(!grepl("Multi Typing", tail(readLogFile(), n = 1)) & grepl("Start Multi Typing", head(readLogFile(), n = 1))) {
-      
-      Typing$multi_result_status <- "start"
-      
-      output$initiate_multi_typing_ui <- NULL
-      
-      output$pending_typing <- renderUI({
-        fluidRow(
-          fluidRow(
-            br(), br(),
-            column(width = 2),
-            column(
-              width = 4,
-              h3(p("Pending Typing ..."), style = "color:white"),
-              br(), br(),
-              fluidRow(
-                column(
-                  width = 5,
-                  HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:24px;color:white;margin-top:5px"></i>'))
-                ),
-                column(
-                  width = 6,
-                  align = "left",
-                  actionButton(
-                    "reset_multi",
-                    "Terminate",
-                    icon = icon("ban")
-                  )
-                )
-              ),
-            )
-          ),
-          br(), br(),
-          fluidRow(
-            column(width = 2),
-            column(
-              width = 10,
-              verbatimTextOutput("logText")
-            )  
-          )
-        )
-      })
-    } else if(grepl("Multi Typing finalized", tail(readLogFile(), n = 1))) {
-      
-      Typing$multi_result_status <- "finalized"
-      
-      Typing$last_scheme <- NULL
-      
-      output$initiate_multi_typing_ui <- NULL
-      
-      output$pending_typing <- renderUI({
-        
-        fluidRow(
-          fluidRow(
-            br(), br(),
-            column(width = 2),
-            column(
-              width = 4,
-              h3(p("Pending Multi Typing ..."), style = "color:white"),
-              br(), br(),
-              HTML(paste("<span style='color: white;'>", 
-                         paste("Typing of", sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "Processing")), "assemblies finalized."),
-                         paste(sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "Successful")), "successes."),
-                         paste(sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "failed")), "failures."),
-                         "Reset to start another typing process.", 
-                         sep = '<br/>')),
-              br(), br(),
-              fluidRow(
-                column(
-                  width = 5,
-                  actionButton(
-                    "reset_multi",
-                    "Reset",
-                    icon = icon("arrows-rotate")
-                  )
-                ),
-                column(
-                  width = 5,
-                  downloadButton(
-                    "print_log",
-                    "Logfile",
-                    icon = icon("floppy-disk")
-                  )
-                )
-              )
-            )
-          ),
-          br(), br(),
-          fluidRow(
-            column(width = 2),
-            column(
-              width = 10,
-              verbatimTextOutput("logTextFull"),
-            )
-          )
-        )
-      })
-    } else if (!grepl("Start Multi Typing", head(readLogFile(), n = 1))){
-      output$pending_typing <- NULL
-      Typing$multi_result_status <- "idle"
-    }
-  })
-  
-  observe({
-    # Get selected Genome in Multi Mode
-    shinyDirChoose(input,
-                   "hash_dir",
-                   roots = c(Home = path_home(), Root = "/"),
-                   defaultRoot = "Home",
-                   session = session,
-                   filetypes = c('', 'fasta', 'fna', 'fa'))
-  })
-  
-  observeEvent(input$hash_start, {
-    dir_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$hash_dir)
-    if (!is_empty(list.files(dir_path)) && all(endsWith(list.files(dir_path), ".fasta"))) {
-      log_print("Hashing directory using utilities")
-      shinyjs::hide("hash_start")
-      shinyjs::show("hash_loading")
-      show_toast(
-        title = "Hashing started!",
-        type = "success",
-        position = "bottom-end",
-        timer = 6000
-      )
-      hash_database(dir_path)
-      shinyjs::hide("hash_loading")
-      shinyjs::show("hash_start")
-      show_toast(
-        title = "Hashing completed!",
-        type = "success",
-        position = "bottom-end",
-        timer = 6000
-      )
-    } else {
-      show_toast(
-        title = "Incorrect folder selected!",
-        type = "error",
-        position = "bottom-end",
-        timer = 6000
-      )
-    }
-  })
-  
-} # end server
-
-# _______________________ ####
-
-# Shiny ----
-
-shinyApp(ui = ui, server = server)
+######## PhyloTrace #########
+
+# _______________________ ####
+# CRAN Packages
+library(shiny)
+library(R.utils)
+library(igraph)
+library(shinyWidgets)
+library(shinydashboard)
+library(dashboardthemes)
+library(ggplot2)
+library(ggnewscale)
+library(ggplotify) 
+library(ape)
+library(tidyverse)
+library(rlang)
+library(tidytree)
+library(shinyFiles)
+library(dplyr)
+library(downloader)
+library(rvest)
+library(rmarkdown)
+library(knitr)
+library(kableExtra)
+library(fs)
+library(data.table)
+library(zoo)
+library(ggnetwork)
+library(rhandsontable)
+library(visNetwork)
+library(proxy)
+library(phangorn)
+library(cowplot)
+library(viridis)
+library(RColorBrewer)
+library(bslib)
+library(bsicons)
+library(DT)
+library(shinyBS)
+library(openssl)
+library(logr)
+# Bioconductor Packages
+library(treeio)
+library(ggtree)
+library(ggtreeExtra)
+
+source(paste0(getwd(), "/www/resources.R"))
+
+options(ignore.negative.edge=TRUE)
+
+# User Interface ----
+
+ui <- dashboardPage(
+  
+  title = "PhyloTrace 1.5.0",
+  
+  # Title
+  dashboardHeader(
+    
+    title = span(
+      div(
+        class = "img_logo",
+        img(
+          src = "PhyloTrace.jpg", width = 190
+        )
+      )
+    ),
+    uiOutput("loaded_scheme"),
+    uiOutput("databasetext"),
+    uiOutput("statustext"),
+    tags$li(class = "dropdown", 
+            tags$span(id = "currentTime", style = "color:white; font-weight:bold;")),
+    disable = FALSE
+  ),
+  
+  ## Sidebar ----
+  dashboardSidebar(
+    tags$head(includeCSS("www/head.css")),
+    tags$style(includeCSS("www/body.css")),
+    tags$style(HTML(
+      "@keyframes pulsate {
+          0% { transform: scale(1); }
+          50% { transform: scale(1.1); }
+          100% { transform: scale(1); }
+        }
+        .pulsating-button {
+          animation: pulsate 1s ease infinite;
+        }
+        .pulsating-button:hover {
+          animation: none;
+        }")),
+    br(), br(),
+    sidebarMenu(
+      id = "tabs",
+      sidebarMenuOutput("menu"),
+      uiOutput("menu_sep2"),
+      conditionalPanel(
+        "input.tabs==='db_browse_entries'",
+        uiOutput("entrytable_sidebar")
+      ),
+      conditionalPanel(
+        "input.tabs==='db_distmatrix'",
+        uiOutput("distmatrix_sidebar")
+      ),
+      conditionalPanel(
+        "input.tabs==='db_missing_values'",
+        uiOutput("missing_values_sidebar")
+      ),
+      conditionalPanel(
+        "input.tabs==='typing'",
+        uiOutput("typing_sidebar")
+      ),
+      conditionalPanel(
+        "input.tabs==='visualization'",
+        uiOutput("visualization_sidebar")
+      ),
+      conditionalPanel(
+        "input.tabs==='gs_profile'",
+        uiOutput("screening_sidebar")
+      )
+    )
+  ),
+  
+  dashboardBody(
+    tags$head(tags$link(rel = "shortcut icon", href = "favicon.ico")),
+    shinyjs::useShinyjs(),
+    
+    shinyDashboardThemeDIY(
+      ### general
+      appFontFamily = "Liberation Sans",
+      appFontColor = "#000000",
+      primaryFontColor = "#ffffff",
+      infoFontColor = "rgb(0,0,0)",
+      successFontColor = "rgb(0,0,0)",
+      warningFontColor = "rgb(0,0,0)",
+      dangerFontColor = "rgb(0,0,0)",
+      bodyBackColor = cssGradientThreeColors(
+        direction = "down",
+        colorStart = "#282f38",
+        colorMiddle = "#384454",
+        colorEnd = "#495d78",
+        colorStartPos = 0,
+        colorMiddlePos = 50,
+        colorEndPos = 100
+      ),
+      
+      ### header
+      logoBackColor = "#282f38",
+      headerButtonBackColor = "#282f38",
+      headerButtonIconColor = "#18ece1",
+      headerButtonBackColorHover = "#282f38",
+      headerButtonIconColorHover = "#ffffff",
+      headerBackColor = "#282f38",
+      headerBoxShadowColor = "#aaaaaa",
+      headerBoxShadowSize = "0px 0px 0px",
+      
+      ### sidebar
+      sidebarBackColor = cssGradientThreeColors(
+        direction = "down",
+        colorStart = "#282f38",
+        colorMiddle = "#384454",
+        colorEnd = "#495d78",
+        colorStartPos = 0,
+        colorMiddlePos = 50,
+        colorEndPos = 100),
+      
+      sidebarPadding = 0,
+      sidebarMenuBackColor = "transparent",
+      sidebarMenuPadding = 0,
+      sidebarMenuBorderRadius = 0,
+      sidebarShadowRadius = "5px 5px 5px",
+      sidebarShadowColor = "#282f38",
+      sidebarUserTextColor = "#ffffff",
+      sidebarSearchBackColor = "rgb(55,72,80)",
+      sidebarSearchIconColor = "rgb(153,153,153)",
+      sidebarSearchBorderColor = "rgb(55,72,80)",
+      sidebarTabTextColor = "rgb(255,255,255)",
+      sidebarTabTextSize = 15,
+      sidebarTabBorderStyle = "none none solid none",
+      sidebarTabBorderColor = "rgb(35,106,135)",
+      sidebarTabBorderWidth = 0,
+      sidebarTabBackColorSelected = cssGradientThreeColors(
+        direction = "right",
+        colorStart = "rgba(44,222,235,1)",
+        colorMiddle = "rgba(44,222,235,1)",
+        colorEnd = "rgba(0,255,213,1)",
+        colorStartPos = 0,
+        colorMiddlePos = 30,
+        colorEndPos = 100
+      ),
+      sidebarTabTextColorSelected = "rgb(0,0,0)",
+      sidebarTabRadiusSelected = "0px 0px 0px 0px",
+      sidebarTabBackColorHover = cssGradientThreeColors(
+        direction = "right",
+        colorStart = "rgba(44,222,235,1)",
+        colorMiddle = "rgba(44,222,235,1)",
+        colorEnd = "rgba(0,255,213,1)",
+        colorStartPos = 0,
+        colorMiddlePos = 30,
+        colorEndPos = 100
+      ),
+      sidebarTabTextColorHover = "rgb(50,50,50)",
+      sidebarTabBorderStyleHover = "none none solid none",
+      sidebarTabBorderColorHover = "rgb(75,126,151)",
+      sidebarTabBorderWidthHover = 0,
+      sidebarTabRadiusHover = "0px 0px 0px 0px",
+      
+      ### boxes
+      boxBackColor = "#ffffff",
+      boxBorderRadius = 7,
+      boxShadowSize = "0px 0px 0px",
+      boxShadowColor = "#ffffff",
+      boxTitleSize = 20,
+      boxDefaultColor = "#00a65a",
+      boxPrimaryColor = "#ffffff",
+      boxInfoColor = "#00a65a",
+      boxSuccessColor = "#00a65a",
+      boxWarningColor = "#ffffff",
+      boxDangerColor = "#ffffff",
+      tabBoxTabColor = "#ffffff",
+      tabBoxTabTextSize = 14,
+      tabBoxTabTextColor = "rgb(0,0,0)",
+      tabBoxTabTextColorSelected = "rgb(0,0,0)",
+      tabBoxBackColor = "#ffffff",
+      tabBoxHighlightColor = "#ffffff",
+      tabBoxBorderRadius = 5,
+      
+      ### inputs
+      buttonBackColor = "#282F38",
+      buttonTextColor = "#ffffff",
+      buttonBorderColor = "#282F38",
+      buttonBorderRadius = 5,
+      buttonBackColorHover = cssGradientThreeColors(
+        direction = "right",
+        colorStart = "rgba(44,222,235,1)",
+        colorMiddle = "rgba(44,222,235,1)",
+        colorEnd = "rgba(0,255,213,1)",
+        colorStartPos = 0,
+        colorMiddlePos = 30,
+        colorEndPos = 100
+      ),
+      buttonTextColorHover = "#000000",
+      buttonBorderColorHover = "transparent",
+      textboxBackColor = "#ffffff",
+      textboxBorderColor = "#ffffff",
+      textboxBorderRadius = 5,
+      textboxBackColorSelect = "#ffffff",
+      textboxBorderColorSelect = "#000000",
+      
+      ### tables
+      tableBackColor = "rgb(255,255,255)",
+      tableBorderColor = "rgb(240,240,240)",
+      tableBorderTopSize = 1,
+      tableBorderRowSize = 1
+    ),
+    
+    uiOutput("start_message"),
+    
+    tabItems(
+      
+      ## Tab Database ----
+      
+      ### Tab Browse Entries ----
+      
+      tabItem(
+        tabName = "db_browse_entries",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Browse Local Database"), style = "color:white")
+          )
+        ),
+        hr(), br(),
+        br(),
+        br(),
+        uiOutput("no_scheme_entries"),
+        uiOutput("db_no_entries"),
+        uiOutput("entry_table_controls"),
+        br(), br(),
+        fluidRow(
+          column(1),
+          column(
+            width = 8,
+            uiOutput("db_entries_table")
+          ),
+          column(
+            width = 3,
+            align = "left",
+            uiOutput("delete_box"),
+            uiOutput("compare_allele_box"),
+            uiOutput("download_entries"),
+            br(), br(), br(), br(), br(), br(), br(), br(),
+            br(), br(), br(), br(), br(), br(), br()
+          )
+        ),
+        br()
+      ),
+      
+      ### Tab Scheme Info  ----  
+      
+      tabItem(
+        tabName = "db_schemeinfo",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Scheme Info"), style = "color:white")
+          )
+        ),
+        hr(), br(), br(), br(),
+        uiOutput("no_scheme_info"),
+        fluidRow(
+          column(2),
+          column(
+            width = 7,
+            align = "center",
+            fluidRow(
+              column(
+                width = 7,
+                align = "right",
+                uiOutput("scheme_header")
+              ),
+              column(
+                width = 2,
+                align = "left",
+                uiOutput("download_scheme_info")
+              )
+            ),
+            br(),
+            br(),
+            uiOutput("scheme_info")
+          )
+        )
+      ),
+      
+      ### Tab Loci Info  ----  
+      
+      tabItem(
+        tabName = "db_loci_info",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Loci Info"), style = "color:white")
+          )
+        ),
+        hr(), br(), br(), br(),
+        fluidRow(
+          column(1),
+          column(
+            width = 10,
+            align = "center",
+            fluidRow(
+              column(
+                width = 6,
+                align = "right",
+                uiOutput("loci_header")
+              ),
+              column(
+                width = 2,
+                align = "left",
+                uiOutput("download_loci")
+              )
+            ),
+            br(),
+            div(class = "loci_table",
+                dataTableOutput("db_loci"))
+          )
+        ),
+        br(), br(),
+        fluidRow(
+          column(1),
+          uiOutput("sequence_selector"), 
+          column(1),
+          column(
+            width = 7,
+            br(),
+            uiOutput("loci_sequences")
+          )
+        )
+      ),
+      
+      ### Tab Distance Matrix  ----  
+      
+      tabItem(
+        tabName = "db_distmatrix",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Distance Matrix"), style = "color:white")
+          )
+        ),
+        hr(), br(), br(), br(),
+        uiOutput("no_scheme_distancematrix"),
+        uiOutput("distancematrix_no_entries"),
+        fluidRow(
+          column(1),
+          uiOutput("distmatrix_show")
+        ),
+        br(), br()
+      ),
+      
+      ### Tab Missing Values ----
+      
+      tabItem(
+        tabName = "db_missing_values",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Missing Values"), style = "color:white")
+          )
+        ),
+        hr(), br(), br(), br(),
+        fluidRow(
+          column(
+            width = 3,
+            uiOutput("missing_values"),
+            fluidRow(
+              column(
+                width = 2,
+                div(
+                  class = "rectangle-red-space" 
+                )
+              ),
+              column(
+                width = 10,
+                align = "left",
+                p(
+                  HTML(
+                    paste(
+                      tags$span(style="color: white; font-size: 15px; margin-left: 75px; position: relative; bottom: -12px", " =  ≥ 5% of loci missing")
+                    )
+                  )
+                )
+              )
+            )
+          ),
+          column(
+            width = 8,
+            rHandsontableOutput("table_missing_values")
+          )
+        )
+      ),
+      
+      ## Tab Manage Schemes  ----  
+      
+      tabItem(
+        tabName = "init",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Select cgMLST Scheme"), style = "color:white")
+          )
+        ),
+        hr(),
+        fluidRow(
+          column(1),
+          column(
+            width = 3,
+            br(),
+            br(),
+            br(),
+            pickerInput(
+              inputId = "select_cgmlst",
+              label = NULL,
+              choices = list(
+                "Acinetobacter baumanii",
+                "Bacillus anthracis",
+                "Bordetella pertussis",
+                "Brucella melitensis",
+                "Brucella spp.",
+                "Burkholderia mallei (FLI)",
+                "Burkholderia mallei (RKI)",
+                "Burkholderia pseudomallei",
+                "Campylobacter jejuni/coli",
+                "Clostridioides difficile",
+                "Clostridium perfringens",
+                "Corynebacterium diphtheriae",
+                "Cronobacter sakazakii/malonaticus",
+                "Enterococcus faecalis",
+                "Enterococcus faecium",
+                "Escherichia coli",
+                "Francisella tularensis",
+                "Klebsiella oxytoca sensu lato",
+                "Klebsiella pneumoniae sensu lato",
+                "Legionella pneumophila",
+                "Listeria monocytogenes",
+                "Mycobacterium tuberculosis complex",
+                "Mycobacteroides abscessus",
+                "Mycoplasma gallisepticum",
+                "Paenibacillus larvae",
+                "Pseudomonas aeruginosa",
+                "Salmonella enterica",
+                "Serratia marcescens",
+                "Staphylococcus aureus",
+                "Staphylococcus capitis",
+                "Streptococcus pyogenes"
+              ),
+              width = "300px",
+              options = list(
+                `live-search` = TRUE,
+                `actions-box` = TRUE,
+                size = 10,
+                style = "background-color: white; border-radius: 5px;"
+              ),
+              multiple = FALSE
+            )
+          ),
+          column(
+            width = 2,
+            br(),
+            br(),
+            br(),
+            h5(textOutput("scheme_update_info"), style = "color: white")
+          ),
+          column(
+            width = 2,
+            br(),
+            br(),
+            br(),
+            actionButton(
+              "download_cgMLST",
+              label = "Download",
+              icon = icon("download")
+            ),
+            shinyjs::hidden(
+              div(id = "loading",
+                  HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
+            )
+          )
+        ),
+        fluidRow(
+          column(1),
+          column(
+            width = 6,
+            align = "center",
+            br(),
+            br(),
+            br(),
+            addSpinner(
+              tableOutput("cgmlst_scheme"),
+              spin = "dots",
+              color = "#ffffff"
+            )
+          )
+        )
+      ),
+      
+      
+      
+      ## Tab Allelic Typing ----------------------------------------------
+      
+      
+      tabItem(
+        tabName = "typing",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Generate Allelic Profile"), style = "color:white")
+          )
+        ),
+        hr(),
+        uiOutput("typing_no_db"),
+        conditionalPanel(
+          "input.typing_mode == 'Single'",
+          fluidRow(
+            uiOutput("initiate_typing_ui"),
+            uiOutput("single_typing_progress"),
+            column(1),
+            uiOutput("metadata_single_box"),
+            column(1),
+            uiOutput("start_typing_ui")
+          )
+        ),
+        conditionalPanel(
+          "input.typing_mode == 'Multi'",
+          fluidRow(
+            uiOutput("initiate_multi_typing_ui"),
+            uiOutput("multi_stop"),
+            column(1),
+            uiOutput("metadata_multi_box"),
+            column(1),
+            uiOutput("start_multi_typing_ui")
+          ),
+          fluidRow(
+            column(
+              width = 6,
+              uiOutput("pending_typing")
+            ),
+            column(
+              width = 6,
+              uiOutput("multi_typing_results")
+            )
+          )
+        )
+      ),
+      
+      
+      ## Tab Visualization -------------------------------------------------------
+      
+      
+      tabItem(
+        tabName = "visualization",
+        fluidRow(
+          tags$script(src = "javascript_functions.js"),
+          column(
+            width = 12,
+            align = "center",
+            br(),
+            conditionalPanel(
+              "input.tree_algo=='Minimum-Spanning'",
+              uiOutput("mst_field")
+            ),
+            conditionalPanel(
+              "input.tree_algo=='Neighbour-Joining'",
+              uiOutput("nj_field")
+            ),
+            conditionalPanel(
+              "input.tree_algo=='UPGMA'",
+              uiOutput("upgma_field")
+            )
+          )
+        ),
+        br(),
+        hr(),
+        
+        ### Control panels MST ----
+        conditionalPanel(
+          "input.tree_algo=='Minimum-Spanning'",
+          fluidRow(
+            column(
+              width = 4,
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "100%",
+                height = "500px",
+                h3(p("Layout"), style = "color:white; position:relative; right:-15px"),
+                hr(),
+                fluidRow(
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Title"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          textInput(
+                            "mst_title",
+                            label = "",
+                            width = "100%",
+                            placeholder = "Plot Title"
+                          ),
+                          fluidRow(
+                            column(
+                              width = 7,
+                              colorPickr(
+                                inputId = "mst_title_color",
+                                selected = "#000000",
+                                label = "",
+                                update = "changestop",
+                                interaction = list(clear = FALSE,
+                                                   save = FALSE),
+                                position = "right-start",
+                                width = "100%"
+                              )
+                            ),
+                            column(
+                              width = 5,
+                              dropMenu(
+                                actionBttn(
+                                  "mst_title_menu",
+                                  label = "",
+                                  color = "default",
+                                  size = "sm",
+                                  style = "material-flat",
+                                  icon = icon("sliders")
+                                ),
+                                placement = "top-start",
+                                theme = "translucent",
+                                numericInput(
+                                  "mst_title_size",
+                                  label = h5("Size", style = "color:white; margin-bottom: 0px;"),
+                                  value = 40,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Subtitle"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          textInput(
+                            "mst_subtitle",
+                            label = "",
+                            width = "100%",
+                            placeholder = "Plot Subtitle"
+                          ),
+                          fluidRow(
+                            column(
+                              width = 7,
+                              colorPickr(
+                                inputId = "mst_subtitle_color",
+                                selected = "#000000",
+                                label = "",
+                                update = "changestop",
+                                interaction = list(clear = FALSE,
+                                                   save = FALSE),
+                                position = "right-start",
+                                width = "100%"
+                              )
+                            ),
+                            column(
+                              width = 5,
+                              dropMenu(
+                                actionBttn(
+                                  "mst_subtitle_menu",
+                                  label = "",
+                                  color = "default",
+                                  size = "sm",
+                                  style = "material-flat",
+                                  icon = icon("sliders")
+                                ),
+                                placement = "top-start",
+                                theme = "translucent",
+                                numericInput(
+                                  "mst_subtitle_size",
+                                  label = h5("Size", style = "color:white; margin-bottom: 0px;"),
+                                  value = 20,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                ),
+                hr(),
+                fluidRow(
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Legend"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 7,
+                              colorPickr(
+                                inputId = "mst_legend_color",
+                                selected = "#000000",
+                                label = "",
+                                update = "changestop",
+                                interaction = list(clear = FALSE,
+                                                   save = FALSE),
+                                position = "right-start",
+                                width = "100%"
+                              )
+                            ),
+                            column(
+                              width = 5,
+                              dropMenu(
+                                actionBttn(
+                                  "mst_legend_menu",
+                                  label = "",
+                                  color = "default",
+                                  size = "sm",
+                                  style = "material-flat",
+                                  icon = icon("sliders")
+                                ),
+                                placement = "top-start",
+                                theme = "translucent",
+                                fluidRow(
+                                  column(
+                                    width = 11,
+                                    sliderInput(
+                                      "mst_font_size",
+                                      label = h5("Font Size", style = "color:white; margin-bottom: 0px;"),
+                                      value = 18,
+                                      min = 15,
+                                      max = 30,
+                                      step = 1,
+                                      ticks = FALSE,
+                                      width = "180px"
+                                    )
+                                  ),
+                                  column(1)
+                                ),
+                                br(),
+                                fluidRow(
+                                  column(
+                                    width = 11,
+                                    sliderInput(
+                                      "mst_symbol_size",
+                                      label = h5("Key Size", style = "color:white; margin-bottom: 0px;"),
+                                      value = 20,
+                                      min = 10,
+                                      max = 30,
+                                      step = 1,
+                                      ticks = FALSE,
+                                      width = "180px"
+                                    )
+                                  ),
+                                  column(1)
+                                )
+                              )
+                            )
+                          ),
+                          fluidRow(
+                            column(
+                              width = 7,
+                              selectInput(
+                                "mst_legend_ori",
+                                label = "",
+                                width = "100%",
+                                choices = c("Left" = "left", "Right" = "right")
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Background"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "left",
+                              div(
+                                class = "mat-switch-mst-nodes",
+                                materialSwitch(
+                                  "mst_background_transparent",
+                                  h5(p("Transparent"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            )
+                          ),
+                          fluidRow(
+                            column(
+                              width = 7,
+                              colorPickr(
+                                inputId = "mst_background_color",
+                                width = "100%",
+                                selected = "#ffffff",
+                                label = "",
+                                update = "changestop",
+                                interaction = list(clear = FALSE,
+                                                   save = FALSE),
+                                position = "right-start"
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            column(
+              width = 4,
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "100%",
+                height = "500px",
+                h3(p("Nodes"), style = "color:white; position:relative; right:-15px"),
+                hr(),
+                fluidRow(
+                  column(
+                    width = 6,
+                    column(
+                      width = 12,
+                      align = "left",
+                      h4(p("Label"), style = "color:white;")
+                    ),
+                    column(
+                      width = 12,
+                      align = "center",
+                      div(
+                        class = "label_sel",
+                        uiOutput("mst_node_label")
+                      ),
+                      fluidRow(
+                        column(
+                          width = 7,
+                          colorPickr(
+                            inputId = "node_font_color",
+                            width = "100%",
+                            selected = "#000000",
+                            label = "",
+                            update = "changestop",
+                            interaction = list(clear = FALSE,
+                                               save = FALSE),
+                            position = "right-start"
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          dropMenu(
+                            actionBttn(
+                              "mst_label_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            numericInput(
+                              "node_label_fontsize",
+                              label = h5("Size", style = "color:white; margin-bottom: 0px;"),
+                              value = 14,
+                              min = 8,
+                              max = 30,
+                              step = 1,
+                              width = "80px"
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Color"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 10,
+                              align = "left",
+                              div(
+                                class = "mat-switch-mst-nodes",
+                                materialSwitch(
+                                  "mst_color_var",
+                                  h5(p("Add Variable"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            column(
+                              width = 2,
+                              bslib::tooltip(
+                                bsicons::bs_icon("info-circle", title = "Only categorical variables can \nbe mapped to the node color", color = "white", 
+                                                 height = "12px", width = "12px", position = "relative", top = "27px", right = "56px"),
+                                "Text shown in the tooltip.",
+                                show = FALSE,
+                                id = "mst_node_col_info"
+                              )
+                            )
+                          ),
+                          uiOutput("mst_color_mapping")
+                        )
+                      )
+                    ), br()
+                  )
+                ),
+                hr(),
+                fluidRow(
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Size"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "left",
+                              div(
+                                class = "mat-switch-mst-nodes",
+                                materialSwitch(
+                                  "scale_nodes",
+                                  h5(p("Scale by Duplicates"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                  value = TRUE,
+                                  right = TRUE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    column(
+                      width = 12,
+                      align = "left",
+                      fluidRow(
+                        column(
+                          width = 3,
+                          align = "left",
+                          conditionalPanel(
+                            "input.scale_nodes==true",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Range')
+                              )
+                            )
+                          ),
+                          conditionalPanel(
+                            "input.scale_nodes==false",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Size')
+                              )
+                            )
+                          )
+                        ),
+                        column(
+                          width = 9,
+                          align = "center",
+                          conditionalPanel(
+                            "input.scale_nodes==true",
+                            div(
+                              class = "mst_scale_slider",
+                              sliderInput(
+                                "mst_node_scale",
+                                label = "",
+                                min = 1,
+                                max = 80,
+                                value = c(20, 40),
+                                ticks = FALSE
+                              )
+                            )
+                          ),
+                          conditionalPanel(
+                            "input.scale_nodes==false",
+                            div(
+                              class = "mst_scale_slider",
+                              sliderInput(
+                                inputId = "mst_node_size",
+                                label = "",
+                                min = 1,
+                                max = 100,
+                                value = 30,
+                                ticks = FALSE
+                              ) 
+                            )
+                          )
+                        )
+                      ),
+                      br()
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Other Elements"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "left",
+                              div(
+                                class = "mat-switch-mst-nodes",
+                                materialSwitch(
+                                  "mst_shadow",
+                                  h5(p("Show Shadow"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                  value = TRUE,
+                                  right = TRUE
+                                )
+                              ),
+                              fluidRow(
+                                column(
+                                  width = 3,
+                                  align = "left",
+                                  HTML(
+                                    paste(
+                                      tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Shape')
+                                    )
+                                  )
+                                ),
+                                column(
+                                  width = 9,
+                                  align = "center",
+                                  div(
+                                    class = "mst_shape_sel",
+                                    selectInput(
+                                      "mst_node_shape",
+                                      "",
+                                      choices = list(`Label inside` = c("Circle" = "circle", "Box" = "box", "Text" = "text"),
+                                                     `Label outside` = c("Diamond" = "diamond", "Hexagon" = "hexagon","Dot" = "dot", "Square" = "square")),
+                                      selected = c("Dot" = "dot"),
+                                      width = "85%"
+                                    )
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            column(
+              width = 4,
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "100%",
+                height = "500px",
+                h3(p("Edges"), style = "color:white; position:relative; right:-15px"),
+                hr(),
+                fluidRow(
+                  column(
+                    width = 6,
+                    column(
+                      width = 12,
+                      align = "left",
+                      h4(p("Label"), style = "color:white;")
+                    ),
+                    column(
+                      width = 12,
+                      align = "center",
+                      div(
+                        class = "label_sel",
+                        selectInput(
+                          "mst_edge_label",
+                          label = "",
+                          choices = c(
+                            `Allelic Distance` = "weight",
+                            Index = "index",
+                            `Assembly ID` = "assembly_id",
+                            `Assembly Name` = "assembly_name",
+                            `Isolation Date` = "isolation_date",
+                            Host = "host",
+                            Country = "country",
+                            City = "city"
+                          ),
+                          selected = c(`Allelic Distance` = "weight"),
+                          width = "100%"
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 7,
+                          colorPickr(
+                            inputId = "mst_edge_font_color",
+                            width = "100%",
+                            selected = "#000000",
+                            label = "",
+                            update = "changestop",
+                            interaction = list(clear = FALSE,
+                                               save = FALSE),
+                            position = "right-start"
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          dropMenu(
+                            actionBttn(
+                              "mst_edgelabel_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            width = 5,
+                            numericInput(
+                              "mst_edge_font_size",
+                              label = h5("Size", style = "color:white; margin-bottom: 0px;"),
+                              value = 18,
+                              step = 1,
+                              min = 8,
+                              max = 30,
+                              width = "80px"
+                            )
+                          )
+                        )
+                      ),
+                      br()
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Color"), style = "color:white; position: relative; right: -15px"),
+                        column(
+                          width = 12,
+                          align = "center",
+                          fluidRow(
+                            column(
+                              width = 7,
+                              div(
+                                class = "node_color",
+                                colorPickr(
+                                  inputId = "mst_color_edge",
+                                  width = "100%",
+                                  selected = "#000000",
+                                  label = "",
+                                  update = "changestop",
+                                  interaction = list(clear = FALSE,
+                                                     save = FALSE),
+                                  position = "right-start"
+                                )
+                              )
+                            ),
+                            column(
+                              width = 5,
+                              dropMenu(
+                                actionBttn(
+                                  "mst_edgecolor_menu",
+                                  label = "",
+                                  color = "default",
+                                  size = "sm",
+                                  style = "material-flat",
+                                  icon = icon("sliders")
+                                ),
+                                placement = "top-start",
+                                theme = "translucent",
+                                width = 5,
+                                sliderInput(
+                                  "mst_edge_opacity",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px;"),
+                                  value = 0.7,
+                                  step = 0.1,
+                                  min = 0,
+                                  max = 1,
+                                  ticks = FALSE,
+                                  width = "150px"
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                ),
+                hr(style = "margin-top: 3px !important"),
+                fluidRow(
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Length multiplier"), style = "color:white; position: relative; right: -15px; margin-bottom: -5px")
+                      )
+                    ),
+                    column(
+                      width = 12,
+                      align = "left",
+                      br(),
+                      div(
+                        class = "switch-mst-edges",
+                        materialSwitch(
+                          "mst_scale_edges",
+                          h5(p("Scale Allelic Distance"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                          value = FALSE,
+                          right = TRUE
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          align = "left",
+                          conditionalPanel(
+                            "input.mst_scale_edges==true",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Multiplier')
+                              )
+                            )
+                          ),
+                          conditionalPanel(
+                            "input.mst_scale_edges==false",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: relative; bottom: -16px; margin-left: 0px ', 'Length')
+                              )
+                            )
+                          )
+                        ),
+                        column(
+                          width = 9,
+                          align = "center",
+                          conditionalPanel(
+                            "input.mst_scale_edges==true",
+                            div(
+                              class = "slider_edge",
+                              sliderInput(
+                                inputId = "mst_edge_length_scale",
+                                label = NULL,
+                                min = 1,
+                                max = 40,
+                                value = 15,
+                                ticks = FALSE
+                              ) 
+                            )
+                          ),
+                          conditionalPanel(
+                            "input.mst_scale_edges==false",
+                            div(
+                              class = "slider_edge",
+                              sliderTextInput(
+                                inputId = "mst_edge_length",
+                                label = NULL,
+                                choices = append(seq(0.1, 1, 0.1), 2:100),
+                                selected = 35,
+                                hide_min_max = FALSE
+                              ) 
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 6,
+                    fluidRow(
+                      column(
+                        width = 6,
+                        align = "left",
+                        h4(p("Clustering"), style = "color:white; text-align: left; position: relative; right: -15px")
+                      ),
+                      column(
+                        width = 2,
+                        bslib::tooltip(
+                          bsicons::bs_icon("info-circle", 
+                                           title = "Cluster threshold according to species-specific\nComplex Type Distance (cgMLST.org)", 
+                                           color = "white", height = "14px", width = "14px", 
+                                           position = "relative", top = "9px", right = "28px"),
+                          "Text shown in the tooltip.",
+                          show = FALSE,
+                          id = "mst_cluster_info"
+                        )
+                      )
+                    ),
+                    br(),
+                    fluidRow(
+                      column(
+                        width = 9,
+                        div(
+                          class = "mst-cluster-switch",
+                          materialSwitch(
+                            "mst_show_clusters",
+                            h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        dropMenu(
+                          actionBttn(
+                            "mst_cluster_col_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          width = 5,
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              selectInput(
+                                "mst_cluster_col_scale",
+                                label = h5("Color Scale", style = "color:white; margin-bottom: 0px;"),
+                                choices = c("Viridis", "Rainbow"),
+                                width = "150px"
+                              ),
+                              br(),
+                              selectInput(
+                                "mst_cluster_type",
+                                label = h5("Cluster Type", style = "color:white; margin-bottom: 0px;"),
+                                choices = c("Area", "Skeleton"),
+                                width = "150px"
+                              ),
+                              br(),
+                              conditionalPanel(
+                                "input.mst_cluster_type=='Skeleton'",
+                                sliderInput(
+                                  "mst_cluster width",
+                                  label = h5("Skeleton Width", style = "color:white; margin-bottom: 0px;"),
+                                  value = 5,
+                                  step = 1,
+                                  min = 1,
+                                  max = 10,
+                                  ticks = FALSE,
+                                  width = "150px"
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    br(),
+                    fluidRow(
+                      column(
+                        width = 4,
+                        HTML(
+                          paste(
+                            tags$span(style='color: white; text-align: left; font-size: 14px; margin-left: 15px', 'Threshold')
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        uiOutput("mst_cluster")
+                      ),
+                      column(
+                        width = 4,
+                        actionButton(
+                          "mst_cluster_reset",
+                          label = "",
+                          icon = icon("rotate")
+                        ),
+                        bsTooltip("mst_cluster_reset", 
+                                  HTML("Reset to default Complex Type Distance"), 
+                                  placement = "top", trigger = "hover")
+                      )
+                    )
+                  ),
+                  br(),
+                )
+              ), br(), br(), br(), br(), br(), br()
+            )
+          )
+        ),
+        
+        ### Control Panels NJ ----
+        
+        conditionalPanel(
+          "input.tree_algo=='Neighbour-Joining'",
+          fluidRow(
+            column(
+              width = 1,
+              radioGroupButtons(
+                inputId = "nj_controls",
+                label = "",
+                choices = c("Layout", "Label", "Elements", "Variables"),
+                direction = "vertical"
+              )
+            ),
+            conditionalPanel(
+              "input.nj_controls=='Layout'",
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Theme"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "center",
+                        selectInput(
+                          inputId = "nj_layout",
+                          label = "",
+                          choices = list(
+                            Linear = list(
+                              "Rectangular" = "rectangular",
+                              "Roundrect" = "roundrect",
+                              "Slanted" = "slanted",
+                              "Ellipse" = "ellipse"
+                            ),
+                            Circular = list("Circular" = "circular",
+                                            "Inward" = "inward")
+                          ),
+                          selected = "rectangular",
+                          width = "90%"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch-layout",
+                          materialSwitch(
+                            "nj_rootedge_show",
+                            h5(p("Rootedge"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "nj_rootedge_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("nj_rootedge_length"),
+                              br(),
+                              selectInput(
+                                "nj_rootedge_line",
+                                label = h5("Rootedge Line", style = "color:white"),
+                                choices = c(Solid = "solid", Dashed = "dashed", Dotted = "dotted"),
+                                selected = c(Dotted = "solid"),
+                                width = "100px"
+                              ),
+                              br(),
+                              conditionalPanel(
+                                "input.nj_layout=='circular'",
+                                sliderInput(
+                                  "nj_xlim",
+                                  label = h5("Adjust Circular", style = "color:white"),
+                                  min = -50,
+                                  max = 0,
+                                  value = -10,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.nj_layout=='inward'",
+                                sliderInput(
+                                  "nj_inward_xlim",
+                                  label = h5("Adjust Circular", style = "color:white"),
+                                  min = 30,
+                                  max = 120,
+                                  value = 50,
+                                  ticks = FALSE,
+                                  width = "150px",
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch-re",
+                          materialSwitch(
+                            "nj_ladder",
+                            h5(p("Ladderize"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                            value = TRUE,
+                            right = TRUE
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Color"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Lines/Text"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
+                      ),
+                      column(
+                        width = 7,
+                        colorPickr(
+                          inputId = "nj_color",
+                          width = "90%",
+                          selected = "#000000",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    br(),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Background"), style = "color:white; position: relative; right: -15px; margin-top: 7px; margin-bottom: 38px")
+                      ),
+                      column(
+                        width = 7,
+                        colorPickr(
+                          inputId = "nj_bg",
+                          width = "90%",
+                          selected = "#ffffff",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ), 
+                    br()
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Title"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      textInput(
+                        "nj_title",
+                        label = "",
+                        width = "100%",
+                        placeholder = "Plot Title"
+                      ),
+                      textInput(
+                        "nj_subtitle",
+                        label = "",
+                        width = "100%",
+                        placeholder = "Plot Subtitle"
+                      ),
+                      br(),
+                      fluidRow(
+                        column(
+                          width = 7,
+                          colorPickr(
+                            inputId = "nj_title_color",
+                            selected = "#000000",
+                            label = "",
+                            update = "changestop",
+                            interaction = list(clear = FALSE,
+                                               save = FALSE),
+                            position = "right-start",
+                            width = "100%"
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "nj_title_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                numericInput(
+                                  "nj_title_size",
+                                  label = h5("Title Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 30,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                ),
+                                br(),
+                                numericInput(
+                                  "nj_subtitle_size",
+                                  label = h5("Subtitle Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 20,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      br()
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Sizing"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      br(),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Ratio", style = "color: white; font-size: 14px;")
+                        ),
+                        column(
+                          width = 6,
+                          align = "left",
+                          div(
+                            class = "ratio-sel",
+                            selectInput(
+                              "nj_ratio",
+                              "",
+                              choices = c("16:10" = (16/10), "16:9" = (16/9), "4:3" = (4/3))
+                            )
+                          )
+                        ),
+                        column(
+                          width = 3,
+                          dropMenu(
+                            actionBttn(
+                              "nj_size_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                sliderInput(
+                                  "nj_v",
+                                  label = h5("Vertical Position", style = "color:white; margin-bottom: 0px"),
+                                  min = -0.5,
+                                  max = 0.5,
+                                  step = 0.01,
+                                  value = 0,
+                                  width = "150px",
+                                  ticks = FALSE
+                                ),
+                                br(),
+                                sliderInput(
+                                  "nj_h",
+                                  label = h5("Horizontal Position", style = "color:white; margin-bottom: 0px"),
+                                  min = -0.5,
+                                  max = 0.5,
+                                  step = 0.01,
+                                  value = 0,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Size", style = "color: white; font-size: 14px; margin-top: 30px")
+                        ),
+                        column(
+                          width = 9,
+                          sliderInput(
+                            "nj_scale",
+                            "",
+                            min = 500,
+                            max = 1200,
+                            value = 800,
+                            step = 5,
+                            width = "95%",
+                            ticks = FALSE
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Zoom", style = "color: white; font-size: 14px; margin-top: 30px")
+                        ),
+                        column(
+                          width = 9,
+                          div(
+                            class = "zoom-slider",
+                            sliderInput(
+                              "nj_zoom",
+                              label = NULL,
+                              min = 0.5,
+                              max = 1.5,
+                              step = 0.05,
+                              value = 0.95,
+                              ticks = FALSE
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Tree Scale"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      fluidRow(
+                        column(
+                          width = 8,
+                          align = "left",
+                          div(
+                            class = "mat-switch-layout",
+                            materialSwitch(
+                              "nj_treescale_show",
+                              h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                              value = TRUE,
+                              right = TRUE
+                            )
+                          ),
+                          br()
+                        ),
+                        column(
+                          width = 4,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "nj_treescale_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                uiOutput("nj_treescale_width"),
+                                br(),
+                                uiOutput("nj_treescale_x"),
+                                br(),
+                                uiOutput("nj_treescale_y")
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Legend"), style = "color:white; position: relative; right: -15px; margin-top: 10px; margin-bottom: -2px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      fluidRow(
+                        column(
+                          width = 7,
+                          align = "left",
+                          prettyRadioButtons(
+                            "nj_legend_orientation",
+                            "",
+                            choices = c(Horizontal = "horizontal",
+                                        Vertical = "vertical"),
+                            selected = c(Vertical = "vertical"),
+                            inline = FALSE
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "nj_legend_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                numericInput(
+                                  "nj_legend_size",
+                                  label = h5("Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 10,
+                                  min = 5,
+                                  max = 25,
+                                  step = 1,
+                                  width = "80px"
+                                ),
+                                br(),
+                                sliderInput(
+                                  "nj_legend_x",
+                                  label = h5("Horizontal Position", style = "color:white; margin-bottom: 0px"),
+                                  value = 0.9,
+                                  min = -0.9,
+                                  max = 1.9,
+                                  step = 0.2,
+                                  width = "150px",
+                                  ticks = FALSE
+                                ),
+                                br(),
+                                sliderInput(
+                                  "nj_legend_y",
+                                  label = h5("Vertical Position", style = "color:white; margin-bottom: 0px"),
+                                  value = 0.2,
+                                  min = -1.5,
+                                  max = 1.5,
+                                  step = 0.1,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.nj_controls=='Label'",
+              column(
+                width = 4,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Tips"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 4,
+                            align = "left",
+                            div(
+                              class = "mat-switch-lab",
+                              materialSwitch(
+                                "nj_tiplab_show",
+                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                                value = TRUE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 4,
+                            align = "center",
+                            uiOutput("nj_tiplab")
+                          ),
+                          column(
+                            width = 3,
+                            div(
+                              class = "mat-switch-align",
+                              materialSwitch(
+                                "nj_align",
+                                h5(p("Align"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 1,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "nj_labeltext_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-start",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  sliderInput(
+                                    "nj_tiplab_alpha",
+                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                    min = 0.1,
+                                    max = 1,
+                                    value = 1,
+                                    width = "150px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  conditionalPanel(
+                                    "!(input.nj_layout=='inward'|input.nj_layout=='circular')",
+                                    sliderInput(
+                                      inputId = "nj_tiplab_nudge_x",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = 0,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  conditionalPanel(
+                                    "input.nj_layout=='circular'",
+                                    sliderInput(
+                                      inputId = "nj_tiplab_position",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = -0.05,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  conditionalPanel(
+                                    "input.nj_layout=='inward'",
+                                    sliderInput(
+                                      inputId = "nj_tiplab_position_inw",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = 1.1,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "nj_tiplab_angle",
+                                    label = h5("Angle", style = "color:white; margin-bottom: 0px"),
+                                    min = -90,
+                                    max = 90,
+                                    value = 0,
+                                    ticks = FALSE,
+                                    width = "150px",
+                                  )      
+                                ),
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  uiOutput("nj_tiplab_size"),
+                                  br(),
+                                  selectInput(
+                                    "nj_tiplab_fontface",
+                                    label = h5("Fontface", style = "color:white; margin-bottom: 5px; margin-top: 16px"),
+                                    width = "250px",
+                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 4,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px")
+                      ),
+                      column(
+                        width = 4,
+                        align = "center",
+                        colorPickr(
+                          inputId = "nj_tiplab_color",
+                          width = "100%",
+                          selected = "#000000",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 4,
+                        align = "left",
+                        br(),
+                        div(
+                          class = "mat-switch-geom",
+                          materialSwitch(
+                            "nj_geom",
+                            h5(p("Panels"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        colorPickr(
+                          inputId = "nj_tiplab_fill",
+                          width = "100%",
+                          selected = "#84D9A0",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "left",
+                        dropMenu(
+                          actionBttn(
+                            "nj_labelformat_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("nj_tiplab_padding"),
+                              br(),
+                              sliderInput(
+                                inputId = "nj_tiplab_labelradius",
+                                label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
+                                min = 0,
+                                max = 0.5,
+                                value = 0.2,
+                                width = "150px",
+                                ticks = FALSE
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 3,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Branches"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 5,
+                            align = "left",
+                            div(
+                              class = "mat-switch-lab",
+                              materialSwitch(
+                                "nj_show_branch_label",
+                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 5,
+                            align = "center",
+                            uiOutput("nj_branch_label")
+                          ),
+                          column(
+                            width = 2,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "nj_branch_label_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-start",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  sliderInput(
+                                    "nj_branchlab_alpha",
+                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                    min = 0.1,
+                                    max = 1,
+                                    value = 0.65,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "nj_branch_x",
+                                    label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+                                    min = -3,
+                                    max = 3,
+                                    value = 0,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "nj_branch_y",
+                                    label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+                                    min = -3,
+                                    max = 3,
+                                    value = 0,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  )
+                                ),
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  uiOutput("nj_branch_size"),
+                                  selectInput(
+                                    "nj_branchlab_fontface",
+                                    label = h5("Fontface", style = "color:white; margin-bottom: 0px;"),
+                                    width = "250px",
+                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    "nj_branch_labelradius",
+                                    label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
+                                    min = 0,
+                                    max = 0.5,
+                                    value = 0.5,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px; margin-bottom: 109px")
+                      ),
+                      column(
+                        width = 5,
+                        colorPickr(
+                          inputId = "nj_branch_label_color",
+                          width = "100%",
+                          selected = "#FFB7B7",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 3,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Custom Labels"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 6,
+                            textInput(
+                              "nj_new_label_name",
+                              "",
+                              placeholder = "New Label"
+                            )
+                          ),
+                          column(
+                            width = 3,
+                            actionButton(
+                              "nj_add_new_label",
+                              "",
+                              icon = icon("plus")
+                            )
+                          ),
+                          column(
+                            width = 2,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "nj_custom_label_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-end",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 12,
+                                  align = "center",
+                                  uiOutput("nj_custom_labelsize"),
+                                  br(),
+                                  uiOutput("nj_sliderInput_y"),
+                                  br(),
+                                  uiOutput("nj_sliderInput_x")
+                                )
+                              )
+                            )
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 6,
+                            uiOutput("nj_custom_label_select")
+                          ),
+                          column(
+                            width = 4,
+                            uiOutput("nj_del_label"),
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 12,
+                            align = "center",
+                            uiOutput("nj_cust_label_save")
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.nj_controls=='Elements'",
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Tip Points"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "nj_tippoint_show",
+                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "nj_tippoint_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              sliderInput(
+                                "nj_tippoint_alpha",
+                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                value = 0.5,
+                                min = 0.1,
+                                max = 1,
+                                width = "150px",
+                                ticks = FALSE
+                              ), 
+                              br(),
+                              uiOutput("nj_tippoint_size")
+                            )
+                          )
+                        )  
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        colorPickr(
+                          inputId = "nj_tippoint_color",
+                          width = "100%",
+                          selected = "#3A4657",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        conditionalPanel(
+                          "input.nj_tipshape_mapping_show==false",
+                          selectInput(
+                            "nj_tippoint_shape",
+                            "",
+                            width = "100%",
+                            choices = c(
+                              Circle = "circle", 
+                              Square = "square", 
+                              Diamond = "diamond", 
+                              Triangle = "triangle",
+                              Cross = "cross", 
+                              Asterisk = "asterisk"
+                            )
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.nj_tipshape_mapping_show==true",
+                          h5(p("Variable assigned"), style = "color:white; position: relative; right: -15px; margin-top: 30px; font-style: italic")
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Node Points"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "nj_nodepoint_show",
+                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "nj_nodepoint_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              sliderInput(
+                                "nj_nodepoint_alpha",
+                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                value = 1,
+                                min = 0.1,
+                                max = 1,
+                                width = "150px",
+                                ticks = FALSE
+                              ), 
+                              br(),
+                              uiOutput("nj_nodepoint_size")
+                            )
+                          )
+                        )  
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        colorPickr(
+                          inputId = "nj_nodepoint_color",
+                          width = "100%",
+                          selected = "#3A4657",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        selectInput(
+                          "nj_nodepoint_shape",
+                          "",
+                          choices = c(
+                            Circle = "circle", 
+                            Square = "square", 
+                            Diamond = "diamond", 
+                            Triangle = "triangle",
+                            Cross = "cross", 
+                            Asterisk = "asterisk"
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 6,
+                        h4(p("Tiles"), style = "color:white; position: relative; right: -15px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        div(
+                          class = "sel-tile-number",
+                          selectInput(
+                            "nj_tile_number",
+                            "",
+                            choices = 1:5,
+                            width = "70px"
+                          )
+                        )
+                      ),
+                      column(
+                        width = 7,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "nj_tile_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              conditionalPanel(
+                                "input.nj_tile_num == 1",
+                                sliderInput(
+                                  "nj_fruit_alpha",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.nj_tile_num == 2",
+                                sliderInput(
+                                  "nj_fruit_alpha_2",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.nj_tile_num == 3",
+                                sliderInput(
+                                  "nj_fruit_alpha_3",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.nj_tile_num == 4",
+                                sliderInput(
+                                  "nj_fruit_alpha_4",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.nj_tile_num == 5",
+                                sliderInput(
+                                  "nj_fruit_alpha_5",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.nj_tile_num == 1",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_width"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 68px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_offset_circ"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.nj_tile_num == 2",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_width2"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_offset_circ_2"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.nj_tile_num == 3",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_width3"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_offset_circ_3"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.nj_tile_num == 4",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_width4"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_offset_circ_4"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.nj_tile_num == 5",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_width5"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("nj_fruit_offset_circ_5"),
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 6,
+                        h4(p("Heatmap"), style = "color:white; position: relative; right: -15px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        h5("Title", style = "color:white; margin-left: 15px; margin-top: 32px;")
+                      ),
+                      column(
+                        width = 6,
+                        align = "center",
+                        textInput(
+                          "nj_heatmap_title",
+                          label = "",
+                          value = "Heatmap",
+                          placeholder = "Heatmap" 
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "nj_heatmap_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("nj_colnames_angle"),
+                              br(),
+                              uiOutput("nj_colnames_y")
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5("Width", style = "color: white; margin-left: 15px; margin-top: 40px;")
+                      ),
+                      column(
+                        width = 7,
+                        uiOutput("nj_heatmap_width")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5("Position", style = "color:white; margin-left: 15px; margin-top: 36px;")
+                      ),
+                      column(
+                        width = 7,
+                        uiOutput("nj_heatmap_offset")
+                      )
+                    ),
+                    br(), br()
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Clade Highlight"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 12,
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "nj_nodelabel_show",
+                            h5(p("Toggle Node View"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        h5(p("Nodes"), style = "color:white; position: relative; right: -15px; margin-top: 20px")
+                      ),
+                      column(
+                        width = 9,
+                        uiOutput("nj_parentnode")
+                      )
+                    ),
+                    uiOutput("nj_clade_scale"),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Form"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
+                      ),
+                      column(
+                        width = 7,
+                        div(
+                          class = "sel-clade",
+                          selectInput(
+                            "nj_clade_type",
+                            "",
+                            choices = c("Rect" = "rect",
+                                        "Round" = "roundrect"),
+                            selected = c("Round" = "roundrect")
+                          ) 
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.nj_controls=='Variables'",
+              column(
+                width = 7,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 3,
+                        align = "center",
+                        h4(p("Element"), style = "color:white; margin-bottom: 20px")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        h4(p("Variable"), style = "color:white; margin-bottom: 20px; margin-right: 30px;")
+                      ),
+                      column(
+                        width = 6,
+                        align = "center",
+                        h4(p("Color Scale"), style = "color:white; margin-bottom: 20px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "nj_mapping_show",
+                            h5(p("Tip Label Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_color_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_tiplab_scale")
+                      ),
+                      uiOutput("nj_tiplab_mapping_info"),
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "nj_tipcolor_mapping_show",
+                            h5(p("Tip Point Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_tipcolor_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_tippoint_scale")
+                      ),
+                      uiOutput("nj_tipcolor_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "nj_tipshape_mapping_show",
+                            h5(p("Tip Point Shape"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_tipshape_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        HTML(
+                          paste(
+                            tags$span(style='color: white; font-size: 14px; font-style: italic; position: relative; bottom: -16px; right: -40px;', 'No scale for shapes')
+                          )
+                        )
+                      ),
+                      uiOutput("nj_tipshape_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        fluidRow(
+                          column(
+                            width = 8,
+                            conditionalPanel(
+                              "input.nj_tile_num == 1",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "nj_tiles_show_1",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px; margin-right: 10px"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.nj_tile_num == 2",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "nj_tiles_show_2",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.nj_tile_num == 3",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "nj_tiles_show_3",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.nj_tile_num == 4",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "nj_tiles_show_4",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.nj_tile_num == 5",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "nj_tiles_show_5",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            )
+                          ), 
+                          column(
+                            width = 4,
+                            align = "left",
+                            div(
+                              class = "tile-sel",
+                              selectInput(
+                                "nj_tile_num",
+                                "",
+                                choices = 1:5,
+                                width = "50px"
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        conditionalPanel(
+                          "input.nj_tile_num == 1",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_fruit_variable")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.nj_tile_num == 2",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_fruit_variable2")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.nj_tile_num == 3",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_fruit_variable3")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.nj_tile_num == 4",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_fruit_variable4")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.nj_tile_num == 5",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_fruit_variable5")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.nj_tile_num == 1",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_tiles_scale_1")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.nj_tile_num == 2",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_tiles_scale_2")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.nj_tile_num == 3",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_tiles_scale_3")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.nj_tile_num == 4",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_tiles_scale_4")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.nj_tile_num == 5",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("nj_tiles_scale_5")
+                          )
+                        )
+                      ),
+                      uiOutput("nj_fruit_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "nj_heatmap_show",
+                            h5(p("Heatmap"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("nj_heatmap_sel")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        div(
+                          class = "heatmap-scale",
+                          uiOutput("nj_heatmap_scale")
+                        )
+                      ),
+                      uiOutput("nj_heatmap_mapping_info")
+                    )
+                  )
+                )
+              )
+            )
+          ),
+          br(), br(), br(), br(), br(), br()
+        ),
+        
+        ### Control Panels UPGMA ----
+        
+        conditionalPanel(
+          "input.tree_algo=='UPGMA'",
+          fluidRow(
+            column(
+              width = 1,
+              radioGroupButtons(
+                inputId = "upgma_controls",
+                label = "",
+                choices = c("Layout", "Label", "Elements", "Variables"),
+                direction = "vertical"
+              )
+            ),
+            conditionalPanel(
+              "input.upgma_controls=='Layout'",
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Theme"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "center",
+                        selectInput(
+                          inputId = "upgma_layout",
+                          label = "",
+                          choices = list(
+                            Linear = list(
+                              "Rectangular" = "rectangular",
+                              "Roundrect" = "roundrect",
+                              "Slanted" = "slanted",
+                              "Ellipse" = "ellipse"
+                            ),
+                            Circular = list("Circular" = "circular",
+                                            "Inward" = "inward")
+                          ),
+                          selected = "rectangular",
+                          width = "90%"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch-layout",
+                          materialSwitch(
+                            "upgma_rootedge_show",
+                            h5(p("Rootedge"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_rootedge_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("upgma_rootedge_length"),
+                              br(),
+                              selectInput(
+                                "upgma_rootedge_line",
+                                label = h5("Rootedge Line", style = "color:white"),
+                                choices = c(Solid = "solid", Dashed = "dashed", Dotted = "dotted"),
+                                selected = c(Dotted = "solid"),
+                                width = "100px"
+                              ),
+                              br(),
+                              conditionalPanel(
+                                "input.upgma_layout=='circular'",
+                                sliderInput(
+                                  "upgma_xlim",
+                                  label = h5("Adjust Circular", style = "color:white"),
+                                  min = -50,
+                                  max = 0,
+                                  value = -10,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.upgma_layout=='inward'",
+                                sliderInput(
+                                  "upgma_inward_xlim",
+                                  label = h5("Adjust Circular", style = "color:white"),
+                                  min = 30,
+                                  max = 120,
+                                  value = 50,
+                                  ticks = FALSE,
+                                  width = "150px",
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch-re",
+                          materialSwitch(
+                            "upgma_ladder",
+                            h5(p("Ladderize"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                            value = TRUE,
+                            right = TRUE
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Color"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Lines/Text"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
+                      ),
+                      column(
+                        width = 7,
+                        colorPickr(
+                          inputId = "upgma_color",
+                          width = "90%",
+                          selected = "#000000",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    br(),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Background"), style = "color:white; position: relative; right: -15px; margin-top: 7px; margin-bottom: 38px")
+                      ),
+                      column(
+                        width = 7,
+                        colorPickr(
+                          inputId = "upgma_bg",
+                          width = "90%",
+                          selected = "#ffffff",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Title"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      textInput(
+                        "upgma_title",
+                        label = "",
+                        width = "100%",
+                        placeholder = "Plot Title"
+                      ),
+                      textInput(
+                        "upgma_subtitle",
+                        label = "",
+                        width = "100%",
+                        placeholder = "Plot Subtitle"
+                      ),
+                      br(),
+                      fluidRow(
+                        column(
+                          width = 7,
+                          colorPickr(
+                            inputId = "upgma_title_color",
+                            selected = "#000000",
+                            label = "",
+                            update = "changestop",
+                            interaction = list(clear = FALSE,
+                                               save = FALSE),
+                            position = "right-start",
+                            width = "100%"
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "upgma_title_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                numericInput(
+                                  "upgma_title_size",
+                                  label = h5("Title Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 30,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                ),
+                                br(),
+                                numericInput(
+                                  "upgma_subtitle_size",
+                                  label = h5("Subtitle Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 20,
+                                  min = 15,
+                                  max = 40,
+                                  step = 1,
+                                  width = "80px"
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Sizing"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      br(),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Ratio", style = "color: white; font-size: 14px;")
+                        ),
+                        column(
+                          width = 6,
+                          align = "left",
+                          div(
+                            class = "ratio-sel",
+                            selectInput(
+                              "upgma_ratio",
+                              "",
+                              choices = c("16:10" = (16/10), "16:9" = (16/9), "4:3" = (4/3))
+                            )
+                          )
+                        ),
+                        column(
+                          width = 3,
+                          dropMenu(
+                            actionBttn(
+                              "upgma_size_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                sliderInput(
+                                  "upgma_v",
+                                  label = "Vertical Position",
+                                  min = -0.5,
+                                  max = 0.5,
+                                  step = 0.01,
+                                  value = 0,
+                                  width = "150px",
+                                  ticks = FALSE
+                                ),
+                                br(),
+                                sliderInput(
+                                  "upgma_h",
+                                  label = "Horizontal Position",
+                                  min = -0.5,
+                                  max = 0.5,
+                                  step = 0.01,
+                                  value = 0,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Size", style = "color: white; font-size: 14px; margin-top: 30px")
+                        ),
+                        column(
+                          width = 9,
+                          sliderInput(
+                            "upgma_scale",
+                            "",
+                            min = 500,
+                            max = 1200,
+                            value = 800,
+                            step = 5,
+                            width = "95%",
+                            ticks = FALSE
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 3,
+                          h5("Zoom", style = "color: white; font-size: 14px; margin-top: 30px")
+                        ),
+                        column(
+                          width = 9,
+                          div(
+                            class = "zoom-slider",
+                            sliderInput(
+                              "upgma_zoom",
+                              label = NULL,
+                              min = 0.5,
+                              max = 1.5,
+                              step = 0.05,
+                              value = 0.95,
+                              ticks = FALSE
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "250px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Tree Scale"), style = "color:white; position: relative; right: -15px"),
+                    column(
+                      width = 12,
+                      fluidRow(
+                        column(
+                          width = 8,
+                          align = "left",
+                          div(
+                            class = "mat-switch-layout",
+                            materialSwitch(
+                              "upgma_treescale_show",
+                              h5(p("Show"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                              value = TRUE,
+                              right = TRUE
+                            )
+                          ),
+                          br()
+                        ),
+                        column(
+                          width = 4,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "upgma_treescale_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                uiOutput("upgma_treescale_width"),
+                                br(),
+                                uiOutput("upgma_treescale_x"),
+                                br(),
+                                uiOutput("upgma_treescale_y")
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  ),
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Legend"), style = "color:white; position: relative; right: -15px; margin-top: 10px; margin-bottom: -2px"),
+                    column(
+                      width = 12,
+                      align = "center",
+                      fluidRow(
+                        column(
+                          width = 7,
+                          align = "left",
+                          prettyRadioButtons(
+                            "upgma_legend_orientation",
+                            "",
+                            choices = c(Horizontal = "horizontal",
+                                        Vertical = "vertical"),
+                            selected = c(Vertical = "vertical"),
+                            inline = FALSE
+                          )
+                        ),
+                        column(
+                          width = 5,
+                          align = "right",
+                          dropMenu(
+                            actionBttn(
+                              "upgma_legend_menu",
+                              label = "",
+                              color = "default",
+                              size = "sm",
+                              style = "material-flat",
+                              icon = icon("sliders")
+                            ),
+                            placement = "top-start",
+                            theme = "translucent",
+                            fluidRow(
+                              column(
+                                width = 12,
+                                align = "center",
+                                numericInput(
+                                  "upgma_legend_size",
+                                  label = h5("Size", style = "color:white; margin-bottom: 0px"),
+                                  value = 10,
+                                  min = 5,
+                                  max = 25,
+                                  step = 1,
+                                  width = "80px"
+                                ),
+                                br(),
+                                sliderInput(
+                                  "upgma_legend_x",
+                                  label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+                                  value = 0.9,
+                                  min = -0.9,
+                                  max = 1.9,
+                                  step = 0.2,
+                                  width = "150px",
+                                  ticks = FALSE
+                                ),
+                                br(),
+                                sliderInput(
+                                  "upgma_legend_y",
+                                  label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+                                  value = 0.2,
+                                  min = -1.5,
+                                  max = 1.5,
+                                  step = 0.1,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.upgma_controls=='Label'",
+              column(
+                width = 4,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Tips"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 4,
+                            align = "left",
+                            div(
+                              class = "mat-switch-lab",
+                              materialSwitch(
+                                "upgma_tiplab_show",
+                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                                value = TRUE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 4,
+                            align = "center",
+                            uiOutput("upgma_tiplab")
+                          ),
+                          column(
+                            width = 3,
+                            div(
+                              class = "mat-switch-align",
+                              materialSwitch(
+                                "upgma_align",
+                                h5(p("Align"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 1,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "upgma_labeltext_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-start",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  sliderInput(
+                                    "upgma_tiplab_alpha",
+                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                    min = 0.1,
+                                    max = 1,
+                                    value = 1,
+                                    width = "150px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  conditionalPanel(
+                                    "!(input.upgma_layout=='inward'|input.upgma_layout=='circular')",
+                                    sliderInput(
+                                      inputId = "upgma_tiplab_nudge_x",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = 0,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  conditionalPanel(
+                                    "input.upgma_layout=='circular'",
+                                    sliderInput(
+                                      inputId = "upgma_tiplab_position",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = -0.05,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  conditionalPanel(
+                                    "input.upgma_layout=='inward'",
+                                    sliderInput(
+                                      inputId = "upgma_tiplab_position_inw",
+                                      label = h5("Position", style = "color:white; margin-bottom: 0px"),
+                                      min = -3,
+                                      max = 3,
+                                      step = 0.05,
+                                      value = 1.1,
+                                      width = "150px",
+                                      ticks = FALSE
+                                    )
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "upgma_tiplab_angle",
+                                    label = h5("Angle", style = "color:white; margin-bottom: 0px"),
+                                    min = -90,
+                                    max = 90,
+                                    value = 0,
+                                    ticks = FALSE,
+                                    width = "150px",
+                                  )      
+                                ),
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  uiOutput("upgma_tiplab_size"),
+                                  br(),
+                                  selectInput(
+                                    "upgma_tiplab_fontface",
+                                    label = h5("Fontface", style = "color:white; margin-bottom: 5px; margin-top: 16px"),
+                                    width = "250px",
+                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 4,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px")
+                      ),
+                      column(
+                        width = 4,
+                        align = "center",
+                        colorPickr(
+                          inputId = "upgma_tiplab_color",
+                          width = "100%",
+                          selected = "#000000",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 4,
+                        align = "left",
+                        br(),
+                        div(
+                          class = "mat-switch-geom",
+                          materialSwitch(
+                            "upgma_geom",
+                            h5(p("Panels"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        colorPickr(
+                          inputId = "upgma_tiplab_fill",
+                          width = "100%",
+                          selected = "#84D9A0",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "left",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_labelformat_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("upgma_tiplab_padding"),
+                              br(),
+                              sliderInput(
+                                inputId = "upgma_tiplab_labelradius",
+                                label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
+                                min = 0,
+                                max = 0.5,
+                                value = 0.2,
+                                width = "150px",
+                                ticks = FALSE
+                              )
+                            )
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 3,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Branches"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 5,
+                            align = "left",
+                            div(
+                              class = "mat-switch-lab",
+                              materialSwitch(
+                                "upgma_show_branch_label",
+                                h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            )
+                          ),
+                          column(
+                            width = 5,
+                            align = "center",
+                            uiOutput("upgma_branch_label")
+                          ),
+                          column(
+                            width = 2,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "upgma_branch_label_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-start",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  sliderInput(
+                                    "upgma_branchlab_alpha",
+                                    label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                    min = 0.1,
+                                    max = 1,
+                                    value = 0.65,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "upgma_branch_x",
+                                    label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+                                    min = -3,
+                                    max = 3,
+                                    value = 0,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    inputId = "upgma_branch_y",
+                                    label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+                                    min = -3,
+                                    max = 3,
+                                    value = 0,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  )
+                                ),
+                                column(
+                                  width = 6,
+                                  align = "center",
+                                  uiOutput("upgma_branch_size"),
+                                  selectInput(
+                                    "upgma_branchlab_fontface",
+                                    label = h5("Fontface", style = "color:white; margin-bottom: 0px;"),
+                                    width = "250px",
+                                    choices = c(Plain = "plain", Bold =  "bold", Italic =  "italic", `B & I` = "bold.italic")
+                                  ),
+                                  br(),
+                                  sliderInput(
+                                    "upgma_branch_labelradius",
+                                    label = h5("Smooth edge", style = "color:white; margin-bottom: 0px"),
+                                    min = 0,
+                                    max = 0.5,
+                                    value = 0.5,
+                                    width = "250px",
+                                    ticks = FALSE
+                                  )
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -14px; margin-top: 23px; margin-bottom: 109px")
+                      ),
+                      column(
+                        width = 5,
+                        colorPickr(
+                          inputId = "upgma_branch_label_color",
+                          width = "100%",
+                          selected = "#FFB7B7",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        ),
+                        br(), br()
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 3,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "280px",
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "left",
+                        h4(p("Custom Labels"), style = "color:white; position: relative; right: -15px"),
+                        fluidRow(
+                          column(
+                            width = 6,
+                            textInput(
+                              "upgma_new_label_name",
+                              "",
+                              placeholder = "New Label"
+                            )
+                          ),
+                          column(
+                            width = 3,
+                            actionButton(
+                              "upgma_add_new_label",
+                              "",
+                              icon = icon("plus")
+                            )
+                          ),
+                          column(
+                            width = 2,
+                            align = "right",
+                            dropMenu(
+                              actionBttn(
+                                "upgma_custom_label_menu",
+                                label = "",
+                                color = "default",
+                                size = "sm",
+                                style = "material-flat",
+                                icon = icon("sliders")
+                              ),
+                              placement = "top-end",
+                              theme = "translucent",
+                              fluidRow(
+                                column(
+                                  width = 12,
+                                  align = "center",
+                                  uiOutput("upgma_custom_labelsize"),
+                                  br(),
+                                  uiOutput("upgma_sliderInput_y"),
+                                  br(),
+                                  uiOutput("upgma_sliderInput_x")
+                                )
+                              )
+                            )
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 6,
+                            uiOutput("upgma_custom_label_select")
+                          ),
+                          column(
+                            width = 4,
+                            uiOutput("upgma_del_label"),
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 12,
+                            align = "center",
+                            uiOutput("upgma_cust_label_save")
+                          )
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.upgma_controls=='Elements'",
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Tip Points"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "upgma_tippoint_show",
+                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_tippoint_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              sliderInput(
+                                "upgma_tippoint_alpha",
+                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                value = 0.5,
+                                min = 0.1,
+                                max = 1,
+                                width = "150px",
+                                ticks = FALSE
+                              ), 
+                              br(),
+                              uiOutput("upgma_tippoint_size")
+                            )
+                          )
+                        )  
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        colorPickr(
+                          inputId = "upgma_tippoint_color",
+                          width = "100%",
+                          selected = "#3A4657",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        align = "left",
+                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        conditionalPanel(
+                          "input.upgma_tipshape_mapping_show==false",
+                          selectInput(
+                            "upgma_tippoint_shape",
+                            "",
+                            width = "100%",
+                            choices = c(
+                              Circle = "circle", 
+                              Square = "square", 
+                              Diamond = "diamond", 
+                              Triangle = "triangle",
+                              Cross = "cross", 
+                              Asterisk = "asterisk"
+                            )
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.upgma_tipshape_mapping_show==true",
+                          h5(p("Variable assigned"), style = "color:white; position: relative; right: -15px; margin-top: 30px; font-style: italic")
+                        ),
+                        br()
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Node Points"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 8,
+                        align = "left",
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "upgma_nodepoint_show",
+                            h5(p("Show"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_nodepoint_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              sliderInput(
+                                "upgma_nodepoint_alpha",
+                                label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                value = 1,
+                                min = 0.1,
+                                max = 1,
+                                width = "150px",
+                                ticks = FALSE
+                              ), 
+                              br(),
+                              uiOutput("upgma_nodepoint_size")
+                            )
+                          )
+                        )  
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Color"), style = "color:white; position: relative; right: -15px; margin-top: 36px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        colorPickr(
+                          inputId = "upgma_nodepoint_color",
+                          width = "100%",
+                          selected = "#3A4657",
+                          label = "",
+                          update = "changestop",
+                          interaction = list(clear = FALSE,
+                                             save = FALSE),
+                          position = "right-start"
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Shape"), style = "color:white; position: relative; right: -15px; margin-top: 30px; margin-bottom: 48px")
+                      ),
+                      column(
+                        width = 7,
+                        align = "center",
+                        selectInput(
+                          "upgma_nodepoint_shape",
+                          "",
+                          choices = c(
+                            Circle = "circle", 
+                            Square = "square", 
+                            Diamond = "diamond", 
+                            Triangle = "triangle",
+                            Cross = "cross", 
+                            Asterisk = "asterisk"
+                          )
+                        ),
+                        br()
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 6,
+                        h4(p("Tiles"), style = "color:white; position: relative; right: -15px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        div(
+                          class = "sel-tile-number",
+                          selectInput(
+                            "upgma_tile_number",
+                            "",
+                            choices = 1:5,
+                            width = "70px"
+                          )
+                        )
+                      ),
+                      column(
+                        width = 7,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_tile_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-start",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              conditionalPanel(
+                                "input.upgma_tile_num == 1",
+                                sliderInput(
+                                  "upgma_fruit_alpha",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.upgma_tile_num == 2",
+                                sliderInput(
+                                  "upgma_fruit_alpha_2",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.upgma_tile_num == 3",
+                                sliderInput(
+                                  "upgma_fruit_alpha_3",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.upgma_tile_num == 4",
+                                sliderInput(
+                                  "upgma_fruit_alpha_4",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.upgma_tile_num == 5",
+                                sliderInput(
+                                  "upgma_fruit_alpha_5",
+                                  label = h5("Opacity", style = "color:white; margin-bottom: 0px"),
+                                  min = 0.1,
+                                  max = 1,
+                                  value = 1,
+                                  step = 0.05,
+                                  width = "150px",
+                                  ticks = FALSE
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.upgma_tile_num == 1",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_width"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 68px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_offset_circ"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.upgma_tile_num == 2",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_width2"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_offset_circ_2"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.upgma_tile_num == 3",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_width3"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_offset_circ_3"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.upgma_tile_num == 4",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_width4"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_offset_circ_4"),
+                          br()
+                        )
+                      )
+                    ),
+                    conditionalPanel(
+                      "input.upgma_tile_num == 5",
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Width", style = "color:white; margin-left: 15px; margin-top: 27px;")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_width5"),
+                          br()
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 5,
+                          h5("Position", style = "color:white; margin-left: 15px; margin-top: 32px; margin-bottom: 54px")
+                        ),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("upgma_fruit_offset_circ_5"),
+                          br()
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 6,
+                        h4(p("Heatmap"), style = "color:white; position: relative; right: -15px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        h5("Title", style = "color:white; margin-left: 15px; margin-top: 32px;")
+                      ),
+                      column(
+                        width = 6,
+                        align = "center",
+                        textInput(
+                          "upgma_heatmap_title",
+                          label = "",
+                          value = "Heatmap",
+                          placeholder = "Heatmap" 
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "right",
+                        dropMenu(
+                          actionBttn(
+                            "upgma_heatmap_menu",
+                            label = "",
+                            color = "default",
+                            size = "sm",
+                            style = "material-flat",
+                            icon = icon("sliders")
+                          ),
+                          placement = "top-end",
+                          theme = "translucent",
+                          fluidRow(
+                            column(
+                              width = 12,
+                              align = "center",
+                              uiOutput("upgma_colnames_angle"),
+                              br(),
+                              uiOutput("upgma_colnames_y")
+                            )
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5("Width", style = "color: white; margin-left: 15px; margin-top: 40px;")
+                      ),
+                      column(
+                        width = 7,
+                        uiOutput("upgma_heatmap_width")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5("Position", style = "color:white; margin-left: 15px; margin-top: 36px;")
+                      ),
+                      column(
+                        width = 7,
+                        uiOutput("upgma_heatmap_offset")
+                      )
+                    ),
+                    br(), br()
+                  )
+                )
+              ),
+              column(
+                width = 2,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  height = "295px",
+                  column(
+                    width = 12,
+                    align = "left",
+                    h4(p("Clade Highlight"), style = "color:white; position: relative; right: -15px"),
+                    fluidRow(
+                      column(
+                        width = 12,
+                        div(
+                          class = "mat-switch",
+                          materialSwitch(
+                            "upgma_nodelabel_show",
+                            h5(p("Toggle Node View"), style = "color:white; padding-left: 5px; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        h5(p("Nodes"), style = "color:white; position: relative; right: -15px; margin-top: 20px")
+                      ),
+                      column(
+                        width = 9,
+                        uiOutput("upgma_parentnode")
+                      )
+                    ),
+                    uiOutput("upgma_clade_scale"),
+                    fluidRow(
+                      column(
+                        width = 5,
+                        h5(p("Form"), style = "color:white; position: relative; right: -15px; margin-top: 30px")
+                      ),
+                      column(
+                        width = 7,
+                        div(
+                          class = "sel-clade",
+                          selectInput(
+                            "upgma_clade_type",
+                            "",
+                            choices = c("Rect" = "rect",
+                                        "Round" = "roundrect"),
+                            selected = c("Round" = "roundrect")
+                          ) 
+                        )
+                      )
+                    )
+                  )
+                )
+              )
+            ),
+            conditionalPanel(
+              "input.upgma_controls=='Variables'",
+              column(
+                width = 7,
+                box(
+                  solidHeader = TRUE,
+                  status = "info",
+                  width = "100%",
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 3,
+                        align = "center",
+                        h4(p("Element"), style = "color:white; margin-bottom: 20px")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        h4(p("Variable"), style = "color:white; margin-bottom: 20px; margin-right: 30px;")
+                      ),
+                      column(
+                        width = 6,
+                        align = "center",
+                        h4(p("Color Scale"), style = "color:white; margin-bottom: 20px")
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "upgma_mapping_show",
+                            h5(p("Tip Label Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_color_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_tiplab_scale")
+                      ),
+                      uiOutput("upgma_tiplab_mapping_info"),
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "upgma_tipcolor_mapping_show",
+                            h5(p("Tip Point Color"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_tipcolor_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_tippoint_scale")
+                      ),
+                      uiOutput("upgma_tipcolor_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "upgma_tipshape_mapping_show",
+                            h5(p("Tip Point Shape"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_tipshape_mapping")
+                      ),
+                      column(
+                        width = 3,
+                        HTML(
+                          paste(
+                            tags$span(style='color: white; font-size: 14px; font-style: italic; position: relative; bottom: -16px; right: -40px;', 'No scale for shapes')
+                          )
+                        )
+                      ),
+                      uiOutput("upgma_tipshape_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        fluidRow(
+                          column(
+                            width = 8,
+                            conditionalPanel(
+                              "input.upgma_tile_num == 1",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "upgma_tiles_show_1",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px; margin-right: 10px"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.upgma_tile_num == 2",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "upgma_tiles_show_2",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.upgma_tile_num == 3",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "upgma_tiles_show_3",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.upgma_tile_num == 4",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "upgma_tiles_show_4",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            ),
+                            conditionalPanel(
+                              "input.upgma_tile_num == 5",
+                              div(
+                                class = "mat-switch-v",
+                                materialSwitch(
+                                  "upgma_tiles_show_5",
+                                  h5(p("Tile"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                                  value = FALSE,
+                                  right = TRUE
+                                )
+                              )
+                            )
+                          ), 
+                          column(
+                            width = 4,
+                            align = "left",
+                            div(
+                              class = "tile-sel",
+                              selectInput(
+                                "upgma_tile_num",
+                                "",
+                                choices = 1:5,
+                                width = "50px"
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        conditionalPanel(
+                          "input.upgma_tile_num == 1",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_fruit_variable")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.upgma_tile_num == 2",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_fruit_variable2")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.upgma_tile_num == 3",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_fruit_variable3")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.upgma_tile_num == 4",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_fruit_variable4")
+                          )
+                        ),
+                        conditionalPanel(
+                          "input.upgma_tile_num == 5",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_fruit_variable5")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.upgma_tile_num == 1",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_tiles_scale_1")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.upgma_tile_num == 2",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_tiles_scale_2")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.upgma_tile_num == 3",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_tiles_scale_3")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.upgma_tile_num == 4",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_tiles_scale_4")
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.upgma_tile_num == 5",
+                        column(
+                          width = 3,
+                          align = "center",
+                          div(
+                            class = "heatmap-scale",
+                            uiOutput("upgma_tiles_scale_5")
+                          )
+                        )
+                      ),
+                      uiOutput("upgma_fruit_mapping_info")
+                    ),
+                    fluidRow(
+                      column(
+                        width = 3,
+                        div(
+                          class = "mat-switch-v",
+                          materialSwitch(
+                            "upgma_heatmap_show",
+                            h5(p("Heatmap"), style = "color:white; position: relative; top: -4px; right: -5px;"),
+                            value = FALSE,
+                            right = TRUE
+                          )
+                        )
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        uiOutput("upgma_heatmap_sel")
+                      ),
+                      column(
+                        width = 3,
+                        align = "center",
+                        div(
+                          class = "heatmap-scale",
+                          uiOutput("upgma_heatmap_scale")
+                        )
+                      ),
+                      uiOutput("upgma_heatmap_mapping_info")
+                    )
+                  )
+                )
+              )
+            )
+          ),
+          br(), br(), br(), br(), br(), br()
+        )
+      ),
+      
+      ## Tab Utilities -------------------------------------------------------
+      
+      tabItem(
+        tabName = "utilities",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Utilities"), style = "color:white")
+          )
+        ),
+        br(),
+        hr(),
+        column(
+          width = 5,
+          align = "left",
+          shinyDirButton(
+            "hash_dir",
+            "Choose folder with .fasta files",
+            title = "Locate folder with loci",
+            buttonType = "default",
+            style = "border-color: white; margin: 10px; min-width: 200px; text-align: center"
+          ),
+          actionButton("hash_start", "Start Hashing", icon = icon("circle-play")),
+          shinyjs::hidden(
+            div(id = "hash_loading",
+                HTML('<i class="fa fa-spinner fa-spin fa-fw fa-2x" style="color:white"></i>'))
+          )
+        )
+          # br(),
+          # actionButton(
+          #   "backup_database",
+          #   "Create backup",
+          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
+          # ),
+          # br(),
+          # actionButton(
+          #   "import_db_backup",
+          #   "Restore backup",
+          #   style = "border-color: white; margin: 10px; min-width: 200px; text-align: left"
+          # )
+      ),
+      
+      
+      ## Tab Screening -------------------------------------------------------
+      
+      tabItem(
+        tabName = "gs_screening",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Screening"), style = "color:white; margin-bottom: -20px;")
+          ),
+          column(
+            width = 7,
+            align = "left",
+            uiOutput("gene_screening_info")
+          )
+        ),
+        br(),
+        hr(),
+        fluidRow(
+          uiOutput("screening_interface")
+        )
+      ),
+      
+      ## Tab Resistance Profile -------------------------------------------------------
+      
+      tabItem(
+        tabName = "gs_profile",
+        fluidRow(
+          column(
+            width = 3,
+            align = "center",
+            h2(p("Browse Entries"), style = "color:white; margin-bottom: -20px")
+          ),
+          column(
+            width = 7,
+            align = "left",
+            uiOutput("gene_resistance_info")
+          )
+        ),
+        br(),
+        hr(),
+        br(), br(),
+        uiOutput("gs_table_selection"),
+        fluidRow(
+          column(1),
+          uiOutput("gs_profile_display")
+        )
+      )
+    ) # End tabItems
+  ) # End dashboardPage
+) # end UI
+
+# _______________________ ####
+
+# Server ----
+
+server <- function(input, output, session) {
+  
+  phylotraceVersion <- paste("1.5.0")
+  
+  #TODO Enable this, or leave disabled
+  # Kill server on session end
+  session$onSessionEnded( function() {
+    stopApp()
+  })
+  
+  # Disable various user inputs (visualization control)
+  shinyjs::disable('mst_edge_label') 
+  
+  ## Functions ----
+  
+  # Function to read and format FASTA sequences
+  format_fasta <- function(filepath) {
+    fasta <- readLines(filepath)
+    formatted_fasta <- list()
+    current_sequence <- ""
+    
+    for (line in fasta) {
+      if (startsWith(line, ">")) {
+        if (current_sequence != "") {
+          formatted_fasta <- append(formatted_fasta, list(current_sequence))
+          current_sequence <- ""
+        }
+        formatted_fasta <- append(formatted_fasta, list(line))
+      } else {
+        current_sequence <- paste0(current_sequence, line)
+      }
+    }
+    if (current_sequence != "") {
+      formatted_fasta <- append(formatted_fasta, list(current_sequence))
+    }
+    
+    formatted_fasta
+  }
+  
+  # Function to color-code the bases in a sequence
+  color_sequence <- function(sequence) {
+    sequence <- gsub("A", "<span class='base-a'>A</span>", sequence)
+    sequence <- gsub("T", "<span class='base-t'>T</span>", sequence)
+    sequence <- gsub("G", "<span class='base-g'>G</span>", sequence)
+    sequence <- gsub("C", "<span class='base-c'>C</span>", sequence)
+    sequence
+  }
+  
+  # Function to log messages to logfile
+  log_message <- function(log_file, message, append = TRUE) {
+    cat(format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "-", message, "\n", file = log_file, append = append)
+  }
+  
+  # Modified gheatmap function
+  gheatmap.mod <- function(p, data, offset=0, width=1, low="green", high="red", color="white",
+                           colnames=TRUE, colnames_position="bottom", colnames_angle=0, colnames_level=NULL,
+                           colnames_offset_x = 0, colnames_offset_y = 0, font.size=4, family="", hjust=0.5, legend_title = "value",
+                           colnames_color = "black") {
+    
+    colnames_position %<>% match.arg(c("bottom", "top"))
+    variable <- value <- lab <- y <- NULL
+    
+    ## if (is.null(width)) {
+    ##     width <- (p$data$x %>% range %>% diff)/30
+    ## }
+    
+    ## convert width to width of each cell
+    width <- width * (p$data$x %>% range(na.rm=TRUE) %>% diff) / ncol(data)
+    
+    isTip <- x <- y <- variable <- value <- from <- to <- NULL
+    
+    ## handle the display of heatmap on collapsed nodes
+    ## https://github.com/GuangchuangYu/ggtree/issues/242
+    ## extract data on leaves (& on collapsed internal nodes) 
+    ## (the latter is extracted only when the input data has data on collapsed
+    ## internal nodes)
+    df <- p$data
+    nodeCo <- intersect(df %>% filter(is.na(x)) %>% 
+                          select(.data$parent, .data$node) %>% unlist(), 
+                        df %>% filter(!is.na(x)) %>% 
+                          select(.data$parent, .data$node) %>% unlist())
+    labCo <- df %>% filter(.data$node %in% nodeCo) %>% 
+      select(.data$label) %>% unlist()
+    selCo <- intersect(labCo, rownames(data))
+    isSel <- df$label %in% selCo
+    
+    df <- df[df$isTip | isSel, ]
+    start <- max(df$x, na.rm=TRUE) + offset
+    
+    dd <- as.data.frame(data)
+    ## dd$lab <- rownames(dd)
+    i <- order(df$y)
+    
+    ## handle collapsed tree
+    ## https://github.com/GuangchuangYu/ggtree/issues/137
+    i <- i[!is.na(df$y[i])]
+    
+    lab <- df$label[i]
+    ## dd <- dd[lab, , drop=FALSE]
+    ## https://github.com/GuangchuangYu/ggtree/issues/182
+    dd <- dd[match(lab, rownames(dd)), , drop = FALSE]
+    
+    
+    dd$y <- sort(df$y)
+    dd$lab <- lab
+    ## dd <- melt(dd, id=c("lab", "y"))
+    dd <- gather(dd, variable, value, -c(lab, y))
+    
+    i <- which(dd$value == "")
+    if (length(i) > 0) {
+      dd$value[i] <- NA
+    }
+    if (is.null(colnames_level)) {
+      dd$variable <- factor(dd$variable, levels=colnames(data))
+    } else {
+      dd$variable <- factor(dd$variable, levels=colnames_level)
+    }
+    V2 <- start + as.numeric(dd$variable) * width
+    mapping <- data.frame(from=dd$variable, to=V2)
+    mapping <- unique(mapping)
+    
+    dd$x <- V2
+    dd$width <- width
+    dd[[".panel"]] <- factor("Tree")
+    if (is.null(color)) {
+      p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, inherit.aes=FALSE)
+    } else {
+      p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, color=color, inherit.aes=FALSE)
+    }
+    if (is(dd$value,"numeric")) {
+      p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value=NA, name = legend_title) # "white")
+    } else {
+      p2 <- p2 + scale_fill_discrete(na.value=NA, name = legend_title) #"white")
+    }
+    
+    if (colnames) {
+      if (colnames_position == "bottom") {
+        y <- 0
+      } else {
+        y <- max(p$data$y) + 1
+      }
+      mapping$y <- y
+      mapping[[".panel"]] <- factor("Tree")
+      p2 <- p2 + geom_text(data=mapping, aes(x=to, y = y, label=from), color = colnames_color, size=font.size, family=family, inherit.aes = FALSE,
+                           angle=colnames_angle, nudge_x=colnames_offset_x, nudge_y = colnames_offset_y, hjust=hjust)
+    }
+    
+    p2 <- p2 + theme(legend.position="right")
+    ## p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))
+    
+    if (!colnames) {
+      ## https://github.com/GuangchuangYu/ggtree/issues/204
+      p2 <- p2 + scale_y_continuous(expand = c(0,0))
+    }
+    
+    attr(p2, "mapping") <- mapping
+    return(p2)
+  }
+  
+  # Get rhandsontable
+  get.entry.table.meta <- reactive({
+    if(!is.null(hot_to_r(input$db_entries))){
+      table <- hot_to_r(input$db_entries)
+      select(select(table, -13), 1:(12 + nrow(DB$cust_var)))
+    }
+  })
+  
+  # Function to find columns with varying values
+  var_alleles <- function(dataframe) {
+    
+    varying_columns <- c()
+    
+    for (col in 1:ncol(dataframe)) {
+      unique_values <- unique(dataframe[, col])
+      
+      if (length(unique_values) > 1) {
+        varying_columns <- c(varying_columns, col)
+      }
+    }
+    
+    return(varying_columns)
+  }
+  
+  # Functions to compute hamming distances dependent on missing value handling
+  hamming.dist <- function(x, y) {
+    sum(x != y)
+  }
+  
+  hamming.distIgnore <- function(x, y) {
+    sum( (x != y) & !is.na(x) & !is.na(y) )
+  }
+  
+  hamming.distCategory <- function(x, y) {
+    sum((x != y | xor(is.na(x), is.na(y))) & !(is.na(x) & is.na(y)))
+  }
+  
+  compute.distMatrix <- function(profile, hamming.method) {
+    mat <- as.matrix(profile)
+    n <- nrow(mat)
+    dist_mat <- matrix(0, n, n)
+    for (i in 1:(n-1)) {
+      for (j in (i+1):n) {
+        dist_mat[i, j] <- hamming.method(x = mat[i, ], y = mat[j, ])
+        dist_mat[j, i] <- dist_mat[i, j]
+      }
+    }
+    return(dist_mat)
+  }
+  
+  # Function to determine entry table height
+  table_height <- reactive({
+    if (input$table_height == TRUE) {
+      NULL
+    } else {900}
+  })
+  
+  # Function to determine distance matrix height
+  distancematrix_height <- reactive({
+    if(DB$distancematrix_nrow > 33) {
+      800
+    } else {NULL}
+  })
+  
+  # Function to missing value table height
+  miss.val.height <- reactive({
+    if(input$miss_val_height == TRUE) {
+      NULL
+    } else {800}
+  })
+  
+  #Function to check custom variable classes
+  column_classes <- function(df) {
+    sapply(df, function(x) {
+      if (class(x) == "numeric") {
+        return("cont")
+      } else if (class(x) == "character") {
+        return("categ")
+      } else {
+        return(class(x))
+      }
+    })
+  }
+  
+  # Function to hash database
+  hash_database <- function(folder) {
+    loci_files <- list.files(folder)
+    loci_names <- sapply(strsplit(loci_files, "[.]"), function(x) x[1])
+    loci_paths <- file.path(folder, loci_files)
+    
+    hashes <- sapply(loci_paths, hash_locus)
+    names(hashes) <- loci_names
+    hashes
+  }
+  
+  # Function to hash a locus
+  hash_locus <- function(locus_path) {
+    locus_file <- readLines(locus_path)
+    seq_list <- locus_file[seq(2, length(locus_file), 3)]
+    seq_hash <- sha256(seq_list)
+    seq_idx <- paste0(">", seq_hash)
+    
+    locus_file[seq(1, length(locus_file), 3)] <- seq_idx
+    writeLines(locus_file, locus_path)
+    
+    seq_hash
+  }
+  
+  # Get locus hashes
+  get_locus_hashes <- function(locus_path) {
+    locus_file <- readLines(locus_path)
+    hash_list <- locus_file[seq(1, length(locus_file), 3)]
+    hash_list <- sapply(strsplit(hash_list, "[>]"), function(x) x[2])
+  }
+  
+  extract_seq <- function(locus_path, hashes) {
+    locus_file <- readLines(locus_path)
+    hash_list <- sapply(strsplit(locus_file[seq(1, length(locus_file), 3)], "[>]"), function(x) x[2])
+    seq_list <- locus_file[seq(2, length(locus_file), 3)]
+    seq_idx <- hash_list %in% hashes
+    
+    list(
+      idx = hash_list[seq_idx],
+      seq = seq_list[seq_idx]
+    )
+  }
+  
+  add_new_sequences <- function(locus_path, sequences) {
+    locus_file <- file(locus_path, open = "a+")
+    for (i in seq_along(sequences$idx)) {
+      writeLines(c("", paste0(">", sequences$idx[i]), sequences$seq[i]), locus_file)
+    }
+    close(locus_file)
+  }
+  
+  # Compute clusters to use in visNetwork
+  compute_clusters <- function(nodes, edges, threshold) {
+    groups <- rep(0, length(nodes$id))
+    edges_groups <- rep(0, length(edges$from))
+    
+    edges_table <- data.frame(
+      from = edges$from,
+      to = edges$to,
+      weight = edges$weight
+    )
+    
+    count <- 0
+    while (any(groups == 0)) {
+      group_na <- groups == 0
+      labels <- nodes$id[group_na]
+      
+      cluster <- nodes$id[group_na][1] # Initialize with 1 label
+      while (!is_empty(labels)) {
+        sub_tb <- edges_table[(edges_table$from %in% cluster | edges_table$to %in% cluster) & edges_table$weight <= threshold,]
+        
+        if (nrow(sub_tb) == 0 | length(unique(c(sub_tb$from, sub_tb$to))) == length(cluster)) {
+          count <- count + 1
+          groups[nodes$id %in% cluster] <- paste("Group", count)
+          edges_groups[edges$from %in% cluster & edges$to %in% cluster] <- paste("Group", count)
+          break
+        } else {
+          cluster <- unique(c(sub_tb$from, sub_tb$to))
+        }
+      }
+    }
+    list(groups = groups,
+         edges = edges_groups)
+  }
+  
+  # Check gene screening status
+  check_status <- function(isolate) {
+    iso_name <- gsub(".zip", "", basename(isolate))
+    if(file.exists(file.path(DB$database, gsub(" ", "_", DB$scheme),
+                             "Isolates", iso_name, "status.txt"))) {
+      if(str_detect(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
+                                        "Isolates", iso_name, "status.txt"))[1], 
+                    "successfully")) {
+        return("success")
+      } else {
+        return("fail")
+      }
+    } else {return("unfinished")}
+  }
+  
+  # Reset gene screening status
+  remove.screening.status <- function(isolate) {
+    if(file.exists(file.path(DB$database, 
+                             gsub(" ", "_", DB$scheme),
+                             "Isolates",
+                             isolate,
+                             "status.txt"))) {
+      file.remove(
+        file.path(DB$database, 
+                  gsub(" ", "_", DB$scheme),
+                  "Isolates",
+                  isolate,
+                  "status.txt")
+      )
+    }
+  }
+  
+  # Truncate hashes
+  truncHash <- function(hash) {
+    if(!is.na(hash)) {
+      paste0(str_sub(hash, 1, 4), "...", str_sub(hash, nchar(hash) - 3, nchar(hash))) 
+    } else {NA}
+  }
+  
+  # Function to check for duplicate isolate IDs for multi typing start
+  dupl_mult_id <- reactive({
+    req(Typing$multi_sel_table)
+    if(!is.null(DB$data)) {
+      selection <- Typing$multi_sel_table[which(unlist(Typing$multi_sel_table$Files) %in% unlist(DB$data["Assembly ID"])),]
+      selection$Files
+    } else {""}
+  })
+  
+  # Function to check single typing log file
+  check_new_entry <- reactive({
+    
+    invalidateLater(5000, session)
+    
+    if(!is.null(DB$database)) {
+      if(file_exists(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))) {
+        
+        Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
+        
+        if(is.null(DB$data)) {
+          if(nrow(Database[["Typing"]]) >= 1) {
+            TRUE
+          } else {FALSE}
+        } else {
+          if(nrow(DB$data) < nrow(Database[["Typing"]])) {
+            TRUE
+          } else {
+            FALSE
+          }
+        }
+      } else {FALSE}
+    }
+  })
+  
+  # Render Entry Table Highlights 
+  
+  diff_allele <- reactive({
+    if (!is.null(DB$data) & !is.null(input$compare_select) & !is.null(DB$cust_var)) {
+      var_alleles(select(DB$data, input$compare_select)) + (13 + nrow(DB$cust_var))
+    }
+  })
+  
+  err_thresh <- reactive({
+    if (!is.null(DB$data) & !is.null(DB$number_loci)) {
+      which(as.numeric(DB$data[["Errors"]]) >= (DB$number_loci * 0.05)) 
+    }
+  })
+  
+  err_thresh_na <- reactive({
+    if (!is.null(DB$na_table) & !is.null(DB$number_loci)) {
+      which(as.numeric(DB$na_table[["Errors"]]) >= (DB$number_loci * 0.05)) 
+    }
+  })
+  
+  true_rows <- reactive({
+    if (!is.null(DB$data)) {
+      which(DB$data$Include == TRUE)
+    }
+  })
+  
+  duplicated_names <- reactive({
+    if (!is.null(DB$meta)) {
+      which(duplicated(DB$meta$`Assembly Name`) | duplicated(DB$meta$`Assembly Name`, fromLast = TRUE))
+    }
+  })
+  
+  duplicated_ids <- reactive({
+    if (!is.null(DB$meta)) {
+      which(duplicated(DB$meta$`Assembly ID`) | duplicated(DB$meta$`Assembly ID`, fromLast = TRUE))
+    }
+  })
+  
+  # _______________________ ####
+  
+  ## Startup ----
+  shinyjs::addClass(selector = "body", class = "sidebar-collapse")
+  shinyjs::removeClass(selector = "body", class = "sidebar-toggle")
+  
+  output$messageMenu <- renderText({
+    HTML(format(Sys.time(), "%Y-%m-%d %H:%M:%S %Z"))
+  })
+  
+  # Initiate logging
+  if(!dir_exists(paste0(getwd(), "/logs"))) {
+    dir_create(paste0(getwd(), "/logs"))
+  }
+  
+  logfile <- file.path(paste0(getwd(), "/logs/phylotrace.log"))
+  
+  log <- log_open(logfile, logdir = FALSE)
+  
+  log_print("Session started")
+  
+  # Clear screening file
+  if(file.exists(paste0(getwd(), "/execute/screening/output_file.tsv"))) {
+    file.remove(paste0(getwd(), "/execute/screening/output_file.tsv"))
+  }
+  
+  if(file.exists(paste0(getwd(), "/execute/screening/error.txt"))) {
+    file.remove(paste0(getwd(), "/execute/screening/error.txt"))
+  }
+  
+  # Declare reactive variables
+  Startup <- reactiveValues(sidebar = TRUE, 
+                            header = TRUE) # reactive variables related to startup process
+  
+  DB <- reactiveValues(data = NULL, 
+                       block_db = FALSE, 
+                       load_selected = TRUE,
+                       no_na_switch = FALSE,
+                       first_look = FALSE) # reactive variables related to local database
+  
+  Typing <- reactiveValues(table = data.frame(), 
+                           single_path = data.frame(),
+                           progress = 0, 
+                           progress_format_start = 0, 
+                           progress_format_end = 0,
+                           result_list = NULL,
+                           status = "") # reactive variables related to typing process
+  
+  Screening <- reactiveValues(status = "idle",
+                              picker_status = TRUE,
+                              first_result = NULL) # reactive variables related to gene screening
+  
+  Vis <- reactiveValues(cluster = NULL, 
+                        metadata = list(),
+                        custom_label_nj = data.frame(),
+                        nj_label_pos_y = list(),
+                        nj_label_pos_x = list(),
+                        nj_label_size = list(),
+                        custom_label_upgma = data.frame(),
+                        upgma_label_pos_y = list(),
+                        upgma_label_pos_x = list(),
+                        upgma_label_size = list()) # reactive variables related to visualization
+  
+  Report <- reactiveValues() # reactive variables related to report functions
+  
+  Scheme <- reactiveValues() # reactive variables related to scheme  functions
+  
+  # Load last used database if possible
+  if(paste0(getwd(), "/execute/last_db.rds") %in% dir_ls(paste0(getwd(), "/execute"))) {
+    DB$last_db <- TRUE
+  }
+  
+  # Locate local Database
+  observe({
+    shinyDirChoose(input,
+                   "db_location",
+                   roots = c(Home = path_home(), Root = "/"),
+                   defaultRoot = "Home",
+                   session = session)
+    
+    if(!is.null(DB$select_new)) {
+      if(DB$select_new == FALSE) {
+        if(DB$block_db == FALSE) {
+          DB$database <- as.character(
+            parseDirPath(
+              roots = c(Home = path_home(), Root = "/"),
+              input$db_location
+            )
+          )
+          
+          DB$exist <- (length(dir_ls(DB$database)) == 0)  # Logical any local database present
+          
+          DB$available <- gsub("_", " ", basename(dir_ls(DB$database))) # List of local schemes available
+        }
+        
+      } else if (DB$select_new ==  TRUE) {
+        DB$database <- paste0(DB$new_database, "/Database")
+        
+      }
+    } else {
+      if(!is.null(DB$last_db) & file.exists(paste0(getwd(), "/execute/last_db.rds"))) {
+        
+        DB$database <- readRDS(paste0(getwd(), "/execute/last_db.rds"))
+        
+        if(dir_exists(DB$database)) {
+          DB$exist <- (length(dir_ls(DB$database)) == 0)  # Logical any local database present
+          
+          DB$available <- gsub("_", " ", basename(dir_ls(DB$database))) # List of local schemes available
+        }
+      }
+    }
+  })
+  
+  ### Set up typing environment ----
+  
+  # Null typing progress trackers
+  writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
+  writeLines("0\n", paste0(getwd(), "/logs/progress.txt"))
+  
+  if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
+    unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
+  }
+  
+  # Reset typing feedback values
+  Typing$pending <- FALSE
+  Typing$multi_started <- FALSE
+  Typing$multi_help <- FALSE
+  saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
+  Typing$last_success <- "0" # Null last multi typing success name
+  Typing$last_failure <- "0" # Null last multi typing failure name
+  
+  ### Landing page UI ----
+  observe({
+    if (Startup$sidebar == FALSE) {
+      shinyjs::removeClass(selector = "body", class = "sidebar-collapse")
+      shinyjs::addClass(selector = "body", class = "sidebar-toggle")
+    }
+  })
+  
+  output$start_message <- renderUI({
+    column(
+      width = 12, 
+      align = "center",
+      br(), br(), br(), br(), br(), br(),
+      div( 
+        class = "image",
+        imageOutput("imageOutput")
+      ),
+      br(), br(), br(),
+      p(
+        HTML(
+          paste(
+            tags$span(style='color: white; font-size: 16px;', 'Proceed by loading a compatible local database or create a new one.')
+          )
+        )
+      ),
+      br(), 
+      fluidRow(
+        column(
+          width = 6,
+          align = "right",
+          shinyDirButton(
+            "db_location",
+            "Browse",
+            icon = icon("folder-open"),
+            title = "Locate the database folder",
+            buttonType = "default",
+            root = path_home()
+          )
+        ),
+        column(
+          width = 6,
+          align = "left",
+          shinyDirButton(
+            "create_new_db",
+            "Create New",
+            icon = icon("plus"),
+            title = "Choose location for new PhyloTrace database",
+            buttonType = "default",
+            root = path_home()
+          )
+        )
+      ),
+      br(), br(),
+      fluidRow(
+        column(
+          width = 12,
+          align = "center",
+          uiOutput("load_db"),
+          br(), br(), br(), br(), br(), br(), br()
+        )
+      )
+    )
+  })
+  
+  # User selection new db or load db
+  observeEvent(input$create_new_db, {
+    log_print("Input create_new_db")
+    DB$select_new <- TRUE
+  })
+  
+  observeEvent(input$db_location, {
+    log_print("Input db_location")
+    DB$select_new <- FALSE
+  })
+  
+  # Load db & scheme selection UI
+  output$load_db <- renderUI({
+    if(!is.null(DB$select_new)) {
+      if(length(DB$new_database) > 0 & DB$select_new) {
+        column(
+          width = 12,
+          p(
+            tags$span(
+              style='color: white; font-size: 15px;',
+              HTML(
+                paste(
+                  'New database will be created in',
+                  DB$new_database
+                )
+              )
+            )
+          ),
+          br(),
+          actionButton(
+            "load",
+            "Create",
+            class = "load-start"
+          )
+        )
+      } else if(length(DB$available) > 0 & !(DB$select_new)) {
+        if(any(!(gsub(" ", "_", DB$available) %in% schemes))) {
+          column(
+            width = 12,
+            p(
+              tags$span(
+                style='color: white; font-size: 15px; font-style: italic;',
+                HTML(
+                  paste('Selected:', DB$database)
+                )
+              )
+            ),
+            uiOutput("scheme_db"),
+            br(), 
+            p(
+              HTML(
+                paste(
+                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
+                            'Warning: Folder contains invalid elements.')
+                )
+              )
+            ),
+            br(),
+            actionButton(
+              "load",
+              "Load",
+              class = "load-start"
+            )
+          )
+        } else {
+          column(
+            width = 12,
+            p(
+              tags$span(
+                style='color: white; font-size: 15px; font-style: italic;',
+                HTML(
+                  paste('Selected:', DB$database)
+                )
+              )
+            ),
+            uiOutput("scheme_db"),
+            br(), br(),
+            actionButton(
+              "load",
+              "Load",
+              class = "load-start"
+            )
+          )
+        }
+      } 
+    } else if((!is.null(DB$last_db)) & (!is.null(DB$available))) {
+      if (DB$last_db == TRUE & (length(DB$available) > 0)) {
+        if(any(!(gsub(" ", "_", DB$available) %in% schemes))) {
+          column(
+            width = 12,
+            p(
+              tags$span(
+                style='color: white; font-size: 15px; font-style: italic;',
+                HTML(
+                  paste('Last used:', DB$database)
+                )
+              )
+            ),
+            uiOutput("scheme_db"),
+            br(), 
+            p(
+              HTML(
+                paste(
+                  tags$span(style='color: #E18B00; font-size: 13px; font-style: italic;', 
+                            'Warning: Folder contains invalid elements.')
+                )
+              )
+            ),
+            br(),
+            actionButton(
+              "load",
+              "Load",
+              class = "load-start"
+            )
+          )
+        } else {
+          column(
+            width = 12,
+            p(
+              tags$span(
+                style='color: white; font-size: 15px; font-style: italic;',
+                HTML(
+                  paste('Last used:', DB$database)
+                )
+              )
+            ),
+            uiOutput("scheme_db"),
+            br(), br(),
+            actionButton(
+              "load",
+              "Load",
+              class = "load-start"
+            )
+          )
+        }
+      } else if (DB$last_db == TRUE & (length(DB$available) == 0)) {
+        column(
+          width = 12,
+          p(
+            tags$span(
+              style='color: white; font-size: 15px; font-style: italic;',
+              HTML(
+                paste('Last used:', DB$database)
+              )
+            )
+          ),
+          br(),
+          actionButton(
+            "load",
+            "Load",
+            class = "load-start"
+          )
+        )
+      }
+    }
+  })
+  
+  output$imageOutput <- renderImage({
+    # Path to your PNG image with a transparent background
+    image_path <- paste0(getwd(), "/www/PhyloTrace.png")
+    
+    # Use HTML to display the image with the <img> tag
+    list(src = image_path,
+         height = 180)
+  }, deleteFile = FALSE)
+  
+  ### Load app event ----
+  
+  observeEvent(input$load, {
+    
+    # Reset reactive screening variables 
+    output$screening_start <- NULL
+    output$screening_result_sel <- NULL
+    output$screening_result <- NULL
+    output$screening_fail <- NULL
+    Screening$status_df <- NULL
+    Screening$choices <- NULL
+    Screening$picker_status <- TRUE
+    Screening$status <- "idle"
+    Screening$first_result <- NULL
+    if(!is.null(input$screening_select)) {
+      if(!is.null(DB$data)) {
+        updatePickerInput(session, "screening_select", selected = character(0))
+      }
+    }
+    
+    log_print("Input load")
+    
+    # set typing start control variable
+    Typing$reload <- TRUE
+    
+    # reset typing status on start(
+    if(Typing$status == "Finalized") {Typing$status <- "Inactive"}
+    if(!is.null(Typing$single_path)) {Typing$single_path <- data.frame()}
+    
+    #### Render status bar ----
+    observe({
+      req(DB$scheme)
+      
+      if(is.null(input$scheme_position)) {
+        output$loaded_scheme <- renderUI({
+          fluidRow(
+            tags$li(
+              class = "dropdown", 
+              tags$span(HTML(
+                paste('<i class="fa-solid fa-layer-group"></i>', 
+                      "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
+                      DB$scheme,
+                      "</i>")), 
+                style = "color:white;")
+            )
+          )
+        })
+      } 
+      
+      if(!is.null(input$scheme_position)) {
+        output$loaded_scheme <- renderUI({
+          fluidRow(
+            tags$li(
+              class = "dropdown", 
+              tags$span(HTML(
+                paste('<i class="fa-solid fa-layer-group"></i>', 
+                      "Selected scheme:&nbsp;&nbsp;&nbsp;<i>",
+                      DB$scheme,
+                      "</i>")), 
+                style = "color:white;"),
+              div(
+                class = "reload-bttn",
+                style = paste0("margin-left:", 30 + input$scheme_position, "px; position: relative; top: -24px;"),
+                actionButton(
+                  "reload_db",
+                  label = "",
+                  icon = icon("rotate")
+                )
+              )
+            )
+          )
+        })
+      }
+    })
+    
+    observe({
+      if(!is.null(DB$database)){
+        if(nchar(DB$database) > 60) {
+          database <- paste0(substring(DB$database, first = 1, last = 60), "...")
+        } else {
+          database <- DB$database
+        }
+        output$databasetext <- renderUI({
+          fluidRow(
+            tags$li(
+              class = "dropdown", 
+              tags$span(HTML(
+                paste('<i class="fa-solid fa-folder-open"></i>', 
+                      "Database:&nbsp;&nbsp;&nbsp;<i>",
+                      database,
+                      "</i>")), 
+                style = "color:white;")
+            ),
+            if(nchar(database) > 60) {bsTooltip("databasetext", 
+                                                HTML(DB$database), 
+                                                placement = "bottom", 
+                                                trigger = "hover")}
+          )
+        })
+      }
+    })
+    
+    observe({
+      if(!is.null(DB$database)) {
+        if(Typing$status == "Finalized"){
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp; <i>typing finalized</i>")),
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(Typing$status == "Attaching"){
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp; <i>evaluating typing results</i>")),
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(Typing$status == "Processing") {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> pending typing</i>")), 
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(Screening$status == "started") {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> pending gene screening</i>")), 
+                  style = "color:white;")
+              )
+            )
+          )
+        } else if(Screening$status == "finished") {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp;<i> gene screening finalized</i>")), 
+                  style = "color:white;")
+              )
+            )
+          )
+        } else {
+          output$statustext <- renderUI(
+            fluidRow(
+              tags$li(
+                class = "dropdown", 
+                tags$span(HTML(
+                  paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                        "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
+                  style = "color:white;")
+              )
+            )
+          )
+        }    
+      }
+    })
+    
+    # Null single typing status
+    if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
+      Typing$progress <- 0
+      
+      Typing$progress_format <- 900000
+      
+      output$single_typing_progress <- NULL
+      
+      output$typing_fin <- NULL
+      
+      output$single_typing_results <- NULL
+      
+      output$typing_formatting <- NULL
+      
+      Typing$single_path <- data.frame()
+      
+      # reset results file 
+      if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
+        unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
+        # Resetting single typing progress logfile bar 
+        con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
+        
+        cat("0\n", file = con)   
+        
+        close(con)
+      }
+    }
+    
+    shinyjs::runjs(
+      'if(document.querySelector("#loaded_scheme > div > li > span") !== null) {
+          // Select the span element
+          let spanElement = document.querySelector("#loaded_scheme > div > li > span");
+                    
+          // Get the bounding rectangle of the span element
+          let rect = spanElement.getBoundingClientRect();
+          
+          // Extract the width
+          let width = rect.width;
+          
+          Shiny.setInputValue("scheme_position", width);            
+        }'
+    )
+    
+    # Load app elements based on database availability and missing value presence
+    if(!is.null(DB$select_new)) {
+      if(DB$select_new & (paste0(DB$new_database, "/Database") %in% dir_ls(DB$new_database))) {
+        
+        log_print("Directory already contains a database")
+        
+        show_toast(
+          title = "Directory already contains a database",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+        DB$load_selected <- FALSE
+        
+      } else if(DB$select_new | (DB$select_new == FALSE & is.null(input$scheme_db))) {
+        
+        log_print(paste0("New database created in ", DB$new_database))
+        
+        DB$check_new_entries <- TRUE
+        DB$data <- NULL
+        DB$meta_gs <- NULL
+        DB$meta <- NULL
+        DB$meta_true <- NULL
+        DB$allelic_profile <- NULL
+        DB$allelic_profile_trunc <- NULL
+        DB$allelic_profile_true <- NULL
+        
+        # null Distance matrix, entry table and plots
+        output$db_distancematrix <- NULL 
+        output$db_entries_table <- NULL
+        output$tree_mst <- NULL
+        output$tree_nj <- NULL
+        output$tree_upgma <- NULL
+        
+        # null report values
+        Report$report_list_mst <- list()
+        Report$report_list_nj <- list()
+        Report$report_list_upgma <- list()
+        
+        # null plots
+        Vis$nj <- NULL
+        Vis$upgma <- NULL
+        Vis$ggraph_1 <- NULL
+        
+        removeModal()
+        
+        #### Render Menu Items ----
+        
+        Startup$sidebar <- FALSE
+        Startup$header <- FALSE
+        
+        output$menu_sep2 <- renderUI(hr())
+        
+        # Hide start message
+        output$start_message <- NULL
+        
+        DB$load_selected <- FALSE
+        
+        # Declare database path
+        DB$database <- file.path(DB$new_database, "Database")
+        
+        # Set database availability screening variables to present database
+        DB$block_db <- TRUE
+        DB$select_new <- FALSE
+        
+        # Render menu with Manage Schemes as start tab and no Missing values tab
+        output$menu <- renderMenu(
+          sidebarMenu(
+            menuItem(
+              text = "Database Browser",
+              tabName = "database",
+              icon = icon("hard-drive"),
+              startExpanded = TRUE,
+              menuSubItem(
+                text = "Browse Entries",
+                tabName = "db_browse_entries"
+              ),
+              menuSubItem(
+                text = "Scheme Info",
+                tabName = "db_schemeinfo"
+              ),
+              menuSubItem(
+                text = "Loci Info",
+                tabName = "db_loci_info"
+              ),
+              menuSubItem(
+                text = "Distance Matrix",
+                tabName = "db_distmatrix"
+              )
+            ),
+            menuItem(
+              text = "Manage Schemes",
+              tabName = "init",
+              icon = icon("layer-group"),
+              selected = TRUE
+            ),
+            menuItem(
+              text = "Allelic Typing",
+              tabName = "typing",
+              icon = icon("gears")
+            ),
+            menuItem(
+              text = "Resistance Profile",
+              tabName = "gene_screening",
+              icon = icon("dna"),
+              startExpanded = TRUE,
+              menuSubItem(
+                text = "Browse Entries",
+                tabName = "gs_profile"
+              ),
+              menuSubItem(
+                text = "Screening",
+                tabName = "gs_screening"
+              )
+            ),
+            menuItem(
+              text = "Visualization",
+              tabName = "visualization",
+              icon = icon("circle-nodes")
+            ),
+            menuItem(
+              text = "Utilities",
+              tabName = "utilities",
+              icon = icon("screwdriver-wrench")
+            )
+          )
+        )
+        
+        # Dont render these elements
+        output$db_no_entries <- NULL
+        output$distancematrix_no_entries <- NULL
+        output$db_entries <- NULL
+        output$edit_index <- NULL
+        output$edit_scheme_d <- NULL
+        output$edit_entries <- NULL
+        output$compare_select <- NULL
+        output$delete_select <- NULL
+        output$del_bttn <- NULL
+        output$compare_allele_box <- NULL
+        output$download_entries <- NULL
+        output$missing_values <- NULL
+        output$delete_box <- NULL
+        output$missing_values_sidebar <- NULL
+        output$distmatrix_sidebar <- NULL
+        output$download_scheme_info <- NULL
+        output$download_loci <- NULL
+        output$entry_table_controls <- NULL
+        output$multi_stop <- NULL
+        output$metadata_multi_box <- NULL
+        output$start_multi_typing_ui <- NULL
+        output$pending_typing <- NULL
+        output$multi_typing_results <- NULL
+        output$single_typing_progress <- NULL
+        output$metadata_single_box <- NULL
+        output$start_typing_ui <- NULL
+        
+      }
+    } else {
+      log_print(paste0("Loading existing ", input$scheme_db, " database from ", DB$database))
+    }
+    
+    if(DB$load_selected == TRUE) {
+      
+      if(gsub(" ", "_", input$scheme_db) %in% schemes) { #Check if selected scheme valid
+        
+        # Save database path for next start
+        saveRDS(DB$database, paste0(getwd(), "/execute/last_db.rds"))
+        
+        DB$check_new_entries <- TRUE
+        DB$data <- NULL
+        DB$meta_gs <- NULL
+        DB$meta <- NULL
+        DB$meta_true <- NULL
+        DB$allelic_profile <- NULL
+        DB$allelic_profile_trunc <- NULL
+        DB$allelic_profile_true <- NULL
+        DB$scheme <- input$scheme_db
+        
+        # null Distance matrix, entry table and plots
+        output$db_distancematrix <- NULL 
+        output$db_entries_table <- NULL
+        output$tree_mst <- NULL
+        output$tree_nj <- NULL
+        output$tree_upgma <- NULL
+        
+        # null typing initiation UI
+        output$multi_stop <- NULL
+        output$metadata_multi_box <- NULL
+        output$start_multi_typing_ui <- NULL
+        output$pending_typing <- NULL
+        output$multi_typing_results <- NULL
+        output$single_typing_progress <- NULL
+        output$metadata_single_box <- NULL
+        output$start_typing_ui <- NULL
+        
+        # null report values
+        Report$report_list_mst <- list()
+        Report$report_list_nj <- list()
+        Report$report_list_upgma <- list()
+        
+        # null plots
+        Vis$nj <- NULL
+        Vis$upgma <- NULL
+        Vis$ggraph_1 <- NULL
+        
+        removeModal()
+        
+        #### Render Menu Items ----
+        
+        Startup$sidebar <- FALSE
+        Startup$header <- FALSE
+        
+        output$menu_sep2 <- renderUI(hr())
+        
+        # Hide start message
+        output$start_message <- NULL
+        
+        if(any(grepl(gsub(" ", "_", DB$scheme), dir_ls(DB$database)))) {
+          
+          if(!any(grepl("alleles", dir_ls(paste0(
+            DB$database, "/", 
+            gsub(" ", "_", DB$scheme)))))) {
+            
+            log_print("Missing loci files")
+            
+            # Show message that loci files are missing
+            showModal(
+              modalDialog(
+                paste0("Whoops! No loci files are present in the local ", 
+                       DB$scheme, 
+                       " folder. Download the scheme again (no influence on already typed assemblies)."),
+                title = "Local Database Error",
+                fade = TRUE,
+                easyClose = TRUE,
+                footer = tagList(
+                  modalButton("Okay")
+                )
+              )
+            )
+            
+            # Render menu with Manage Schemes as start tab
+            output$menu <- renderMenu(
+              sidebarMenu(
+                menuItem(
+                  text = "Database Browser",
+                  tabName = "database",
+                  icon = icon("hard-drive"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "db_browse_entries"
+                  ),
+                  menuSubItem(
+                    text = "Scheme Info",
+                    tabName = "db_schemeinfo"
+                  ),
+                  menuSubItem(
+                    text = "Loci Info",
+                    tabName = "db_loci_info"
+                  ),
+                  menuSubItem(
+                    text = "Distance Matrix",
+                    tabName = "db_distmatrix"
+                  ),
+                  menuSubItem(
+                    text = "Missing Values",
+                    tabName = "db_missing_values",
+                    icon = icon("triangle-exclamation")
+                  )
+                ),
+                menuItem(
+                  text = "Manage Schemes",
+                  tabName = "init",
+                  icon = icon("layer-group"),
+                  selected = TRUE
+                ),
+                menuItem(
+                  text = "Allelic Typing",
+                  tabName = "typing",
+                  icon = icon("gears")
+                ),
+                menuItem(
+                  text = "Resistance Profile",
+                  tabName = "gene_screening",
+                  icon = icon("dna"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "gs_profile"
+                  ),
+                  menuSubItem(
+                    text = "Screening",
+                    tabName = "gs_screening"
+                  )
+                ),
+                menuItem(
+                  text = "Visualization",
+                  tabName = "visualization",
+                  icon = icon("circle-nodes")
+                ),
+                menuItem(
+                  text = "Utilities",
+                  tabName = "utilities",
+                  icon = icon("screwdriver-wrench")
+                )
+              )
+            )
+          } else if (!any(grepl("scheme_info.html", dir_ls(paste0(
+            DB$database, "/", 
+            gsub(" ", "_", DB$scheme)))))) {
+            
+            output$download_scheme_info <- NULL
+            
+            log_print("Scheme info file missing")
+            
+            # Show message that scheme info is missing
+            showModal(
+              modalDialog(
+                paste0("Whoops! Scheme info of the local ", 
+                       DB$scheme, 
+                       " database is missing. Download the scheme again (no influence on already typed assemblies)."),
+                title = "Local Database Error",
+                fade = TRUE,
+                easyClose = TRUE,
+                footer = tagList(
+                  modalButton("Okay")
+                )
+              )
+            )
+            
+            # Render menu with Manage Schemes as start tab
+            output$menu <- renderMenu(
+              sidebarMenu(
+                menuItem(
+                  text = "Database Browser",
+                  tabName = "database",
+                  icon = icon("hard-drive"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "db_browse_entries"
+                  ),
+                  menuSubItem(
+                    text = "Scheme Info",
+                    tabName = "db_schemeinfo"
+                  ),
+                  menuSubItem(
+                    text = "Loci Info",
+                    tabName = "db_loci_info"
+                  ),
+                  menuSubItem(
+                    text = "Distance Matrix",
+                    tabName = "db_distmatrix"
+                  ),
+                  menuSubItem(
+                    text = "Missing Values",
+                    tabName = "db_missing_values",
+                    icon = icon("triangle-exclamation")
+                  )
+                ),
+                menuItem(
+                  text = "Manage Schemes",
+                  tabName = "init",
+                  icon = icon("layer-group"),
+                  selected = TRUE
+                ),
+                menuItem(
+                  text = "Allelic Typing",
+                  tabName = "typing",
+                  icon = icon("gears")
+                ),
+                menuItem(
+                  text = "Resistance Profile",
+                  tabName = "gene_screening",
+                  icon = icon("dna"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "gs_profile"
+                  ),
+                  menuSubItem(
+                    text = "Screening",
+                    tabName = "gs_screening"
+                  )
+                ),
+                menuItem(
+                  text = "Visualization",
+                  tabName = "visualization",
+                  icon = icon("circle-nodes")
+                ),
+                menuItem(
+                  text = "Utilities",
+                  tabName = "utilities",
+                  icon = icon("screwdriver-wrench")
+                )
+              )
+            )
+            
+          } else if (!any(grepl("targets.csv", dir_ls(paste0(
+            DB$database, "/", 
+            gsub(" ", "_", DB$scheme)))))) {
+            
+            # Dont render target download button
+            output$download_loci <- NULL
+            
+            log_print("Missing loci info (targets.csv)")
+            
+            # Show message that scheme info is missing
+            showModal(
+              modalDialog(
+                paste0("Whoops! Loci info of the local ", 
+                       DB$scheme, 
+                       " database is missing. Download the scheme again (no influence on already typed assemblies)."),
+                title = "Local Database Error",
+                fade = TRUE,
+                easyClose = TRUE,
+                footer = tagList(
+                  modalButton("Okay")
+                )
+              )
+            )
+            
+            # Render menu with Manage Schemes as start tab
+            output$menu <- renderMenu(
+              sidebarMenu(
+                menuItem(
+                  text = "Database Browser",
+                  tabName = "database",
+                  icon = icon("hard-drive"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "db_browse_entries"
+                  ),
+                  menuSubItem(
+                    text = "Scheme Info",
+                    tabName = "db_schemeinfo"
+                  ),
+                  menuSubItem(
+                    text = "Loci Info",
+                    tabName = "db_loci_info"
+                  ),
+                  menuSubItem(
+                    text = "Distance Matrix",
+                    tabName = "db_distmatrix"
+                  ),
+                  menuSubItem(
+                    text = "Missing Values",
+                    tabName = "db_missing_values",
+                    icon = icon("triangle-exclamation")
+                  )
+                ),
+                menuItem(
+                  text = "Manage Schemes",
+                  tabName = "init",
+                  icon = icon("layer-group"),
+                  selected = TRUE
+                ),
+                menuItem(
+                  text = "Allelic Typing",
+                  tabName = "typing",
+                  icon = icon("gears")
+                ),
+                menuItem(
+                  text = "Resistance Profile",
+                  tabName = "gene_screening",
+                  icon = icon("dna"),
+                  startExpanded = TRUE,
+                  menuSubItem(
+                    text = "Browse Entries",
+                    tabName = "gs_profile"
+                  ),
+                  menuSubItem(
+                    text = "Screening",
+                    tabName = "gs_screening"
+                  )
+                ),
+                menuItem(
+                  text = "Visualization",
+                  tabName = "visualization",
+                  icon = icon("circle-nodes")
+                ),
+                menuItem(
+                  text = "Utilities",
+                  tabName = "utilities",
+                  icon = icon("screwdriver-wrench")
+                )
+              )
+            )
+            
+          } else {
+            # Produce Scheme Info Table
+            schemeinfo <-
+              read_html(paste0(
+                DB$database, "/",
+                gsub(" ", "_", DB$scheme),
+                "/scheme_info.html"
+              )) %>%
+              html_table(header = FALSE) %>%
+              as.data.frame(stringsAsFactors = FALSE)
+            names(schemeinfo) <- NULL
+            DB$schemeinfo <- schemeinfo
+            number_loci <- as.vector(DB$schemeinfo[6, 2])
+            DB$number_loci <- as.numeric(gsub(",", "", number_loci))
+            
+            # Produce Loci Info table
+            DB$loci_info <- read.csv(
+              file.path(DB$database, gsub(" ", "_", DB$scheme), "targets.csv"),
+              header = TRUE,
+              sep = "\t",
+              row.names = NULL,
+              colClasses = c(
+                "NULL",
+                "character",
+                "character",
+                "integer",
+                "integer",
+                "character",
+                "integer",
+                "NULL"
+              )
+            )
+            
+            # Check if number of loci/fastq-files of alleles is coherent with number of targets in scheme
+            if(DB$number_loci > length(dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")))) {
+              
+              log_print(paste0("Loci files are missing in the local ", DB$scheme, " folder"))
+              
+              # Show message that loci files are missing
+              showModal(
+                modalDialog(
+                  paste0("Whoops! Some loci files are missing in the local ", 
+                         DB$scheme, 
+                         " folder. Download the scheme again (no influence on already typed assemblies)."),
+                  title = "Local Database Error",
+                  fade = TRUE,
+                  easyClose = TRUE,
+                  footer = tagList(
+                    modalButton("Okay")
+                  )
+                )
+              )
+              
+              # Render menu with Manage Schemes as start tab
+              output$menu <- renderMenu(
+                sidebarMenu(
+                  menuItem(
+                    text = "Database Browser",
+                    tabName = "database",
+                    icon = icon("hard-drive"),
+                    startExpanded = TRUE,
+                    menuSubItem(
+                      text = "Browse Entries",
+                      tabName = "db_browse_entries"
+                    ),
+                    menuSubItem(
+                      text = "Scheme Info",
+                      tabName = "db_schemeinfo"
+                    ),
+                    menuSubItem(
+                      text = "Loci Info",
+                      tabName = "db_loci_info"
+                    ),
+                    menuSubItem(
+                      text = "Distance Matrix",
+                      tabName = "db_distmatrix"
+                    ),
+                    menuSubItem(
+                      text = "Missing Values",
+                      tabName = "db_missing_values",
+                      icon = icon("triangle-exclamation")
+                    )
+                  ),
+                  menuItem(
+                    text = "Manage Schemes",
+                    tabName = "init",
+                    icon = icon("layer-group"),
+                    selected = TRUE
+                  ),
+                  menuItem(
+                    text = "Allelic Typing",
+                    tabName = "typing",
+                    icon = icon("gears")
+                  ),
+                  menuItem(
+                    text = "Resistance Profile",
+                    tabName = "gene_screening",
+                    icon = icon("dna"),
+                    startExpanded = TRUE,
+                    menuSubItem(
+                      text = "Browse Entries",
+                      tabName = "gs_profile"
+                    ),
+                    menuSubItem(
+                      text = "Screening",
+                      tabName = "gs_screening"
+                    )
+                  ),
+                  menuItem(
+                    text = "Visualization",
+                    tabName = "visualization",
+                    icon = icon("circle-nodes")
+                  ),
+                  menuItem(
+                    text = "Utilities",
+                    tabName = "utilities",
+                    icon = icon("screwdriver-wrench")
+                  )
+                )
+              )
+              
+            } else {
+              ###### Alle checks bestanden -> Laden der DTB
+              # If typed entries present
+              if (any(grepl("Typing.rds", dir_ls(paste0(
+                DB$database, "/", gsub(" ", "_", DB$scheme)
+              ))))) {
+                
+                # Load database from files  
+                Database <- readRDS(file.path(DB$database, 
+                                              gsub(" ", "_", DB$scheme), 
+                                              "Typing.rds"))
+                
+                DB$data <- Database[["Typing"]]
+                
+                if(!is.null(DB$data)){
+                  if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+                    cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+                    DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
+                  } else {
+                    DB$cust_var <- data.frame()
+                  }
+                }
+                
+                DB$change <- FALSE
+                DB$meta_gs <- select(DB$data, c(1, 3:13))
+                DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+                DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+                DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+                DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
+                DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+                
+                # Null pipe 
+                con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
+                
+                cat("0\n", file = con)
+                
+                # Close the file connection
+                close(con)
+                
+                # Reset other reactive typing variables
+                Typing$progress_format_end <- 0 
+                Typing$progress_format_start <- 0
+                Typing$pending_format <- 0
+                Typing$entry_added <- 0
+                Typing$progress <- 0
+                Typing$progress_format <- 900000
+                output$single_typing_progress <- NULL
+                output$typing_fin <- NULL
+                output$single_typing_results <- NULL
+                output$typing_formatting <- NULL
+                Typing$single_path <- data.frame()
+                
+                # Null multi typing feedback variable
+                Typing$reset <- TRUE
+                
+                # Check need for new missing vlaue display
+                if(DB$first_look == TRUE) {
+                  if(sum(apply(DB$data, 1, anyNA)) >= 1) {
+                    DB$no_na_switch <- TRUE
+                  } else {
+                    DB$no_na_switch <- FALSE
+                  }
+                }
+                
+                DB$first_look <- TRUE
+                
+                output$initiate_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(),
+                    br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyFilesButton(
+                          "genome_file",
+                          "Browse" ,
+                          icon = icon("file"),
+                          title = "Select the assembly in .fasta/.fna/.fa format:",
+                          multiple = FALSE,
+                          buttonType = "default",
+                          class = NULL,
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("genome_path"),
+                        br()
+                      )
+                    )
+                  )
+                })
+                
+                output$initiate_multi_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(), br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyDirButton(
+                          "genome_file_multi",
+                          "Browse",
+                          icon = icon("folder-open"),
+                          title = "Select the folder containing the genome assemblies (FASTA)",
+                          buttonType = "default",
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("multi_select_info"),
+                        br()
+                      )
+                    ),
+                    uiOutput("multi_select_tab_ctrls"),
+                    br(),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "left",
+                        rHandsontableOutput("multi_select_table")
+                      )
+                    )
+                  )
+                })
+                
+                if(!anyNA(DB$allelic_profile)) {
+                  
+                  # no NA's -> dont render missing values sidebar elements
+                  output$missing_values_sidebar <- NULL
+                  
+                  # Render menu if no NA's present
+                  output$menu <- renderMenu(
+                    sidebarMenu(
+                      menuItem(
+                        text = "Database Browser",
+                        tabName = "database",
+                        icon = icon("hard-drive"),
+                        startExpanded = TRUE,
+                        menuSubItem(
+                          text = "Browse Entries",
+                          tabName = "db_browse_entries"
+                        ),
+                        menuSubItem(
+                          text = "Scheme Info",
+                          tabName = "db_schemeinfo"
+                        ),
+                        menuSubItem(
+                          text = "Loci Info",
+                          tabName = "db_loci_info"
+                        ),
+                        menuSubItem(
+                          text = "Distance Matrix",
+                          tabName = "db_distmatrix"
+                        )
+                      ),
+                      menuItem(
+                        text = "Manage Schemes",
+                        tabName = "init",
+                        icon = icon("layer-group")
+                      ),
+                      menuItem(
+                        text = "Allelic Typing",
+                        tabName = "typing",
+                        icon = icon("gears")
+                      ),
+                      menuItem(
+                        text = "Resistance Profile",
+                        tabName = "gene_screening",
+                        icon = icon("dna"),
+                        startExpanded = TRUE,
+                        menuSubItem(
+                          text = "Browse Entries",
+                          tabName = "gs_profile"
+                        ),
+                        menuSubItem(
+                          text = "Screening",
+                          tabName = "gs_screening"
+                        )
+                      ),
+                      menuItem(
+                        text = "Visualization",
+                        tabName = "visualization",
+                        icon = icon("circle-nodes")
+                      ),
+                      menuItem(
+                        text = "Utilities",
+                        tabName = "utilities",
+                        icon = icon("screwdriver-wrench")
+                      )
+                    )
+                  )
+                } else {
+                  output$menu <- renderMenu(
+                    sidebarMenu(
+                      menuItem(
+                        text = "Database Browser",
+                        tabName = "database",
+                        icon = icon("hard-drive"),
+                        startExpanded = TRUE,
+                        menuSubItem(
+                          text = "Browse Entries",
+                          tabName = "db_browse_entries",
+                          selected = TRUE
+                        ),
+                        menuSubItem(
+                          text = "Scheme Info",
+                          tabName = "db_schemeinfo"
+                        ),
+                        menuSubItem(
+                          text = "Loci Info",
+                          tabName = "db_loci_info"
+                        ),
+                        menuSubItem(
+                          text = "Distance Matrix",
+                          tabName = "db_distmatrix"
+                        ),
+                        menuSubItem(
+                          text = "Missing Values",
+                          tabName = "db_missing_values",
+                          icon = icon("triangle-exclamation")
+                        )
+                      ),
+                      menuItem(
+                        text = "Manage Schemes",
+                        tabName = "init",
+                        icon = icon("layer-group")
+                      ),
+                      menuItem(
+                        text = "Allelic Typing",
+                        tabName = "typing",
+                        icon = icon("gears")
+                      ),
+                      menuItem(
+                        text = "Resistance Profile",
+                        tabName = "gene_screening",
+                        icon = icon("dna"),
+                        startExpanded = TRUE,
+                        menuSubItem(
+                          text = "Browse Entries",
+                          tabName = "gs_profile"
+                        ),
+                        menuSubItem(
+                          text = "Screening",
+                          tabName = "gs_screening"
+                        )
+                      ),
+                      menuItem(
+                        text = "Visualization",
+                        tabName = "visualization",
+                        icon = icon("circle-nodes")
+                      ),
+                      menuItem(
+                        text = "Utilities",
+                        tabName = "utilities",
+                        icon = icon("screwdriver-wrench")
+                      )
+                    )
+                  )
+                }
+                
+                # Render custom variable display
+                output$show_cust_var <- renderTable(
+                  width = "100%", 
+                  {
+                    if((!is.null(DB$cust_var)) & (!is.null(input$cust_var_select))) {
+                      if(nrow(DB$cust_var) > 5) {
+                        low <- -4
+                        high <- 0
+                        for (i in 1:input$cust_var_select) {
+                          low <- low + 5
+                          if((nrow(DB$cust_var) %% 5) != 0) {
+                            if(i == ceiling(nrow(DB$cust_var) / 5 )) {
+                              high <- high + nrow(DB$cust_var) %% 5
+                            } else {
+                              high <- high + 5
+                            }
+                          } else {
+                            high <- high + 5
+                          }
+                        }
+                        DB$cust_var[low:high,]
+                      } else {
+                        DB$cust_var
+                      }
+                    } else if (!is.null(DB$cust_var)) {
+                      DB$cust_var
+                    }
+                  })
+                
+                # render visualization sidebar elements
+                observe({
+                  Vis$tree_algo <- input$tree_algo
+                })
+                
+                output$visualization_sidebar <- renderUI({
+                  if(!is.null(DB$data)) {
+                    column(
+                      width = 12,
+                      br(),
+                      fluidRow(
+                        column(1),
+                        column(
+                          width = 11,
+                          align = "left",
+                          prettyRadioButtons(
+                            "tree_algo",
+                            choices = c("Minimum-Spanning", "Neighbour-Joining", "UPGMA"),
+                            label = "",
+                            selected = if(!is.null(Vis$tree_algo)){Vis$tree_algo} else {"Minimum-Spanning"}
+                          ),
+                        )
+                      ),
+                      br(),
+                      fluidRow(
+                        column(
+                          width = 12,
+                          align = "center",
+                          tags$div(
+                            id = "button-wrapper",
+                            actionButton(
+                              "create_tree",
+                              h5("Create Tree", style = "position: relative; left: 15px; color: white; font-size: 15px;"),
+                              width = "100%"
+                            ),
+                            tags$img(
+                              src = "phylo.png",
+                              alt = "icon",
+                              class = "icon"
+                            )
+                          )
+                        )
+                      ), 
+                      br(),
+                      hr(),
+                      conditionalPanel(
+                        "input.tree_algo=='Minimum-Spanning'",
+                        fluidRow(
+                          column(
+                            width = 12,
+                            align = "left",
+                            br(),
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 16px; margin-left: 15px', "Sizing")
+                              )
+                            )
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 12,
+                            radioGroupButtons(
+                              "mst_ratio",
+                              "",
+                              choiceNames = c("16:10", "16:9", "4:3"),
+                              choiceValues = c((16/10), (16/9), (4/3)),
+                              width = "100%"
+                            ),
+                            br(),
+                            sliderInput(
+                              "mst_scale",
+                              "",
+                              min = 500,
+                              max = 1200,
+                              step = 5,
+                              value = 800,
+                              width = "95%",
+                              ticks = FALSE
+                            )
+                          )
+                        ),
+                        br(),
+                        hr(),
+                        fluidRow(
+                          column(
+                            width = 12,
+                            column(
+                              width = 5,
+                              align = "left",
+                              conditionalPanel(
+                                "input.mst_plot_format=='jpeg'",
+                                actionBttn(
+                                  "save_plot_jpeg",
+                                  style = "simple",
+                                  label = "Save Plot",
+                                  size = "sm",
+                                  icon = NULL,
+                                  color = "primary"
+                                )  
+                              ),
+                              conditionalPanel(
+                                "input.mst_plot_format=='png'",
+                                actionBttn(
+                                  "save_plot_png",
+                                  style = "simple",
+                                  label = "Save Plot",
+                                  size = "sm",
+                                  icon = NULL,
+                                  color = "primary"
+                                )
+                              ),
+                              conditionalPanel(
+                                "input.mst_plot_format=='bmp'",
+                                actionBttn(
+                                  "save_plot_bmp",
+                                  style = "simple",
+                                  label = "Save Plot",
+                                  size = "sm",
+                                  icon = NULL,
+                                  color = "primary"
+                                )  
+                              ),
+                              conditionalPanel(
+                                "input.mst_plot_format=='html'",
+                                downloadBttn(
+                                  "save_plot_html",
+                                  style = "simple",
+                                  label = "Save Plot",
+                                  size = "sm",
+                                  icon = NULL,
+                                  color = "primary"
+                                )
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              div(
+                                style = "max-width: 150px",
+                                class = "format",
+                                selectInput(
+                                  inputId = "mst_plot_format",
+                                  label = "",
+                                  choices = c("html", "jpeg", "png", "bmp")
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.tree_algo=='Neighbour-Joining'",
+                        fluidRow(
+                          column(
+                            width = 12,
+                            column(
+                              width = 5,
+                              align = "left",
+                              downloadBttn(
+                                "download_nj",
+                                style = "simple",
+                                label = "Save Plot",
+                                size = "sm",
+                                icon = NULL,
+                                color = "primary"
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              div(
+                                style = "max-width: 150px",
+                                class = "format",
+                                selectInput(
+                                  inputId = "filetype_nj",
+                                  label = "",
+                                  choices = c("png", "jpeg", "bmp", "svg")
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      conditionalPanel(
+                        "input.tree_algo=='UPGMA'",
+                        fluidRow(
+                          column(
+                            width = 12,
+                            column(
+                              width = 5,
+                              align = "left",
+                              downloadBttn(
+                                "download_upgma",
+                                style = "simple",
+                                label = "Save Plot",
+                                size = "sm",
+                                icon = NULL,
+                                color = "primary"
+                              )
+                            ),
+                            column(
+                              width = 7,
+                              div(
+                                style = "max-width: 150px",
+                                class = "format",
+                                selectInput(
+                                  inputId = "filetype_upgma",
+                                  label = "",
+                                  choices = c("png", "jpeg", "bmp", "svg")
+                                )
+                              )
+                            )
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 6,
+                          align = "left",
+                          br(),
+                          actionButton(
+                            "create_rep",
+                            "Print Report"
+                          )
+                        )
+                      )
+                    )
+                  }
+                })
+                
+                # Render entry table sidebar elements
+                output$entrytable_sidebar <- renderUI({
+                  if(!is.null(DB$data)) {
+                    column(
+                      width = 12,
+                      align = "center",
+                      br(), 
+                      fluidRow(
+                        column(1),
+                        column(
+                          width = 10,
+                          align = "left",
+                          if(nrow(DB$data) > 40) {
+                            div(
+                              class = "mat-switch-db-tab",
+                              materialSwitch(
+                                "table_height",
+                                h5(p("Show Full Table"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            )
+                          }
+                        )
+                      ),
+                      br(), br(), 
+                      fluidRow(
+                        column(
+                          width = 12,
+                          HTML(
+                            paste(
+                              tags$span(style='color: white; font-size: 18px; margin-bottom: 0px', 'Custom Variables')
+                            )
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 8,
+                          textInput(
+                            "new_var_name",
+                            label = "",
+                            placeholder = "New Variable"
+                          )
+                        ),
+                        column(
+                          width = 2,
+                          actionButton(
+                            "add_new_variable",
+                            "",
+                            icon = icon("plus")
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(
+                          width = 8,
+                          align = "left",
+                          div(
+                            class = "textinput_var",
+                            selectInput(
+                              "del_which_var",
+                              "",
+                              DB$cust_var$Variable
+                            )
+                          )
+                        ),
+                        column(
+                          width = 2,
+                          align = "left",
+                          actionButton(
+                            "delete_new_variable",
+                            "",
+                            icon = icon("minus")
+                          )
+                        )
+                      ),
+                      br(), 
+                      fluidRow(
+                        column(1),
+                        column(
+                          width = 4,
+                          uiOutput("cust_var_info")
+                        )
+                      ),
+                      fluidRow(
+                        column(1),
+                        column(
+                          width = 11,
+                          align = "center",
+                          tableOutput("show_cust_var")
+                        )
+                      ),
+                      fluidRow(
+                        column(4),
+                        column(
+                          width = 7,
+                          align = "center",
+                          uiOutput("cust_var_select")
+                        )
+                      )
+                    )
+                  } 
+                })
+                
+                # Render missing values sidebar elements
+                output$missing_values_sidebar <- renderUI({
+                  column(
+                    width = 12,
+                    fluidRow(
+                      column(
+                        width = 12,
+                        br(),
+                        materialSwitch(
+                          "miss_val_height",
+                          h5(p("Show Full Table"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                          value = FALSE,
+                          right = TRUE
+                        )
+                      ),
+                      br()
+                    ),
+                    fluidRow(
+                      column(
+                        width = 6,
+                        HTML(
+                          paste(
+                            tags$span(style='color: white; font-size: 14px; position: relative; bottom: -23px; right: -15px', 
+                                      'Download CSV')
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        downloadBttn(
+                          "download_na_matrix",
+                          style = "simple",
+                          label = "",
+                          size = "sm",
+                          icon = icon("download")
+                        )
+                      )
+                    )
+                  )
+                })
+                
+                # Render scheme info download button
+                output$download_loci <- renderUI({
+                  column(
+                    12,
+                    downloadBttn(
+                      "download_loci_info",
+                      style = "simple",
+                      label = "",
+                      size = "sm",
+                      icon = icon("download"),
+                      color = "primary"
+                    ),
+                    bsTooltip("download_loci_info_bttn", HTML("Save loci information <br> (without sequence)"), placement = "top", trigger = "hover")
+                  )
+                })
+                
+                # Render scheme info download button
+                output$download_scheme_info <- renderUI({
+                  downloadBttn(
+                    "download_schemeinfo",
+                    style = "simple",
+                    label = "",
+                    size = "sm",
+                    icon = icon("download"),
+                    color = "primary"
+                  )
+                })
+                
+                # Render distance matrix sidebar
+                output$distmatrix_sidebar <- renderUI({
+                  column(
+                    width = 12,
+                    align = "left",
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "center",
+                        selectInput(
+                          "distmatrix_label",
+                          label = "",
+                          choices = c("Index", "Assembly Name", "Assembly ID"),
+                          selected = c("Assembly Name"),
+                          width = "100%"
+                        ),
+                        br()
+                      )
+                    ),
+                    div(
+                      class = "mat-switch-dmatrix",
+                      materialSwitch(
+                        "distmatrix_true",
+                        h5(p("Only Included Entries"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                        value = FALSE,
+                        right = TRUE
+                      )
+                    ),
+                    div(
+                      class = "mat-switch-dmatrix",
+                      materialSwitch(
+                        "distmatrix_triangle",
+                        h5(p("Show Upper Triangle"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                        value = FALSE,
+                        right = TRUE
+                      )
+                    ),
+                    div(
+                      class = "mat-switch-dmatrix-last",
+                      materialSwitch(
+                        "distmatrix_diag",
+                        h5(p("Show Diagonal"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                        value = TRUE,
+                        right = TRUE
+                      )
+                    ),
+                    fluidRow(
+                      column(
+                        width = 6,
+                        HTML(
+                          paste(
+                            tags$span(style='color: white; font-size: 14px; position: relative; bottom: 37px; right: -15px', 
+                                      'Download CSV')
+                          )
+                        )
+                      ),
+                      column(
+                        width = 4,
+                        downloadBttn(
+                          "download_distmatrix",
+                          style = "simple",
+                          label = "",
+                          size = "sm",
+                          icon = icon("download")
+                        )
+                      )
+                    )
+                  )
+                })
+                
+                # Render select input to choose displayed loci
+                output$compare_select <- renderUI({
+                  
+                  if(nrow(DB$data) == 1) {
+                    HTML(
+                      paste(
+                        tags$span(style='color: white; font-size: 15px;', "Type at least two assemblies to compare")
+                      )
+                    )
+                  } else {
+                    if(!is.null(input$compare_difference)) {
+                      if (input$compare_difference == FALSE) {
+                        pickerInput(
+                          inputId = "compare_select",
+                          label = "",
+                          width = "85%",
+                          choices = names(DB$allelic_profile),
+                          selected = names(DB$allelic_profile)[1:20],
+                          options = list(
+                            `live-search` = TRUE,
+                            `actions-box` = TRUE,
+                            size = 10,
+                            style = "background-color: white; border-radius: 5px;"
+                          ),
+                          multiple = TRUE
+                        )
+                      } else {
+                        pickerInput(
+                          inputId = "compare_select",
+                          label = "",
+                          width = "85%",
+                          choices = names(DB$allelic_profile),
+                          selected = names(DB$allelic_profile)[var_alleles(DB$allelic_profile)],
+                          options = list(
+                            `live-search` = TRUE,
+                            `actions-box` = TRUE,
+                            size = 10,
+                            style = "background-color: white; border-radius: 5px;"
+                          ),
+                          multiple = TRUE
+                        )
+                      }
+                    }
+                  }
+                })
+                
+                #### Render Entry Data Table ----
+                output$db_entries_table <- renderUI({
+                  if(!is.null(DB$data)) {
+                    if(between(nrow(DB$data), 1, 30)) {
+                      rHandsontableOutput("db_entries")
+                    } else {
+                      addSpinner(
+                        rHandsontableOutput("db_entries"),
+                        spin = "dots",
+                        color = "#ffffff"
+                      )
+                    }
+                  }
+                })
+                
+                if (!is.null(DB$data)) {
+                  
+                  observe({
+                    
+                    if (!is.null(DB$data)) {
+                      if (nrow(DB$data) == 1) {
+                        if(!is.null(DB$data) & !is.null(DB$cust_var)) {
+                          output$db_entries <- renderRHandsontable({
+                            rhandsontable(
+                              select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                              error_highlight = err_thresh() - 1,                              
+                              rowHeaders = NULL,
+                              contextMenu = FALSE,
+                              highlightCol = TRUE, 
+                              highlightRow = TRUE
+                            ) %>%
+                              hot_col(1, 
+                                      valign = "htMiddle",
+                                      halign = "htCenter") %>%
+                              hot_col(3, readOnly = TRUE) %>%
+                              hot_col(c(1, 5, 10, 11, 12, 13),
+                                      readOnly = TRUE) %>%
+                              hot_col(3:(13 + nrow(DB$cust_var)), 
+                                      valign = "htMiddle",
+                                      halign = "htLeft") %>%
+                              hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                              hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                              hot_col(8, type = "dropdown", source = country_names) %>%
+                              hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                                      validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                              hot_cols(fixedColumnsLeft = 1) %>%
+                              hot_col(2, type = "checkbox", width = "auto",
+                                      valign = "htTop",
+                                      halign = "htCenter") %>%
+                              hot_rows(fixedRowsTop = 0) %>%
+                              hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+                          })
+                        }
+                      } else if (between(nrow(DB$data), 2, 40)) {
+                        if (length(input$compare_select) > 0) {
+                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
+                            output$db_entries <- renderRHandsontable({
+                              
+                              entry_data <- DB$data %>%
+                                select(1:(13 + nrow(DB$cust_var))) %>%
+                                add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                              
+                              rhandsontable(
+                                entry_data,
+                                col_highlight = diff_allele() - 1,
+                                dup_names_high = duplicated_names() - 1,
+                                dup_ids_high = duplicated_ids() - 1,
+                                row_highlight = true_rows() - 1,
+                                error_highlight = err_thresh() - 1,
+                                rowHeaders = NULL,
+                                highlightCol = TRUE, 
+                                highlightRow = TRUE,
+                                contextMenu = FALSE
+                              )  %>%
+                                hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
+                                        valign = "htMiddle",
+                                        halign = "htCenter",
+                                        readOnly = TRUE) %>%
+                                hot_col(1, 
+                                        valign = "htMiddle",
+                                        halign = "htCenter") %>%
+                                hot_col(3, readOnly = TRUE) %>%
+                                hot_col(c(1, 5, 10, 11, 12, 13),
+                                        readOnly = TRUE) %>%
+                                hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
+                                        valign = "htMiddle",
+                                        halign = "htLeft") %>%
+                                hot_col(8, type = "dropdown", source = country_names) %>%
+                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                                        validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                                hot_col(2, type = "checkbox", width = "auto",
+                                        valign = "htTop",
+                                        halign = "htCenter",
+                                        strict = TRUE,
+                                        allowInvalid = FALSE,
+                                        copyable = TRUE) %>%
+                                hot_cols(fixedColumnsLeft = 1) %>%
+                                hot_rows(fixedRowsTop = 0) %>%
+                                hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+  
+                       }
+              }") %>%
+                                hot_col(diff_allele(),
+                                        renderer = "
+                  function(instance, td, row, col, prop, value, cellProperties) {
+                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
+  
+                    if (instance.params) {
+                          hcols = instance.params.col_highlight;
+                          hcols = hcols instanceof Array ? hcols : [hcols];
+                        }
+  
+                    if (instance.params && hcols.includes(col)) {
+                      td.style.background = 'rgb(116, 188, 139)';
+                    }
+                }"
+                                ) %>%
+                                hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+                            })
+                          }
+                        } else {
+                          if(!is.null(DB$data) & !is.null(DB$cust_var)) {
+                            output$db_entries <- renderRHandsontable({
+                              rhandsontable(
+                                select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                                rowHeaders = NULL,
+                                row_highlight = true_rows() - 1,
+                                dup_names_high = duplicated_names()- 1,
+                                dup_ids_high = duplicated_ids() - 1,
+                                error_highlight = err_thresh() - 1,
+                                contextMenu = FALSE,
+                                highlightCol = TRUE, 
+                                highlightRow = TRUE
+                              ) %>%
+                                hot_cols(fixedColumnsLeft = 1) %>%
+                                hot_col(1, 
+                                        valign = "htMiddle",
+                                        halign = "htCenter") %>%
+                                hot_col(3, readOnly = TRUE) %>%
+                                hot_col(c(1, 5, 10, 11, 12, 13),
+                                        readOnly = TRUE) %>%
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
+                                        valign = "htMiddle",
+                                        halign = "htLeft") %>%
+                                hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(8, type = "dropdown", source = country_names) %>%
+                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                                        validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                                hot_col(2, type = "checkbox", width = "auto",
+                                        valign = "htTop",
+                                        halign = "htCenter") %>%
+                                hot_rows(fixedRowsTop = 0) %>%
+                                hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+  
+                       }
+              }") %>%
+                                hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+                            })    
+                          }
+                        }
+                      } else {
+                        if (length(input$compare_select) > 0) {
+                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
+                            output$db_entries <- renderRHandsontable({
+                              
+                              entry_data <- DB$data %>%
+                                select(1:(13 + nrow(DB$cust_var))) %>%
+                                add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                              
+                              rhandsontable(
+                                entry_data,
+                                col_highlight = diff_allele() - 1,
+                                rowHeaders = NULL,
+                                height = table_height(),
+                                row_highlight = true_rows() - 1,
+                                dup_names_high = duplicated_names() - 1,
+                                dup_ids_high = duplicated_ids() - 1,
+                                error_highlight = err_thresh() - 1,
+                                contextMenu = FALSE,
+                                highlightCol = TRUE, 
+                                highlightRow = TRUE
+                              ) %>%
+                                hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
+                                        readOnly = TRUE, 
+                                        valign = "htMiddle",
+                                        halign = "htCenter") %>%
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
+                                        valign = "htMiddle",
+                                        halign = "htLeft") %>%
+                                hot_col(3, readOnly = TRUE) %>%
+                                hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(c(1, 5, 10, 11, 12, 13),
+                                        readOnly = TRUE) %>%
+                                hot_col(8, type = "dropdown", source = country_names) %>%
+                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                                        validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                                hot_col(1, 
+                                        valign = "htMiddle",
+                                        halign = "htCenter") %>%
+                                hot_col(2, type = "checkbox", width = "auto",
+                                        valign = "htTop",
+                                        halign = "htCenter",
+                                        allowInvalid = FALSE,
+                                        copyable = TRUE) %>%
+                                hot_cols(fixedColumnsLeft = 1) %>%
+                                hot_rows(fixedRowsTop = 0) %>%
+                                hot_col(1, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.row_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                                                             }
+                                                           }
+                                                       }") %>%
+                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") %>%
+                                hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(diff_allele(),
+                                        renderer = "
+                  function(instance, td, row, col, prop, value, cellProperties) {
+                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
+  
+                    if (instance.params) {
+                          hcols = instance.params.col_highlight;
+                          hcols = hcols instanceof Array ? hcols : [hcols];
+                        }
+  
+                    if (instance.params && hcols.includes(col)) {
+                      td.style.background = 'rgb(116, 188, 139)';
+                    }
+                }") 
+                            })    
+                          }
+                        } else {
+                          if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
+                            output$db_entries <- renderRHandsontable({
+                              rhandsontable(
+                                select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                                rowHeaders = NULL,
+                                height = table_height(),
+                                dup_names_high = duplicated_names() - 1,
+                                dup_ids_high = duplicated_ids() - 1,
+                                row_highlight = true_rows() - 1,
+                                error_highlight = err_thresh() - 1,
+                                contextMenu = FALSE,
+                                highlightCol = TRUE, 
+                                highlightRow = TRUE
+                              ) %>%
+                                hot_cols(fixedColumnsLeft = 1) %>%
+                                hot_col(1, 
+                                        valign = "htMiddle",
+                                        halign = "htCenter") %>%
+                                hot_col(3, readOnly = TRUE) %>%
+                                hot_col(c(1, 5, 10, 11, 12, 13),
+                                        readOnly = TRUE) %>%
+                                hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                                hot_col(8, type = "dropdown", source = country_names) %>%
+                                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                                        validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                                hot_col(3:(13 + nrow(DB$cust_var)), 
+                                        valign = "htMiddle",
+                                        halign = "htLeft") %>%
+                                hot_rows(fixedRowsTop = 0) %>%
+                                hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(2, type = "checkbox", width = "auto",
+                                        valign = "htTop", halign = "htCenter") %>%
+                                hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+                            })
+                          }
+                        }
+                      }
+                    }
+                    
+                    # Dynamic save button when rhandsontable changes or new entries
+                    output$edit_entry_table <- renderUI({
+                      if(check_new_entry() & DB$check_new_entries) {
+                        Typing$reload <- FALSE
+                        fluidRow(
+                          column(
+                            width = 8,
+                            align = "left",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: absolute; bottom: -30px; right: -5px', 
+                                          'New entries - reload database')
+                              )
+                            )
+                          ),
+                          column(
+                            width = 4,
+                            actionButton(
+                              "load",
+                              "",
+                              icon = icon("rotate"),
+                              class = "pulsating-button"
+                            )
+                          )
+                        )
+                      } else if(Typing$status == "Attaching") {
+                        fluidRow(
+                          column(
+                            width = 11,
+                            align = "left",
+                            HTML(
+                              paste(
+                                tags$span(style='color: white; font-size: 14px; position: absolute; bottom: -30px; right: -5px', 'No database changes possible - pending entry addition')
+                              )
+                            )
+                          ),
+                          column(
+                            width = 1,
+                            HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px; color:white; margin-top: 10px"></i>'))
+                          )
+                        )
+                      } else if((DB$change == TRUE) | !identical(get.entry.table.meta(), select(DB$meta, -13))) {
+                        
+                        if(!is.null(input$db_entries)) {
+                          fluidRow(
+                            column(
+                              width = 5,
+                              HTML(
+                                paste(
+                                  tags$span(style='color: white; font-size: 16px; position: absolute; bottom: -30px; right: -5px', 'Confirm changes')
+                                )
+                              )
+                            ),
+                            column(
+                              width = 3,
+                              actionButton(
+                                "edit_button",
+                                "",
+                                icon = icon("bookmark"),
+                                class = "pulsating-button"
+                              )
+                            ),
+                            column(
+                              width = 4,
+                              actionButton(
+                                "undo_changes",
+                                "Undo",
+                                icon = icon("repeat")
+                              )
+                            )
+                          )
+                        }
+                      } else {NULL}
+                    })
+                    
+                  })
+                  
+                  # Hide no entry message
+                  output$db_no_entries <- NULL
+                  output$distancematrix_no_entries <- NULL
+                  
+                } else {
+                  
+                  # If database loading not successful dont show entry table
+                  output$db_entries_table <- NULL
+                  output$entry_table_controls <- NULL
+                }
+                
+                # Render Entry table controls
+                output$entry_table_controls <- renderUI({
+                  fluidRow(
+                    column(1),
+                    column(
+                      width = 3,
+                      align = "center",
+                      fluidRow(
+                        column(
+                          width = 4,
+                          align = "center",
+                          actionButton(
+                            "sel_all_entries",
+                            "Select All",
+                            icon = icon("check")
+                          )
+                        ),
+                        column(
+                          width = 4,
+                          align = "left",
+                          actionButton(
+                            "desel_all_entries",
+                            "Deselect All",
+                            icon = icon("xmark")
+                          )
+                        )
+                      )
+                    ),
+                    column(
+                      width = 3,
+                      uiOutput("edit_entry_table")
+                    )
+                  )
+                })
+                
+                #### Render Distance Matrix ----
+                observe({
+                  if(!is.null(DB$data)) {
+                    
+                    if(any(duplicated(DB$meta$`Assembly Name`)) | any(duplicated(DB$meta$`Assembly ID`))) {
+                      output$db_distancematrix <- NULL
+                      
+                      if( (sum(duplicated(DB$meta$`Assembly Name`)) > 0) & (sum(duplicated(DB$meta$`Assembly ID`)) == 0) ) {
+                        duplicated_txt <- paste0(
+                          paste(
+                            paste0("Name  # ", which(duplicated(DB$meta$`Assembly Name`)), " - "),
+                            DB$meta$`Assembly Name`[which(duplicated(DB$meta$`Assembly Name`))]
+                          ),
+                          "<br>"
+                        )
+                      } else if ( (sum(duplicated(DB$meta$`Assembly ID`)) > 0) & (sum(duplicated(DB$meta$`Assembly Name`)) == 0) ){
+                        duplicated_txt <- paste0(
+                          paste(
+                            paste0("ID  # ", which(duplicated(DB$meta$`Assembly ID`)), " - "),
+                            DB$meta$`Assembly ID`[which(duplicated(DB$meta$`Assembly ID`))]
+                          ),
+                          "<br>"
+                        )
+                      } else {
+                        duplicated_txt <- c(
+                          paste0(
+                            paste(
+                              paste0("Name  # ", which(duplicated(DB$meta$`Assembly Name`)), " - "),
+                              DB$meta$`Assembly Name`[which(duplicated(DB$meta$`Assembly Name`))]
+                            ),
+                            "<br>"
+                          ),
+                          paste0(
+                            paste(
+                              paste0("ID  # ", which(duplicated(DB$meta$`Assembly ID`)), " - "),
+                              DB$meta$`Assembly ID`[which(duplicated(DB$meta$`Assembly ID`))]
+                            ),
+                            "<br>"
+                          )
+                        )
+                      }
+                      
+                      output$distancematrix_duplicated <- renderUI({
+                        column(
+                          width = 12,
+                          tags$span(style = "font-size: 15; color: white",
+                                    "Change duplicated entry names to display distance matrix."),
+                          br(), br(), br(),
+                          actionButton("change_entries", "Go to Entry Table", class = "btn btn-default"),
+                          br(), br(), br(),
+                          tags$span(
+                            style = "font-size: 15; color: white",
+                            HTML(
+                              append(
+                                "Duplicated:",
+                                append(
+                                  "<br>",
+                                  duplicated_txt
+                                )
+                              )
+                            )
+                          )
+                        )
+                      })
+                    } else {
+                      output$distancematrix_duplicated <- NULL
+                      if(!is.null(DB$data) & !is.null(DB$allelic_profile) & !is.null(DB$allelic_profile_true) & !is.null(DB$cust_var) & !is.null(input$distmatrix_label) & !is.null(input$distmatrix_diag) & !is.null(input$distmatrix_triangle)) {
+                        output$db_distancematrix <- renderRHandsontable({
+                          rhandsontable(hamming_df(), 
+                                        digits = 1, 
+                                        readOnly = TRUE,
+                                        contextMenu = FALSE,
+                                        highlightCol = TRUE, 
+                                        highlightRow = TRUE,
+                                        height = distancematrix_height(), rowHeaders = NULL) %>%
+                            hot_heatmap(renderer = paste0("
+                            function (instance, td, row, col, prop, value, cellProperties) {
+                              Handsontable.renderers.TextRenderer.apply(this, arguments);
+                              heatmapScale  = chroma.scale(['#17F556', '#ED6D47']);
+                            
+                              if (instance.heatmap[col]) {
+                                mn = ", DB$matrix_min, ";
+                                mx = ", DB$matrix_max, ";
+                            
+                                pt = (parseInt(value, 10) - mn) / (mx - mn);    
+                            
+                                td.style.backgroundColor = heatmapScale(pt).hex();
+                              }
+                            }")) %>%
+                            hot_rows(fixedRowsTop = 0) %>%
+                            hot_cols(fixedColumnsLeft = 1) %>%
+                            hot_col(1:(dim(DB$ham_matrix)[1]+1),
+                                    halign = "htCenter",
+                                    valign = "htMiddle") %>%
+                            hot_col(1, renderer = "
+                            function(instance, td, row, col, prop, value, cellProperties) {
+                              Handsontable.renderers.NumericRenderer.apply(this, arguments);
+                              td.style.background = '#F0F0F0'
+                            }"
+                            )
+                        })  
+                      }
+                    }
+                    
+                    # Render Distance Matrix UI
+                    
+                    output$distmatrix_show <- renderUI({
+                      if(!is.null(DB$data)) {
+                        if(nrow(DB$data) > 1) {
+                          column(
+                            width = 10,
+                            uiOutput("distancematrix_duplicated"),
+                            div(
+                              class = "distmatrix",
+                              rHandsontableOutput("db_distancematrix")
+                            )
+                          )
+                        } else {
+                          column(
+                            width = 10,
+                            align = "left",
+                            p(
+                              HTML(
+                                paste(
+                                  tags$span(style='color: white; font-size: 15px;', "Type at least two assemblies to display a distance matrix.")
+                                )
+                              )
+                            ),
+                            br(),
+                            br()
+                          )
+                        }
+                      }
+                    })
+                    
+                  }
+                })
+                
+                
+                # Render delete entry box UI
+                output$delete_box <- renderUI({
+                  box(
+                    solidHeader = TRUE,
+                    status = "primary",
+                    width = "100%",
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "center",
+                        h3(p("Delete Entries"), style = "color:white")
+                      )
+                    ),
+                    hr(),
+                    fluidRow(
+                      column(
+                        width = 2,
+                        offset = 1,
+                        align = "right",
+                        br(),
+                        h5("Index", style = "color:white; margin-bottom: 0px;")
+                      ),
+                      column(
+                        width = 6,
+                        align = "center",
+                        uiOutput("delete_select")
+                      ),
+                      column(
+                        width = 2,
+                        align = "center",
+                        br(),
+                        uiOutput("del_bttn")
+                      )
+                    ),
+                    br()
+                  )
+                })
+                
+                # Render loci comparison box UI
+                output$compare_allele_box <- renderUI({
+                  box(
+                    solidHeader = TRUE,
+                    status = "primary",
+                    width = "100%",
+                    fluidRow(
+                      column(
+                        width = 12,
+                        align = "center",
+                        h3(p("Compare Loci"), style = "color:white")
+                      )
+                    ),
+                    hr(),
+                    column(
+                      width = 12,
+                      align = "center",
+                      br(),
+                      uiOutput("compare_select"),
+                      br(),
+                      column(2),
+                      column(
+                        width = 10,
+                        align = "left",
+                        uiOutput("compare_difference_box")
+                      )
+                    ),
+                    br()
+                  )
+                })
+                
+                # Render entry table download box UI
+                output$download_entries <- renderUI({
+                  fluidRow(
+                    column(
+                      width = 12,
+                      box(
+                        solidHeader = TRUE,
+                        status = "primary",
+                        width = "100%",
+                        fluidRow(
+                          column(
+                            width = 12,
+                            align = "center",
+                            h3(p("Download Table"), style = "color:white")
+                          )
+                        ),
+                        hr(),
+                        fluidRow(
+                          column(2),
+                          column(
+                            width = 10,
+                            align = "left",
+                            br(),
+                            div(
+                              class = "mat-switch-db",
+                              materialSwitch(
+                                "download_table_include",
+                                h5(p("Only Included Entries"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            ),
+                            div(
+                              class = "mat-switch-db",
+                              materialSwitch(
+                                "download_table_loci",
+                                h5(p("Include Displayed Loci"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+                                value = FALSE,
+                                right = TRUE
+                              )
+                            ),
+                            br(),
+                          )
+                        ),
+                        fluidRow(
+                          column(
+                            width = 12,
+                            align = "center",
+                            downloadBttn(
+                              "download_entry_table",
+                              style = "simple",
+                              label = "",
+                              size = "sm",
+                              icon = icon("download"),
+                              color = "primary"
+                            )
+                          )
+                        ),
+                        br()
+                      )
+                    ),
+                    column(
+                      width = 12,
+                      fluidRow(
+                        column(
+                          width = 2,
+                          div(
+                            class = "rectangle-blue" 
+                          ),
+                          div(
+                            class = "rectangle-orange" 
+                          ),
+                          div(
+                            class = "rectangle-red" 
+                          ),
+                          div(
+                            class = "rectangle-green" 
+                          )
+                        ),
+                        column(
+                          width = 10,
+                          align = "left",
+                          p(
+                            HTML(
+                              paste(
+                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -12px", " = included for analyses")
+                              )
+                            )
+                          ),
+                          p(
+                            HTML(
+                              paste(
+                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -13px", " =  duplicated name/ID")
+                              )
+                            )
+                          ),
+                          p(
+                            HTML(
+                              paste(
+                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -14px", " =  ≥ 5% of loci missing")
+                              )
+                            )
+                          ),
+                          p(
+                            HTML(
+                              paste(
+                                tags$span(style="color: white; font-size: 15px; margin-left: 25px; position: relative; bottom: -15px", " =  locus contains multiple variants")
+                              )
+                            )
+                          ),
+                        )
+                      )
+                    )
+                  )
+                })
+                
+                # Render entry deletion select input
+                output$delete_select <- renderUI({
+                  pickerInput("select_delete",
+                              label = "",
+                              choices = DB$data[, "Index"],
+                              options = list(
+                                `live-search` = TRUE,
+                                `actions-box` = TRUE,
+                                size = 10,
+                                style = "background-color: white; border-radius: 5px;"
+                              ),
+                              multiple = TRUE)
+                })
+                
+                # Render delete entry button
+                output$del_bttn <- renderUI({
+                  actionBttn(
+                    "del_button",
+                    label = "",
+                    color = "danger",
+                    size = "sm",
+                    style = "material-circle",
+                    icon = icon("xmark")
+                  )
+                })
+                
+                #### Missing Values UI ----
+                
+                # Missing values calculations and table 
+                observe({
+                  
+                  if (!is.null(DB$allelic_profile)) {
+                    NA_table <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) != 0]
+                    
+                    NA_table <- NA_table[rowSums(is.na(NA_table)) != 0,]
+                    
+                    NA_table[is.na(NA_table)] <- "NA"
+                    
+                    NA_table <- NA_table %>% 
+                      cbind("Assembly Name" = DB$meta[rownames(NA_table),]$`Assembly Name`) %>%
+                      cbind("Errors" = DB$meta[rownames(NA_table),]$Errors) %>%
+                      relocate("Assembly Name", "Errors")
+                    
+                    DB$na_table <- NA_table
+                    
+                    if(!is.null(input$miss_val_height)) {
+                      if(nrow(DB$na_table) < 31) {
+                        output$table_missing_values <- renderRHandsontable({
+                          rhandsontable(
+                            DB$na_table,
+                            readOnly = TRUE,
+                            rowHeaders = NULL,
+                            contextMenu = FALSE,
+                            highlightCol = TRUE, 
+                            highlightRow = TRUE,
+                            error_highlight = err_thresh_na() - 1
+                          ) %>%
+                            hot_cols(fixedColumnsLeft = 1) %>%
+                            hot_rows(fixedRowsTop = 0) %>%
+                            hot_col(1:ncol(DB$na_table), valign = "htMiddle", halign = "htLeft") %>%
+                            hot_col(2, renderer = "
+                            function (instance, td, row, col, prop, value, cellProperties) {
+                              Handsontable.renderers.TextRenderer.apply(this, arguments);
+                              if (instance.params) {
+                                hrows = instance.params.error_highlight
+                                hrows = hrows instanceof Array ? hrows : [hrows]
+                                if (hrows.includes(row)) { 
+                                  td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
+                                }
+                              }
+                            }") %>%
+                            hot_col(3:ncol(DB$na_table), renderer = htmlwidgets::JS(
+                              "function(instance, td, row, col, prop, value, cellProperties) {
+                                if (value.length > 8) {
+                                  value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                                }
+                                td.innerHTML = value;
+                                td.style.textAlign = 'center';
+                                return td;
+                               }"
+                            ))
+                        })
+                      } else {
+                        output$table_missing_values <- renderRHandsontable({
+                          rhandsontable(
+                            DB$na_table,
+                            readOnly = TRUE,
+                            rowHeaders = NULL,
+                            height = miss.val.height(),
+                            contextMenu = FALSE,
+                            highlightCol = TRUE, 
+                            highlightRow = TRUE,
+                            error_highlight = err_thresh() - 1
+                          ) %>%
+                            hot_cols(fixedColumnsLeft = 1) %>%
+                            hot_rows(fixedRowsTop = 0) %>%
+                            hot_col(1:ncol(DB$na_table), valign = "htMiddle", halign = "htLeft") %>%
+                            hot_col(2, renderer = "
+                            function (instance, td, row, col, prop, value, cellProperties) {
+                              Handsontable.renderers.TextRenderer.apply(this, arguments);
+                              if (instance.params) {
+                                hrows = instance.params.error_highlight
+                                hrows = hrows instanceof Array ? hrows : [hrows]
+                                if (hrows.includes(row)) { 
+                                  td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
+                                }
+                              }
+                            }") %>%
+                            hot_col(3:ncol(DB$na_table), renderer = htmlwidgets::JS(
+                              "function(instance, td, row, col, prop, value, cellProperties) {
+                                if (value.length > 8) {
+                                  value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                                }
+                                td.innerHTML = value;
+                                td.style.textAlign = 'center';
+                                return td;
+                               }"
+                            ))
+                        })
+                      }
+                    }
+                  }
+                  
+                })
+                
+                # Render missing value informatiojn box UI
+                output$missing_values <- renderUI({
+                  div(
+                    class = "miss_val_box",
+                    box(
+                      solidHeader = TRUE,
+                      status = "primary",
+                      width = "100%",
+                      fluidRow(
+                        div(
+                          class = "white",
+                          column(
+                            width = 12,
+                            align = "left",
+                            br(), 
+                            HTML(
+                              paste0("There are ", 
+                                     strong(as.character(sum(is.na(DB$data)))), 
+                                     " unsuccessful allele allocations (NA). ",
+                                     strong(sum(sapply(DB$allelic_profile, anyNA))),
+                                     " out of ",
+                                     strong(ncol(DB$allelic_profile)),
+                                     " total loci in this scheme contain NA's (",
+                                     strong(round((sum(sapply(DB$allelic_profile, anyNA)) / ncol(DB$allelic_profile) * 100), 1)),
+                                     " %). ",
+                                     "Decide how these missing values should be treated:")
+                              
+                            ),
+                            br()
+                          )
+                        )
+                      ),
+                      fluidRow(
+                        column(1),
+                        column(
+                          width = 11,
+                          align = "left",
+                          br(),
+                          prettyRadioButtons(
+                            "na_handling",
+                            "",
+                            choiceNames = c("Ignore missing values for pairwise comparison",
+                                            "Omit loci with missing values for all assemblies",
+                                            "Treat missing values as allele variant"),
+                            choiceValues = c("ignore_na", "omit", "category"),
+                            shape = "curve",
+                            selected = c("ignore_na")
+                          ),
+                          br()
+                        )
+                      )
+                    )
+                  )
+                })  
+                
+              } else { 
+                #if no typed assemblies present
+                
+                # null underlying database
+                
+                DB$data <- NULL
+                DB$meta <- NULL
+                DB$meta_gs <- NULL
+                DB$meta_true <- NULL
+                DB$allelic_profile <- NULL
+                DB$allelic_profile_trunc <- NULL
+                DB$allelic_profile_true <- NULL
+                
+                # Render menu without missing values tab
+                output$menu <- renderMenu(
+                  sidebarMenu(
+                    menuItem(
+                      text = "Database Browser",
+                      tabName = "database",
+                      icon = icon("hard-drive"),
+                      startExpanded = TRUE,
+                      selected = TRUE,
+                      menuSubItem(
+                        text = "Browse Entries",
+                        tabName = "db_browse_entries"
+                      ),
+                      menuSubItem(
+                        text = "Scheme Info",
+                        tabName = "db_schemeinfo"
+                      ),
+                      menuSubItem(
+                        text = "Loci Info",
+                        tabName = "db_loci_info"
+                      ),
+                      menuSubItem(
+                        text = "Distance Matrix",
+                        tabName = "db_distmatrix"
+                      )
+                    ),
+                    menuItem(
+                      text = "Manage Schemes",
+                      tabName = "init",
+                      icon = icon("layer-group")
+                    ),
+                    menuItem(
+                      text = "Allelic Typing",
+                      tabName = "typing",
+                      icon = icon("gears")
+                    ),
+                    menuItem(
+                      text = "Resistance Profile",
+                      tabName = "gene_screening",
+                      icon = icon("dna"),
+                      startExpanded = TRUE,
+                      menuSubItem(
+                        text = "Browse Entries",
+                        tabName = "gs_profile"
+                      ),
+                      menuSubItem(
+                        text = "Screening",
+                        tabName = "gs_screening"
+                      )
+                    ),
+                    menuItem(
+                      text = "Visualization",
+                      tabName = "visualization",
+                      icon = icon("circle-nodes")
+                    ),
+                    menuItem(
+                      text = "Utilities",
+                      tabName = "utilities",
+                      icon = icon("screwdriver-wrench")
+                    )
+                  )
+                )
+                
+                observe({
+                  if(is.null(DB$data)) {
+                    if(check_new_entry()) {
+                      output$db_no_entries <- renderUI(
+                        column(
+                          width = 12,
+                          fluidRow(
+                            column(1),
+                            column(
+                              width = 3,
+                              align = "left",
+                              HTML(
+                                paste(
+                                  tags$span(style='color: white; font-size: 15px; position: absolute; bottom: -30px; right: -5px', 'New entries - reload database')
+                                )
+                              )
+                            ),
+                            column(
+                              width = 4,
+                              actionButton(
+                                "load",
+                                "",
+                                icon = icon("rotate"),
+                                class = "pulsating-button"
+                              )
+                            )
+                          )
+                        )
+                      )
+                    } else {
+                      output$db_no_entries <- renderUI(
+                        column(
+                          width = 12,
+                          fluidRow(
+                            column(1),
+                            column(
+                              width = 11,
+                              align = "left",
+                              HTML(
+                                paste(
+                                  "<span style='color: white;'>",
+                                  "No Entries for this scheme available.\n",
+                                  "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
+                                  sep = '<br/>'
+                                )
+                              )
+                            )
+                          )
+                        )
+                      )
+                    }
+                  }
+                })
+                
+                output$distancematrix_no_entries <- renderUI(
+                  fluidRow(
+                    column(1),
+                    column(
+                      width = 11,
+                      align = "left",
+                      HTML(paste(
+                        "<span style='color: white;'>",
+                        "No Entries for this scheme available.",
+                        "Type a genome in the section <strong>Allelic Typing</strong> and add the result to the local database.",
+                        sep = '<br/>'
+                      ))
+                    )
+                  )
+                )
+                
+                output$db_entries <- NULL
+                output$edit_index <- NULL
+                output$edit_scheme_d <- NULL
+                output$edit_entries <- NULL
+                output$compare_select <- NULL
+                output$delete_select <- NULL
+                output$del_bttn <- NULL
+                output$compare_allele_box <- NULL
+                output$download_entries <- NULL
+                output$missing_values <- NULL
+                output$delete_box <- NULL
+                output$entry_table_controls <- NULL
+                output$multi_stop <- NULL
+                output$metadata_multi_box <- NULL
+                output$start_multi_typing_ui <- NULL
+                output$pending_typing <- NULL
+                output$multi_typing_results <- NULL
+                output$single_typing_progress <- NULL
+                output$metadata_single_box <- NULL
+                output$start_typing_ui <- NULL
+                
+                output$initiate_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(),
+                    br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyFilesButton(
+                          "genome_file",
+                          "Browse" ,
+                          icon = icon("file"),
+                          title = "Select the assembly in .fasta/.fna/.fa format:",
+                          multiple = FALSE,
+                          buttonType = "default",
+                          class = NULL,
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("genome_path"),
+                        br()
+                      )
+                    )
+                  )
+                })
+                
+                output$initiate_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(),
+                    br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyFilesButton(
+                          "genome_file",
+                          "Browse" ,
+                          icon = icon("file"),
+                          title = "Select the assembly in .fasta/.fna/.fa format:",
+                          multiple = FALSE,
+                          buttonType = "default",
+                          class = NULL,
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("genome_path"),
+                        br()
+                      )
+                    )
+                  )
+                })
+                
+                output$initiate_multi_typing_ui <- renderUI({
+                  column(
+                    width = 4,
+                    align = "center",
+                    br(),
+                    br(),
+                    h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+                    br(), br(),
+                    p(
+                      HTML(
+                        paste(
+                          tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+                        )
+                      )
+                    ),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "center",
+                        shinyDirButton(
+                          "genome_file_multi",
+                          "Browse",
+                          icon = icon("folder-open"),
+                          title = "Select the folder containing the genome assemblies (FASTA)",
+                          buttonType = "default",
+                          root = path_home()
+                        ),
+                        br(),
+                        br(),
+                        uiOutput("multi_select_info"),
+                        br()
+                      )
+                    ),
+                    uiOutput("multi_select_tab_ctrls"),
+                    br(),
+                    fluidRow(
+                      column(1),
+                      column(
+                        width = 11,
+                        align = "left",
+                        rHandsontableOutput("multi_select_table")
+                      )
+                    )
+                  )
+                })
+              }
+            }
+          }
+        }
+      } else {
+        
+        log_print("Invalid scheme folder")
+        show_toast(
+          title = "Invalid scheme folder",
+          type = "warning",
+          position = "bottom-end",
+          timer = 4000
+        )
+      }
+    }
+    
+  })
+  
+  # _______________________ ####
+  
+  ## Database ----
+  
+  ### Conditional UI Elements rendering ----
+  
+  # Contro custom variables table
+  output$cust_var_select <- renderUI({
+    if(nrow(DB$cust_var) > 5) {
+      selectInput(
+        "cust_var_select",
+        "",
+        choices = 1:ceiling(nrow(DB$cust_var) / 5 )
+      )
+    }
+  })
+  
+  output$cust_var_info <- renderUI({
+    if((!is.null(DB$cust_var)) & (!is.null(input$cust_var_select))) {
+      if(nrow(DB$cust_var) > 5) {
+        low <- -4
+        high <- 0
+        for (i in 1:input$cust_var_select) {
+          low <- low + 5
+          if((nrow(DB$cust_var) %% 5) != 0) {
+            if(i == ceiling(nrow(DB$cust_var) / 5 )) {
+              high <- high + nrow(DB$cust_var) %% 5
+            } else {
+              high <- high + 5
+            }
+          } else {
+            high <- high + 5
+          }
+        }
+        h5(paste0("Showing ", low, " to ", high," of ", nrow(DB$cust_var), " variables"), style = "color: white; font-size: 10px;")
+      }
+    }
+  })
+  
+  # Message on Database tabs if no scheme available yet
+  observe({
+    if(!is.null(DB$exist)) {
+      if(DB$exist){
+        
+        # Message for tab Browse Entries
+        output$no_scheme_entries <- renderUI({
+          fluidRow(
+            column(1),
+            column(
+              width = 4,
+              align = "left",
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'No scheme available.')
+                  )
+                )
+              ),
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'Download a scheme first and type assemblies in the section Allelic Typing.')
+                  )
+                )
+              )
+            )
+          )
+        })
+        
+        # Message for Tab Scheme Info
+        output$no_scheme_info <- renderUI({
+          fluidRow(
+            column(1),
+            column(
+              width = 10,
+              align = "left",
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'No scheme available.')
+                  )
+                )
+              ),
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'Download a scheme first and type assemblies in the section Allelic Typing.')
+                  )
+                )
+              )
+            )
+          )
+        })
+        
+        # Message for Tab Distance Matrix
+        output$no_scheme_distancematrix <- renderUI({
+          fluidRow(
+            column(1),
+            column(
+              width = 10,
+              align = "left",
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'No scheme available.')
+                  )
+                )
+              ),
+              p(
+                HTML(
+                  paste(
+                    tags$span(style='color: white; font-size: 15px; ', 
+                              'Download a scheme first and type assemblies in the section Allelic Typing.')
+                  )
+                )
+              )
+            )
+          )
+        })
+        
+      } else {
+        output$no_scheme_entries <- NULL
+        output$no_scheme_info <- NULL
+        output$no_scheme_distancematrix <- NULL
+      }
+    }
+    
+  })
+  
+  observe({
+    # Conditional Missing Values Tab
+    if(!is.null(DB$allelic_profile)) {
+      if(anyNA(DB$allelic_profile)) {
+        if(DB$no_na_switch == FALSE) {
+          output$menu <- renderMenu(
+            sidebarMenu(
+              menuItem(
+                text = "Database Browser",
+                tabName = "database",
+                icon = icon("hard-drive"),
+                startExpanded = TRUE,
+                menuSubItem(
+                  text = "Browse Entries",
+                  tabName = "db_browse_entries"
+                ),
+                menuSubItem(
+                  text = "Scheme Info",
+                  tabName = "db_schemeinfo"
+                ),
+                menuSubItem(
+                  text = "Loci Info",
+                  tabName = "db_loci_info"
+                ),
+                menuSubItem(
+                  text = "Distance Matrix",
+                  tabName = "db_distmatrix"
+                ),
+                menuSubItem(
+                  text = "Missing Values",
+                  tabName = "db_missing_values",
+                  selected = TRUE,
+                  icon = icon("triangle-exclamation")
+                )
+              ),
+              menuItem(
+                text = "Manage Schemes",
+                tabName = "init",
+                icon = icon("layer-group")
+              ),
+              menuItem(
+                text = "Allelic Typing",
+                tabName = "typing",
+                icon = icon("gears")
+              ),
+              menuItem(
+                text = "Resistance Profile",
+                tabName = "gene_screening",
+                icon = icon("dna"),
+                startExpanded = TRUE,
+                menuSubItem(
+                  text = "Browse Entries",
+                  tabName = "gs_profile"
+                ),
+                menuSubItem(
+                  text = "Screening",
+                  tabName = "gs_screening"
+                )
+              ),
+              menuItem(
+                text = "Visualization",
+                tabName = "visualization",
+                icon = icon("circle-nodes")
+              ),
+              menuItem(
+                text = "Utilities",
+                tabName = "utilities",
+                icon = icon("screwdriver-wrench")
+              )
+            )
+          )
+        }
+        
+      } else {
+        output$menu <- renderMenu(
+          sidebarMenu(
+            menuItem(
+              text = "Database Browser",
+              tabName = "database",
+              icon = icon("hard-drive"),
+              startExpanded = TRUE,
+              menuSubItem(
+                text = "Browse Entries",
+                tabName = "db_browse_entries"
+              ),
+              menuSubItem(
+                text = "Scheme Info",
+                tabName = "db_schemeinfo"
+              ),
+              menuSubItem(
+                text = "Loci Info",
+                tabName = "db_loci_info"
+              ),
+              menuSubItem(
+                text = "Distance Matrix",
+                tabName = "db_distmatrix"
+              )
+            ),
+            menuItem(
+              text = "Manage Schemes",
+              tabName = "init",
+              icon = icon("layer-group")
+            ),
+            menuItem(
+              text = "Allelic Typing",
+              tabName = "typing",
+              icon = icon("gears")
+            ),
+            menuItem(
+              text = "Resistance Profile",
+              tabName = "gene_screening",
+              icon = icon("dna"),
+              startExpanded = TRUE,
+              menuSubItem(
+                text = "Browse Entries",
+                tabName = "gs_profile"
+              ),
+              menuSubItem(
+                text = "Screening",
+                tabName = "gs_screening"
+              )
+            ),
+            menuItem(
+              text = "Visualization",
+              tabName = "visualization",
+              icon = icon("circle-nodes")
+            ),
+            menuItem(
+              text = "Utilities",
+              tabName = "utilities",
+              icon = icon("screwdriver-wrench")
+            )
+          )
+        )
+      }
+    }
+    
+  })
+  
+  observe({
+    
+    if (!is.null(DB$available)) {
+      output$scheme_db <- renderUI({
+        if (length(DB$available) > 5) {
+          selectInput(
+            "scheme_db",
+            label = "",
+            choices = if(!is.null(Typing$last_scheme)) {
+              Typing$last_scheme
+            } else {DB$available},
+            selected = if(!is.null(Typing$last_scheme)) {
+              Typing$last_scheme
+            } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}
+          )
+        } else {
+          prettyRadioButtons(
+            "scheme_db",
+            label = "",
+            choices = if(!is.null(Typing$last_scheme)) {
+              Typing$last_scheme
+            } else {DB$available},
+            selected = if(!is.null(Typing$last_scheme)) {
+              Typing$last_scheme
+            } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}
+          )
+        }
+      })
+      
+      if (!is.null(DB$schemeinfo)) {
+        
+        output$scheme_info <- renderTable({
+          DB$schemeinfo
+        })
+        
+        output$scheme_header <- renderUI(h3(p("cgMLST Scheme"), style = "color:white"))
+        
+      } else {
+        
+        output$scheme_info <- NULL
+        output$scheme_header <- NULL
+        
+      }
+      
+      if (!is.null(DB$loci_info)) {
+        loci_info <- DB$loci_info
+        names(loci_info)[6] <- "Allele Count"
+        
+        output$db_loci <- renderDataTable(
+          loci_info,
+          selection = "single",
+          options = list(pageLength = 10,
+                         columnDefs = list(list(searchable = TRUE,
+                                                targets = "_all")),
+                         initComplete = DT::JS(
+                           "function(settings, json) {",
+                           "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                           "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                           "}"
+                         ),
+                         drawCallback = DT::JS(
+                           "function(settings) {",
+                           "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                           "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                           "}"
+                         ))
+        )
+        
+        output$loci_header <- renderUI(h3(p("Loci"), style = "color:white"))
+        
+      } else {
+        output$db_loci <- NULL
+        output$loci_header <- NULL
+      }
+    } 
+  })
+  
+  # If only one entry available disable varying loci checkbox
+  
+  output$compare_difference_box <- renderUI({
+    if(!is.null(DB$data)) {
+      if(nrow(DB$data) > 1) {
+        div(
+          class = "mat-switch-db",
+          materialSwitch(
+            "compare_difference",
+            h5(p("Only Varying Loci"), style = "color:white; padding-left: 0px; position: relative; top: -4px; right: -5px;"),
+            value = FALSE,
+            right = TRUE
+          )
+        )
+      }
+    }
+  })
+  
+  ### Database Events ----
+  
+  # Invalid entries table input
+  observe({
+    req(DB$data, input$db_entries)
+    if (isTRUE(input$invalid_date)) {
+      show_toast(
+        title = "Invalid date",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+      DB$inhibit_change <- TRUE
+    } else if (isTRUE(input$empty_name)) {
+      show_toast(
+        title = "Empty name",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+      DB$inhibit_change <- TRUE
+    } else if (isTRUE(input$empty_id)) {
+      show_toast(
+        title = "Empty ID",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+      DB$inhibit_change <- TRUE
+    } else {
+      DB$inhibit_change <- FALSE
+    }
+  })
+  
+  # Change scheme
+  observeEvent(input$reload_db, {
+    log_print("Input reload_db")
+    
+    if(tail(readLines(paste0(getwd(), "/logs/script_log.txt")), 1)!= "0") {
+      show_toast(
+        title = "Pending Multi Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if(Screening$status == "started") {
+      show_toast(
+        title = "Pending Screening",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      showModal(
+        modalDialog(
+          selectInput(
+            "scheme_db",
+            label = "",
+            choices = DB$available,
+            selected = DB$scheme),
+          title = "Select a local database to load.",
+          easyClose = TRUE,
+          footer = tagList(
+            modalButton("Cancel"),
+            actionButton("load", "Load", class = "btn btn-default")
+          )
+        )
+      )
+    }
+  })
+  
+  # Create new database
+  observe({
+    shinyDirChoose(input,
+                   "create_new_db",
+                   roots = c(Home = path_home(), Root = "/"),
+                   defaultRoot = "Home",
+                   session = session)
+    
+    if(!is.null(input$create_new_db)) {
+      DB$new_database <- as.character(
+        parseDirPath(
+          roots = c(Home = path_home(), Root = "/"),
+          input$create_new_db
+        )
+      )
+    }
+  })
+  
+  # Undo db changes
+  observeEvent(input$undo_changes, {
+    log_print("Input undo_changes")
+    
+    DB$inhibit_change <- FALSE
+    
+    Data <- readRDS(paste0(
+      DB$database, "/",
+      gsub(" ", "_", DB$scheme),
+      "/Typing.rds"
+    ))
+    
+    DB$data <- Data[["Typing"]]
+    
+    if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+      cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+      DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
+    } else {
+      DB$cust_var <- data.frame()
+    }
+    
+    DB$change <- FALSE
+    DB$count <- 0
+    DB$no_na_switch <- TRUE
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
+    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+    DB$deleted_entries <- character(0)
+    
+    observe({
+      if (!is.null(DB$data)) {
+        if (nrow(DB$data) == 1) {
+          if(!is.null(DB$data) & !is.null(DB$cust_var)) {
+            output$db_entries <- renderRHandsontable({
+              rhandsontable(
+                select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                error_highlight = err_thresh() - 1,                              
+                rowHeaders = NULL,
+                contextMenu = FALSE,
+                highlightCol = TRUE, 
+                highlightRow = TRUE
+              ) %>%
+                hot_col(1, 
+                        valign = "htMiddle",
+                        halign = "htCenter") %>%
+                hot_col(3, readOnly = TRUE) %>%
+                hot_col(c(1, 5, 10, 11, 12, 13),
+                        readOnly = TRUE) %>%
+                hot_col(3:(13 + nrow(DB$cust_var)), 
+                        valign = "htMiddle",
+                        halign = "htLeft") %>%
+                hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                hot_col(8, type = "dropdown", source = country_names) %>%
+                hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                        validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                hot_cols(fixedColumnsLeft = 1) %>%
+                hot_col(2, type = "checkbox", width = "auto",
+                        valign = "htTop",
+                        halign = "htCenter") %>%
+                hot_rows(fixedRowsTop = 0) %>%
+                hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgbA(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+            })
+          }
+        } else if (between(nrow(DB$data), 1, 40)) {
+          if (length(input$compare_select) > 0) {
+            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$compare_select)) {
+              output$db_entries <- renderRHandsontable({
+                
+                entry_data <- DB$data %>%
+                  select(1:(13 + nrow(DB$cust_var))) %>%
+                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                
+                rhandsontable(
+                  entry_data,
+                  col_highlight = diff_allele() - 1,
+                  dup_names_high = duplicated_names() - 1,
+                  dup_ids_high = duplicated_ids() - 1,
+                  row_highlight = true_rows() - 1,
+                  error_highlight = err_thresh() - 1,
+                  rowHeaders = NULL,
+                  highlightCol = TRUE, 
+                  highlightRow = TRUE,
+                  contextMenu = FALSE
+                )  %>%
+                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)), 
+                          valign = "htMiddle",
+                          halign = "htCenter",
+                          readOnly = TRUE) %>%
+                  hot_col(1, 
+                          valign = "htMiddle",
+                          halign = "htCenter") %>%
+                  hot_col(3, readOnly = TRUE) %>%
+                  hot_col(c(1, 5, 10, 11, 12, 13),
+                          readOnly = TRUE) %>%
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
+                          valign = "htMiddle",
+                          halign = "htLeft") %>%
+                  hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(8, type = "dropdown", source = country_names) %>%
+                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                          validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                  hot_col(2, type = "checkbox", width = "auto",
+                          valign = "htTop",
+                          halign = "htCenter",
+                          strict = TRUE,
+                          allowInvalid = FALSE,
+                          copyable = TRUE) %>%
+                  hot_cols(fixedColumnsLeft = 1) %>%
+                  hot_rows(fixedRowsTop = 0) %>%
+                  hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+  
+                       }
+              }") %>%
+                  hot_col(diff_allele(),
+                          renderer = "
+                  function(instance, td, row, col, prop, value, cellProperties) {
+                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
+  
+                    if (instance.params) {
+                          hcols = instance.params.col_highlight;
+                          hcols = hcols instanceof Array ? hcols : [hcols];
+                        }
+  
+                    if (instance.params && hcols.includes(col)) {
+                      td.style.background = 'rgb(116, 188, 139)';
+                    }
+                }"
+                  ) %>%
+                  hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+              })
+            }
+          } else {
+            if(!is.null(DB$data) & !is.null(DB$cust_var)) {
+              output$db_entries <- renderRHandsontable({
+                rhandsontable(
+                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                  rowHeaders = NULL,
+                  row_highlight = true_rows() - 1,
+                  dup_names_high = duplicated_names()- 1,
+                  dup_ids_high = duplicated_ids() - 1,
+                  error_highlight = err_thresh() - 1,
+                  contextMenu = FALSE,
+                  highlightCol = TRUE, 
+                  highlightRow = TRUE
+                ) %>%
+                  hot_cols(fixedColumnsLeft = 1) %>%
+                  hot_col(1, 
+                          valign = "htMiddle",
+                          halign = "htCenter") %>%
+                  hot_col(3, readOnly = TRUE) %>%
+                  hot_col(c(1, 5, 10, 11, 12, 13),
+                          readOnly = TRUE) %>%
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
+                          valign = "htMiddle",
+                          halign = "htLeft") %>%
+                  hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(8, type = "dropdown", source = country_names) %>%
+                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                          validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                  hot_col(2, type = "checkbox", width = "auto",
+                          valign = "htTop",
+                          halign = "htCenter") %>%
+                  hot_rows(fixedRowsTop = 0) %>%
+                  hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+  
+                       }
+              }") %>%
+                  hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+              })    
+            }
+          }
+        } else {
+          if (length(input$compare_select) > 0) {
+            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height) & !is.null(input$compare_select)) {
+              output$db_entries <- renderRHandsontable({
+                
+                entry_data <- DB$data %>%
+                  select(1:(13 + nrow(DB$cust_var))) %>%
+                  add_column(select(DB$allelic_profile_trunc, input$compare_select))
+                
+                rhandsontable(
+                  entry_data,
+                  col_highlight = diff_allele() - 1,
+                  rowHeaders = NULL,
+                  height = table_height(),
+                  row_highlight = true_rows() - 1,
+                  dup_names_high = duplicated_names() - 1,
+                  dup_ids_high = duplicated_ids() - 1,
+                  error_highlight = err_thresh() - 1,
+                  contextMenu = FALSE,
+                  highlightCol = TRUE, 
+                  highlightRow = TRUE
+                ) %>%
+                  hot_col((14 + nrow(DB$cust_var)):((13 + nrow(DB$cust_var)) + length(input$compare_select)),
+                          readOnly = TRUE, 
+                          valign = "htMiddle",
+                          halign = "htCenter") %>%
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
+                          valign = "htMiddle",
+                          halign = "htLeft") %>%
+                  hot_col(3, readOnly = TRUE) %>%
+                  hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(c(1, 5, 10, 11, 12, 13),
+                          readOnly = TRUE) %>%
+                  hot_col(8, type = "dropdown", source = country_names) %>%
+                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                          validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                  hot_col(1, 
+                          valign = "htMiddle",
+                          halign = "htCenter") %>%
+                  hot_col(2, type = "checkbox", width = "auto",
+                          valign = "htTop",
+                          halign = "htCenter",
+                          allowInvalid = FALSE,
+                          copyable = TRUE) %>%
+                  hot_cols(fixedColumnsLeft = 1) %>%
+                  hot_rows(fixedRowsTop = 0) %>%
+                  hot_col(1, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.row_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                                                             }
+                                                           }
+                                                       }") %>%
+                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") %>%
+                  hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(diff_allele(),
+                          renderer = "
+                  function(instance, td, row, col, prop, value, cellProperties) {
+                    Handsontable.renderers.NumericRenderer.apply(this, arguments);
+  
+                    if (instance.params) {
+                          hcols = instance.params.col_highlight;
+                          hcols = hcols instanceof Array ? hcols : [hcols];
+                        }
+  
+                    if (instance.params && hcols.includes(col)) {
+                      td.style.background = 'rgb(116, 188, 139)';
+                    }
+                }") 
+              })    
+            }
+          } else {
+            if(!is.null(DB$data) & !is.null(DB$cust_var) & !is.null(input$table_height)) {
+              output$db_entries <- renderRHandsontable({
+                rhandsontable(
+                  select(DB$data, 1:(13 + nrow(DB$cust_var))),
+                  rowHeaders = NULL,
+                  height = table_height(),
+                  dup_names_high = duplicated_names() - 1,
+                  dup_ids_high = duplicated_ids() - 1,
+                  row_highlight = true_rows() - 1,
+                  error_highlight = err_thresh() - 1,
+                  contextMenu = FALSE,
+                  highlightCol = TRUE, 
+                  highlightRow = TRUE
+                ) %>%
+                  hot_cols(fixedColumnsLeft = 1) %>%
+                  hot_col(1, 
+                          valign = "htMiddle",
+                          halign = "htCenter") %>%
+                  hot_col(c(1, 5, 10, 11, 12, 13),
+                          readOnly = TRUE) %>%
+                  hot_col(3, readOnly = TRUE) %>%
+                  hot_col(3, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_id', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_id', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(4, validator = "
+                                  function(value, callback) {
+                                    try {
+                                      if (value === null || value.trim() === '') {
+                                        callback(false); // Cell is empty
+                                        Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                      } else {
+                                        callback(true); // Cell is not empty
+                                        Shiny.setInputValue('empty_name', false); // Reset to false when cell is not empty
+                                      }
+                                    } catch (err) {
+                                      console.log(err);
+                                      callback(false); // In case of error, consider it as invalid
+                                      Shiny.setInputValue('empty_name', true); // Notify Shiny of empty cell
+                                    }
+                                  }
+                                ") %>%
+                  hot_col(8, type = "dropdown", source = country_names) %>%
+                  hot_col(6, dateFormat = "YYYY-MM-DD", type = "date", strict = TRUE, allowInvalid = TRUE,
+                          validator = "
+                                function (value, callback) {
+                                  var today_date = new Date();
+                                  today_date.setHours(0, 0, 0, 0);
+                                  
+                                  var new_date = new Date(value);
+                                  new_date.setHours(0, 0, 0, 0);
+                                  
+                                  try {
+                                    if (new_date <= today_date) {
+                                      callback(true);
+                                      Shiny.setInputValue('invalid_date', false);
+                                    } else {
+                                      callback(false); 
+                                      Shiny.setInputValue('invalid_date', true);
+                                    }
+                                  } catch (err) {
+                                    console.log(err);
+                                    callback(false); 
+                                    Shiny.setInputValue('invalid_date', true);
+                                  }
+                                }") %>%
+                  hot_col(3:(13 + nrow(DB$cust_var)), 
+                          valign = "htMiddle",
+                          halign = "htLeft") %>%
+                  hot_rows(fixedRowsTop = 0) %>%
+                  hot_col(1, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.row_highlight
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgba(44, 222, 235, 0.6)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(2, type = "checkbox", width = "auto",
+                          valign = "htTop", halign = "htCenter") %>%
+                  hot_col(4, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_names_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(3, renderer = "
+              function (instance, td, row, col, prop, value, cellProperties) {
+                       Handsontable.renderers.TextRenderer.apply(this, arguments);
+  
+                       if (instance.params) {
+                         hrows = instance.params.dup_ids_high
+                         hrows = hrows instanceof Array ? hrows : [hrows]
+  
+                         if (hrows.includes(row)) { 
+                           td.style.backgroundColor = 'rgb(224, 179, 0)' 
+                         }
+                       }
+              }") %>%
+                  hot_col(12, renderer = "function (instance, td, row, col, prop, value, cellProperties) {
+                                                           Handsontable.renderers.TextRenderer.apply(this, arguments);
+                                                           if (instance.params) {
+                                                             hrows = instance.params.error_highlight
+                                                             hrows = hrows instanceof Array ? hrows : [hrows]
+                                                             if (hrows.includes(row)) { 
+                                                               td.style.backgroundColor = 'rgba(255, 80, 1, 0.8)' 
+                                                             }
+                                                           }
+                                                       }") 
+              })
+            }
+          }
+        }
+      }
+    })
+  })
+  
+  observe({
+    if(!is.null(DB$data)){
+      if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+        cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+        DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
+        
+      } else {
+        DB$cust_var <- data.frame()
+      }
+    }
+  })
+  
+  DB$count <- 0
+  
+  observeEvent(input$add_new_variable, {
+    log_print("Input add_new_variable")
+    
+    if(nchar(input$new_var_name) > 12) {
+      log_print("Add variable; max. 10 character")
+      show_toast(
+        title = "Max. 10 characters",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      if (input$new_var_name == "") {
+        log_print("Add variable; min. 1 character")
+        show_toast(
+          title = "Min. 1 character",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+      } else {
+        if(trimws(input$new_var_name) %in% names(DB$meta)) {
+          log_print("Add variable; name already existing")
+          show_toast(
+            title = "Variable name already existing",
+            type = "warning",
+            position = "bottom-end",
+            timer = 6000
+          )
+        } else {
+          showModal(
+            modalDialog(
+              selectInput(
+                "new_var_type",
+                label = "",
+                choices = c("Categorical (character)",
+                            "Continous (numeric)")),
+              title = paste0("Select Data Type"),
+              easyClose = TRUE,
+              footer = tagList(
+                modalButton("Cancel"),
+                actionButton("conf_new_var", "Confirm", class = "btn btn-default")
+              )
+            )
+          )
+        }
+      }
+    }
+  })
+  
+  observeEvent(input$conf_new_var, {
+    log_print("Input conf_new_var")
+    
+    # User feedback variables
+    removeModal()
+    DB$count <- DB$count + 1
+    DB$change <- TRUE
+    
+    # Format variable name
+    name <- trimws(input$new_var_name)
+    
+    if(input$new_var_type == "Categorical (character)") {
+      DB$data <- DB$data %>%
+        mutate("{name}" := character(nrow(DB$data)), .after = 13)
+      
+      DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "categ"))
+    } else {
+      DB$data <- DB$data %>%
+        mutate("{name}" := numeric(nrow(DB$data)), .after = 13)
+      
+      DB$cust_var <- rbind(DB$cust_var, data.frame(Variable = name, Type = "cont"))
+    }
+    
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+    
+    log_print(paste0("New custom variable added: ", input$new_var_name))
+    
+    show_toast(
+      title = paste0("Variable ", trimws(input$new_var_name), " added"),
+      type = "success",
+      position = "bottom-end",
+      timer = 6000
+    )
+    
+  })
+  
+  observeEvent(input$delete_new_variable, {
+    log_print("Input delete_new_variable")
+    
+    if (input$del_which_var == "") {
+      log_print("Delete custom variables; no custom variable")
+      show_toast(
+        title = "No custom variables",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      showModal(
+        modalDialog(
+          paste0(
+            "Confirmation will lead to irreversible deletion of the custom ",
+            input$del_which_var,
+            " variable. Continue?"
+          ),
+          title = "Delete custom variables",
+          fade = TRUE,
+          easyClose = TRUE,
+          footer = tagList(
+            modalButton("Cancel"),
+            actionButton("conf_var_del", "Delete", class = "btn btn-danger")
+          )
+        )
+      )
+    }
+  })
+  
+  observeEvent(input$conf_var_del, {
+    log_print("Input conf_var_del")
+    
+    DB$change <- TRUE
+    
+    removeModal()
+    
+    if(DB$count >= 1) {
+      DB$count <- DB$count - 1
+    } 
+    
+    show_toast(
+      title = paste0("Variable ", input$del_which_var, " removed"),
+      type = "warning",
+      position = "bottom-end",
+      timer = 6000
+    )
+    
+    log_print(paste0("Variable ", input$del_which_var, " removed"))
+    
+    DB$cust_var <- DB$cust_var[-which(DB$cust_var$Variable == input$del_which_var),]
+    DB$data <- select(DB$data, -(input$del_which_var))
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
+    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+  })
+  
+  # Select all button
+  
+  observeEvent(input$sel_all_entries, {
+    log_print("Input sel_all_entries")
+    
+    DB$data$Include <- TRUE
+  })
+  
+  observeEvent(input$desel_all_entries, {
+    log_print("Input desel_all_entries")
+    
+    DB$data$Include <- FALSE
+  })
+  
+  # Switch to entry table
+  
+  observeEvent(input$change_entries, {
+    log_print("Input change_entries")
+    
+    removeModal()
+    updateTabItems(session, "tabs", selected = "db_browse_entries")
+  })
+  
+  #### Save Missing Value as CSV ----
+  
+  output$download_na_matrix <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save missing values table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")))
+      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Missing_Values.csv")
+    },
+    content = function(file) {
+      download_matrix <- hot_to_r(input$table_missing_values)
+      write.csv(download_matrix, file, sep = ",", row.names=FALSE, quote=FALSE) 
+    }
+  )
+  
+  #### Save scheme info table as CSV ----
+  
+  output$download_schemeinfo <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save scheme info table ", paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")))
+      
+      paste0(gsub(" ", "_", DB$scheme), "_scheme.csv")
+    },
+    content = function(file) {
+      pub_index <- which(DB$schemeinfo[,1] == "Publications")
+      write.table(
+        DB$schemeinfo[1:(pub_index-1),],
+        file, 
+        sep = ";",
+        row.names = FALSE, 
+        quote = FALSE
+      ) 
+    }
+  )
+  
+  #### Save Loci info table as CSV ----
+  
+  output$download_loci_info <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save loci info table ", paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")))
+      
+      paste0(gsub(" ", "_", DB$scheme), "_Loci.csv")
+    },
+    content = function(file) {
+      write.table(
+        DB$loci_info,
+        file, 
+        sep = ";",
+        row.names = FALSE, 
+        quote = FALSE
+      ) 
+    }
+  )
+  
+  #### Save entry table as CSV ----
+  
+  output$download_entry_table <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save entry table ", paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")))
+      
+      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Entries.csv")
+    },
+    content = function(file) {
+      download_matrix <- hot_to_r(input$db_entries)
+      
+      if (input$download_table_include == TRUE) {
+        download_matrix <- download_matrix[which(download_matrix$Include == TRUE),]
+      }
+      
+      if (input$download_table_loci == FALSE) {
+        download_matrix <- select(download_matrix, 1:(13 + nrow(DB$cust_var)))
+      } 
+      
+      write.csv(download_matrix, file, row.names=FALSE, quote=FALSE) 
+    }
+  )
+  
+  # Save Edits Button
+  
+  observeEvent(input$edit_button, {
+    if(nrow(hot_to_r(input$db_entries)) > nrow(DB$data)) {
+      show_toast(
+        title = "Invalid rows entered. Saving not possible.",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      if(!isTRUE(DB$inhibit_change)) {
+        log_print("Input edit_button")
+        
+        showModal(
+          modalDialog(
+            if(length(DB$deleted_entries > 0)) {
+              paste0(
+                "Overwriting previous metadata of local ",
+                DB$scheme,
+                " database. Deleted entries will be irreversibly removed. Continue?"
+              )
+            } else {
+              paste0(
+                "Overwriting previous metadata of local ",
+                DB$scheme,
+                " database. Continue?"
+              )
+            },
+            title = "Save Database",
+            fade = TRUE,
+            easyClose = TRUE,
+            footer = tagList(
+              modalButton("Cancel"),
+              actionButton("conf_db_save", "Save", class = "btn btn-default")
+            )
+          )
+        )
+      } else {
+        log_print("Input edit_button, invalid values.")
+        show_toast(
+          title = "Invalid values entered. Saving not possible.",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+      }
+    }
+  })
+  
+  observeEvent(input$Cancel, {
+    log_print("Input Cancel")
+    removeModal()
+  })
+  
+  observeEvent(input$conf_db_save, {
+    log_print("Input conf_db_save")
+    
+    # Remove isolate assembly file if present
+    if(!is.null(DB$remove_iso)) {
+      if(length(DB$remove_iso) > 0) {
+        lapply(DB$remove_iso, unlink, recursive = TRUE, force = FALSE, expand = TRUE)
+      }
+    }
+    DB$remove_iso <- NULL
+    
+    Data <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme),"Typing.rds"))
+    
+    if ((ncol(Data[["Typing"]]) - 13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+      cust_vars_pre <- select(Data[["Typing"]], 
+                              14:(ncol(Data[["Typing"]]) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+      cust_vars_pre <- names(cust_vars_pre)
+    } else {
+      cust_vars_pre <- character()
+    }
+    
+    Data[["Typing"]] <- select(Data[["Typing"]], -(1:(13 + length(cust_vars_pre))))
+    
+    meta_hot <- hot_to_r(input$db_entries)
+    
+    if(length(DB$deleted_entries > 0)) {
+      
+      meta_hot <- mutate(meta_hot, Index = as.character(1:nrow(DB$data)))
+      
+      Data[["Typing"]] <- mutate(Data[["Typing"]][-as.numeric(DB$deleted_entries),  ], 
+                                 meta_hot, .before = 1)
+      rownames(Data[["Typing"]]) <- Data[["Typing"]]$Index
+    } else {
+      Data[["Typing"]] <- mutate(Data[["Typing"]], meta_hot, .before = 1)
+    }
+    
+    # Ensure correct logical data type
+    Data[["Typing"]][["Include"]] <- as.logical(Data[["Typing"]][["Include"]])
+    saveRDS(Data, file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+    
+    # Load database from files  
+    Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+    
+    DB$data <- Database[["Typing"]]
+    
+    if(!is.null(DB$data)){
+      if ((ncol(DB$data)-13) != as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))) {
+        cust_var <- select(DB$data, 14:(ncol(DB$data) - as.numeric(gsub(",", "", as.vector(DB$schemeinfo[6, 2])))))
+        DB$cust_var <- data.frame(Variable = names(cust_var), Type = column_classes(cust_var))
+      } else {
+        DB$cust_var <- data.frame()
+      }
+    }
+    
+    DB$change <- FALSE
+    DB$count <- 0
+    DB$no_na_switch <- TRUE
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
+    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+    DB$deleted_entries <- character(0)
+    
+    removeModal()
+    
+    show_toast(
+      title = "Database successfully saved",
+      type = "success",
+      position = "bottom-end",
+      timer = 4000
+    )
+  })
+  
+  observeEvent(input$del_button, {
+    log_print("Input del_button")
+    
+    if (length(input$select_delete) < 1) {
+      log_print("Delete entries; no entry selected")
+      show_toast(
+        title = "No entry selected",
+        type = "warning",
+        position = "bottom-end",
+        timer = 4000
+      )
+    } else if((readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") |
+              (tail(readLogFile(), 1) != "0")) {
+      log_print("Delete entries; pending typing")
+      
+      show_toast(
+        title = "Pending Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 4000
+      )
+    } else {
+      if( (length(input$select_delete) - nrow(DB$data) ) == 0) {
+        showModal(
+          modalDialog(
+            paste0("Deleting will lead to removal of all entries and assemblies from local ", DB$scheme, " database. The data can not be recovered afterwards. Continue?"),
+            easyClose = TRUE,
+            title = "Deleting Entries",
+            footer = tagList(
+              modalButton("Cancel"),
+              actionButton("conf_delete_all", "Delete", class = "btn btn-danger")
+            )
+          )
+        )
+      } else {
+        showModal(
+          modalDialog(
+            paste0(
+              "Confirmation will lead to irreversible removal of selected entries and the respectively saved assembly. Continue?"
+            ),
+            title = "Deleting Entries",
+            fade = TRUE,
+            easyClose = TRUE,
+            footer = tagList(
+              modalButton("Cancel"),
+              actionButton(
+                "conf_delete", 
+                "Delete", 
+                class = "btn btn-danger")
+            )
+          )
+        )
+      }
+    }
+  })
+  
+  observeEvent(input$conf_delete_all, {
+    log_print("Input conf_delete_all")
+    
+    # remove file with typing data
+    file.remove(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+    unlink(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates"), recursive = TRUE, force = FALSE, expand =TRUE)
+    
+    showModal(
+      modalDialog(
+        selectInput(
+          "scheme_db",
+          label = "",
+          choices = if(!is.null(Typing$last_scheme)) {
+            Typing$last_scheme
+          } else {DB$available},
+          selected = if(!is.null(Typing$last_scheme)) {
+            Typing$last_scheme
+          } else {if(!is.null(DB$scheme)) {DB$scheme} else {DB$available[1]}}),
+        title = "All entries have been removed. Select a local database to load.",
+        footer = tagList(
+          actionButton("load", "Load", class = "btn btn-default")
+        )
+      )
+    )
+    
+  })
+  
+  DB$deleted_entries <- character(0)
+  
+  observeEvent(input$conf_delete, {
+    
+    log_print("Input conf_delete")
+    
+    # Get isolates selected for deletion
+    DB$deleted_entries <- append(DB$deleted_entries, DB$data$Index[as.numeric(input$select_delete)])
+    
+    # Set reactive status variables
+    DB$no_na_switch <- TRUE
+    DB$change <- TRUE
+    DB$check_new_entries <- FALSE
+    
+    # Set isolate directory deletion variables
+    isopath <- dir_ls(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates"))
+    DB$remove_iso <- isopath[which(basename(isopath) == DB$data$`Assembly ID`[as.numeric(input$select_delete)])]
+    
+    # Reload updated database reactive variables
+    DB$data <- DB$data[!(DB$data$Index %in% as.numeric(input$select_delete)),]
+    DB$meta_gs <- select(DB$data, c(1, 3:13))
+    DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+    DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+    DB$allelic_profile <- select(DB$data, -(1:(13 + nrow(DB$cust_var))))
+    DB$allelic_profile_trunc <- as.data.frame(lapply(DB$allelic_profile, function(x) sapply(x, truncHash)))
+    DB$allelic_profile_true <- DB$allelic_profile[which(DB$data$Include == TRUE),]
+    
+    # User feedback
+    removeModal()
+    
+    if(length(input$select_delete) > 1) {
+      show_toast(
+        title = "Entries deleted",
+        type = "success",
+        position = "bottom-end",
+        timer = 4000
+      )
+    } else {
+      show_toast(
+        title = "Entry deleted",
+        type = "success",
+        position = "bottom-end",
+        timer = 4000
+      )
+    }
+  })
+  
+  
+  ### Distance Matrix ---- 
+  
+  hamming_df <- reactive({
+    if(input$distmatrix_true == TRUE) {
+      if(anyNA(DB$allelic_profile)) {
+        if(input$na_handling == "omit") {
+          allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
+          
+          allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
+          
+          hamming_mat <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
+          
+        } else if(input$na_handling == "ignore_na"){
+          hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
+          
+        } else {
+          hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
+          
+        } 
+      } else {
+        hamming_mat <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
+      }
+    } else {
+      if(anyNA(DB$allelic_profile)) {
+        if(input$na_handling == "omit") {
+          allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
+          hamming_mat <- compute.distMatrix(allelic_profile_noNA, hamming.dist)
+        } else if(input$na_handling == "ignore_na"){
+          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distIgnore)
+        } else {
+          hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.distCategory)
+        }  
+      } else {
+        hamming_mat <- compute.distMatrix(DB$allelic_profile, hamming.dist)
+      }
+    }
+    
+    # Extreme values for distance matrix heatmap display
+    DB$matrix_min <- min(hamming_mat, na.rm = TRUE)
+    DB$matrix_max <- max(hamming_mat, na.rm = TRUE)
+    
+    if(input$distmatrix_triangle == FALSE) {
+      hamming_mat[upper.tri(hamming_mat, diag = !input$distmatrix_diag)] <- NA
+    } 
+    
+    # Row- and colnames change
+    if(input$distmatrix_true == TRUE) {
+      rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label][which(DB$data$Include == TRUE),])
+    } else {
+      rownames(hamming_mat) <- unlist(DB$data[input$distmatrix_label])
+    }
+    colnames(hamming_mat) <- rownames(hamming_mat)
+    
+    mode(hamming_mat) <- "integer"
+    
+    DB$ham_matrix <- hamming_mat %>%
+      as.data.frame() %>%
+      mutate(Index = colnames(hamming_mat)) %>%
+      relocate(Index)
+    DB$distancematrix_nrow <- nrow(DB$ham_matrix)
+    
+    DB$ham_matrix
+  })
+  
+  output$download_distmatrix <- downloadHandler(
+    filename = function() {
+      paste0(Sys.Date(), "_", gsub(" ", "_", DB$scheme), "_Distance_Matrix.csv")
+    },
+    content = function(file) {
+      download_matrix <- hot_to_r(input$db_distancematrix)
+      download_matrix[is.na(download_matrix)] <- ""
+      write.csv(download_matrix, file, row.names=FALSE, quote=FALSE) 
+    }
+  )
+  
+  # _______________________ ####
+  
+  ## Locus sequences ----
+  
+  observe({
+    if(!is.null(DB$database) & !is.null(DB$scheme)) {
+      DB$loci <- list.files(
+        path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
+        pattern = "\\.(fasta|fa|fna)$",
+        full.names = TRUE
+      )
+    }
+  })
+  
+  output$loci_sequences <- renderUI({
+    req(input$db_loci_rows_selected, DB$database, DB$scheme, input$seq_sel)
+    
+    DB$loci <- list.files(
+      path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
+      pattern = "\\.(fasta|fa|fna)$",
+      full.names = TRUE
+    )
+    
+    fasta <- format_fasta(DB$loci[input$db_loci_rows_selected])
+    
+    seq <- fasta[[which(fasta == paste0(">", gsub("Allele ", "", sub(" -.*", "", input$seq_sel)))) + 1]]
+    
+    DB$seq <- seq
+    
+    column(
+      width = 12,
+      HTML(
+        paste(
+          tags$span(style='color: white; font-size: 15px; position: relative; top: -15px; left: -50px', 
+                    sub(" -.*", "", input$seq_sel))
+        )
+      ),
+      tags$pre(HTML(color_sequence(seq)), class = "sequence")
+    )
+  })
+  
+  output$sequence_selector <- renderUI({
+    if(!is.null(input$db_loci_rows_selected)) {
+      
+      req(input$db_loci_rows_selected, DB$database, DB$scheme)
+      
+      DB$loci <- list.files(
+        path = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles"),
+        pattern = "\\.(fasta|fa|fna)$",
+        full.names = TRUE
+      )
+      
+      fasta <- format_fasta(DB$loci[input$db_loci_rows_selected])
+      
+      seq_names <- c()
+      for (i in seq_along(fasta)) {
+        if (startsWith(fasta[[i]], ">")) {
+          name <- sub(">", "", fasta[[i]])
+          seq_names <- c(seq_names, name)
+        }
+      }
+      
+      var_count <- table(DB$allelic_profile[gsub(".fasta", "", (basename(DB$loci[input$db_loci_rows_selected])))])
+      
+      vec <- prop.table(var_count)
+      
+      perc <- sapply(unname(vec), scales::percent, accuracy = 0.1)
+      
+      names(perc) <- names(vec)
+      
+      choices <- seq_names
+      
+      present <- which(choices %in% names(vec))
+      absent <- which(!(choices %in% names(vec)))
+      
+      choices[present] <- paste0("Allele ", choices[present], " - ", unname(var_count), " times in DB (", unname(perc), ")")
+      
+      choices[absent] <- paste0("Allele ", choices[absent], " - not present")
+      
+      choices <- c(choices[present], choices[absent])
+      
+      names(choices) <- sapply(choices, function(x) {
+        x <- strsplit(x, " ")[[1]]
+        x[2] <- paste0(substr(x[2], 1, 4), "...", substr(x[2], nchar(x[2])-3, nchar(x[2])))
+        paste(x, collapse = " ")
+      })
+      
+      column(
+        width = 3,
+        selectInput(
+          "seq_sel",
+          h5("Select Variant", style = "color:white;"),
+          choices = choices,
+          width = "80%"
+        ),
+        br(),
+        fluidRow(
+          column(
+            width = 8,
+            align = "left",
+            actionButton("copy_seq", "Copy Sequence",
+                         icon = icon("copy")),
+            bsTooltip("copy_seq", "Copy the variant sequence <br> to clipboard", placement = "top", trigger = "hover")
+          )
+        ),
+        br(),
+        fluidRow(
+          column(
+            width = 8,
+            align = "left",
+            downloadBttn(
+              "get_locus",
+              style = "simple",
+              label = "Save .fasta",
+              size = "sm",
+              icon = icon("download")
+            ),
+            bsTooltip("get_locus_bttn", "Save locus file with all variants", placement = "top", trigger = "hover")
+          )
+        ),
+        br(), br(), br(), br(), br(), br(), br()
+      )
+    }
+  })
+  
+  observeEvent(input$copy_seq, {
+    if(!is.null(DB$seq)) {
+      session$sendCustomMessage("txt", DB$seq)
+    }
+    show_toast(
+      title = "Copied sequence",
+      type = "success",
+      position = "bottom-end",
+      timer = 3000
+    )
+  })
+  
+  output$get_locus <- downloadHandler(
+    filename = function() {
+      fname <- basename(DB$loci[input$db_loci_rows_selected])
+      log_print(paste0("Get locus fasta ", fname))
+      fname
+    },
+    content = function(file) {
+      cont <- readLines(DB$loci[input$db_loci_rows_selected])
+      writeLines(cont, file)
+    }
+  )
+  
+  # _______________________ ####
+  
+  ## Download cgMLST ----
+  
+  observe({
+    if (input$select_cgmlst == "Acinetobacter baumanii") {
+      species <- "Abaumannii1907"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- Scheme$folder_name <- "Acinetobacter_baumanii"
+    } else if (input$select_cgmlst == "Bacillus anthracis") {
+      species <- "Banthracis1917"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Bacillus_anthracis"
+    } else if (input$select_cgmlst == "Bordetella pertussis") {
+      species <- "Bpertussis1917"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Bordetella_pertussis"
+    } else if (input$select_cgmlst == "Brucella melitensis") {
+      species <- "Bmelitensis1912"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Brucella_melitensis"
+    } else if (input$select_cgmlst == "Brucella spp.") {
+      species <- "Brucella1914"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Brucella_spp"
+    } else if (input$select_cgmlst == "Burkholderia mallei (FLI)") {
+      species <- "Bmallei_fli1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Burkholderia_mallei_FLI"
+    } else if (input$select_cgmlst == "Burkholderia mallei (RKI)") {
+      species <- "Bmallei_rki1909"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Burkholderia_mallei_RKI"
+    } else if (input$select_cgmlst == "Burkholderia pseudomallei") {
+      species <- "Bpseudomallei1906"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Burkholderia_pseudomallei"
+    } else if (input$select_cgmlst == "Campylobacter jejuni/coli") {
+      species <- "Cjejuni1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Campylobacter_jejuni_coli"
+    } else if (input$select_cgmlst == "Clostridioides difficile") {
+      species <- "Cdifficile1905"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Clostridioides_difficile"
+    } else if (input$select_cgmlst == "Clostridium perfringens") {
+      species <- "Cperfringens1907"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Clostridium_perfringens"
+    } else if (input$select_cgmlst == "Corynebacterium diphtheriae") {
+      species <- "Cdiphtheriae1907"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Corynebacterium_diphtheriae"
+    } else if (input$select_cgmlst == "Cronobacter sakazakii/malonaticus") {
+      species <- "Csakazakii1910"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Cronobacter_sakazakii_malonaticus"
+    } else if (input$select_cgmlst == "Enterococcus faecalis") {
+      species <- "Efaecalis1912"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Enterococcus_faecalis"
+    } else if (input$select_cgmlst == "Enterococcus faecium") {
+      species <- "Efaecium1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Enterococcus_faecium"
+    } else if (input$select_cgmlst == "Escherichia coli") {
+      species <- "Ecoli1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Escherichia_coli"
+    } else if (input$select_cgmlst == "Francisella tularensis") {
+      species <- "Ftularensis1913"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Francisella_tularensis"
+    } else if (input$select_cgmlst == "Klebsiella oxytoca sensu lato") {
+      species <- "Koxytoca717"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Klebsiella_oxytoca_sensu_lato"
+    } else if (input$select_cgmlst == "Klebsiella pneumoniae sensu lato") {
+      species <- "Kpneumoniae1909"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Klebsiella_pneumoniae_sensu_lato"
+    } else if (input$select_cgmlst == "Legionella pneumophila") {
+      species <- "Lpneumophila1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Legionella_pneumophila"
+    } else if (input$select_cgmlst == "Listeria monocytogenes") {
+      species <- "Lmonocytogenes1910"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Listeria_monocytogenes"
+    } else if (input$select_cgmlst == "Mycobacterium tuberculosis complex") {
+      species <- "Mtuberculosis1909"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Mycobacterium_tuberculosis_complex"
+    } else if (input$select_cgmlst == "Mycobacteroides abscessus") {
+      species <- "Mabscessus1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Mycobacteroides_abscessus"
+    } else if (input$select_cgmlst == "Mycoplasma gallisepticum") {
+      species <- "Mgallisepticum1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Mycoplasma_gallisepticum"
+    } else if (input$select_cgmlst == "Paenibacillus larvae") {
+      species <- "Plarvae1902"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Paenibacillus_larvae"
+    } else if (input$select_cgmlst == "Pseudomonas aeruginosa") {
+      species <- "Paeruginosa1911"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Pseudomonas_aeruginosa"
+    } else if (input$select_cgmlst == "Salmonella enterica") {
+      species <- "Senterica1913"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Salmonella_enterica"
+    } else if (input$select_cgmlst == "Serratia marcescens") {
+      species <- "Smarcescens1912"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Serratia_marcescens"
+    } else if (input$select_cgmlst == "Staphylococcus aureus") {
+      species <- "Saureus1908"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Staphylococcus_aureus"
+    } else if (input$select_cgmlst == "Staphylococcus capitis") {
+      species <- "Scapitis1905"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Staphylococcus_capitis"
+    } else if (input$select_cgmlst == "Streptococcus pyogenes") {
+      species <- "Spyogenes1904"
+      Scheme$link_scheme <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/")
+      Scheme$link_cgmlst <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/alleles/")
+      Scheme$link_targets <- paste0("https://www.cgmlst.org/ncs/schema/", species, "/locus/?content-type=csv")
+      Scheme$folder_name <- "Streptococcus_pyogenes"
+    }
+  })
+  
+  observeEvent(input$download_cgMLST, {
+    log_print(paste0("Started download of scheme for ", Scheme$folder_name))
+    
+    shinyjs::hide("download_cgMLST")
+    shinyjs::show("loading")
+    
+    output$statustext <- renderUI(
+      fluidRow(
+        tags$li(
+          class = "dropdown", 
+          tags$span(HTML(
+            paste('<i class="fa-solid fa-circle-dot" style="color:orange !important;"></i>', 
+                  "Status:&nbsp;&nbsp;&nbsp; <i>Downloading scheme...</i>")),
+            style = "color:white;")
+        )
+      )
+    )
+    
+    show_toast(
+      title = "Download started",
+      type = "success",
+      position = "bottom-end",
+      timer = 5000
+    )
+    
+    if(length(DB$available) == 0) {
+      saveRDS(DB$new_database, paste0(getwd(), "/execute/new_db.rds"))
+      dir.create(file.path(readRDS(paste0(getwd(), "/execute/new_db.rds")), "Database"), recursive = TRUE)
+    }
+    
+    DB$load_selected <- TRUE
+    
+    # Check if .downloaded_schemes folder exists and if not create it
+    if (!dir.exists(file.path(DB$database, ".downloaded_schemes"))) {
+      dir.create(file.path(DB$database, ".downloaded_schemes"), recursive = TRUE)
+    }
+    
+    # Check if remains of old temporary folder exists and remove them
+    if (dir.exists(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")))) {
+      unlink(file.path(DB$database, Scheme$folder_name, paste0(Scheme$folder_name, ".tmp")), recursive = TRUE)
+    }
+    
+    # Download Loci Fasta Files
+    options(timeout = 600)
+    
+    tryCatch({
+      download.file(Scheme$link_cgmlst, 
+                    file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")))
+      "Download successful!"
+    }, error = function(e) {
+      paste("Error: ", e$message)
+    })
+    
+    # Unzip the scheme in temporary folder
+    unzip(
+      zipfile = file.path(DB$database, ".downloaded_schemes", paste0(Scheme$folder_name, ".zip")),
+      exdir = file.path(DB$database, 
+                        Scheme$folder_name, 
+                        paste0(Scheme$folder_name, ".tmp")
+      )
+    )
+    
+    log_print("Hashing downloaded database")
+    # Hash temporary folder
+    hash_database(file.path(DB$database, 
+                            Scheme$folder_name, 
+                            paste0(Scheme$folder_name, ".tmp")))
+    
+    # Get list from local database
+    local_db_filelist <- list.files(file.path(DB$database, 
+                                              Scheme$folder_name, 
+                                              paste0(Scheme$folder_name, "_alleles")))
+    if (!is_empty(local_db_filelist)) {
+      # Get list from temporary database
+      tmp_db_filelist <- list.files(file.path(DB$database,
+                                              Scheme$folder_name,
+                                              paste0(Scheme$folder_name, ".tmp")))
+      
+      # Find the difference (extra files in local database)
+      local_db_extra <- setdiff(local_db_filelist, tmp_db_filelist)
+      
+      # Copy extra files to temporary folder
+      file.copy(file.path(DB$database,
+                          Scheme$folder_name, 
+                          paste0(Scheme$folder_name, "_alleles"), local_db_extra),
+                file.path(DB$database,
+                          Scheme$folder_name,
+                          paste0(Scheme$folder_name, ".tmp")))
+      
+      # Check differences in file pairs
+      local_db_hashes <- tools::md5sum(file.path(DB$database,
+                                                 Scheme$folder_name,
+                                                 paste0(Scheme$folder_name, "_alleles"),
+                                                 local_db_filelist))
+      tmp_db_hashes <- tools::md5sum(file.path(DB$database,
+                                               Scheme$folder_name,
+                                               paste0(Scheme$folder_name, ".tmp"),
+                                               local_db_filelist))
+      
+      diff_files <- local_db_hashes %in% tmp_db_hashes
+      diff_loci <- names(local_db_hashes)[diff_files == FALSE]
+      diff_loci <- sapply(strsplit(diff_loci, "/"), function(x) x[length(x)])
+      
+      # Check locus hashes
+      for (locus in diff_loci) {
+        local_db_hashes <- get_locus_hashes(file.path(DB$database,
+                                                      Scheme$folder_name,
+                                                      paste0(Scheme$folder_name, "_alleles"),
+                                                      locus))
+        tmp_db_hashes <- get_locus_hashes(file.path(DB$database,
+                                                    Scheme$folder_name,
+                                                    paste0(Scheme$folder_name, ".tmp"),
+                                                    locus))
+        diff_hashes <- setdiff(local_db_hashes, tmp_db_hashes)
+        
+        sequences <- extract_seq(file.path(DB$database,
+                                           Scheme$folder_name,
+                                           paste0(Scheme$folder_name, "_alleles"),
+                                           locus), diff_hashes)
+        if (!is_empty(sequences$idx) && !is_empty(sequences$seq) &&
+            length(sequences$idx) == length(sequences$seq)) {
+          add_new_sequences(file.path(DB$database,
+                                      Scheme$folder_name,
+                                      paste0(Scheme$folder_name, ".tmp"),
+                                      locus), sequences)
+        }
+      }
+    }
+    
+    unlink(file.path(DB$database, Scheme$folder_name, 
+                     paste0(Scheme$folder_name, "_alleles")), recursive = TRUE)
+    
+    file.rename(file.path(DB$database, Scheme$folder_name,
+                          paste0(Scheme$folder_name, ".tmp")),
+                file.path(DB$database, Scheme$folder_name,
+                          paste0(Scheme$folder_name, "_alleles")))
+    
+    # Download Scheme Info
+    download(
+      Scheme$link_scheme,
+      dest = file.path(DB$database, Scheme$folder_name, "scheme_info.html"),
+      mode = "wb"
+    )
+    
+    # Download Loci Info	
+    download(	
+      Scheme$link_targets,	
+      dest = file.path(DB$database, Scheme$folder_name, "targets.csv"),
+      mode = "wb"
+    )
+    
+    # Send downloaded scheme to database browser overview
+    DB$available <- gsub("_", " ", basename(dir_ls(DB$database)))
+    
+    Scheme$target_table <- read.csv(
+      file.path(DB$database, Scheme$folder_name, "targets.csv"),
+      header = TRUE,	
+      sep = "\t",	
+      row.names = NULL,	
+      colClasses = c(	
+        "NULL",	
+        "character",	
+        "character",	
+        "integer",	
+        "integer",	
+        "character",	
+        "integer",	
+        "NULL"	
+      )	
+    )
+    
+    DB$exist <- length(dir_ls(DB$database)) == 0
+    
+    shinyjs::show("download_cgMLST")
+    shinyjs::hide("loading")
+    
+    output$statustext <- renderUI(
+      fluidRow(
+        tags$li(
+          class = "dropdown", 
+          tags$span(HTML(
+            paste('<i class="fa-solid fa-circle-dot" style="color:lightgreen !important;"></i>', 
+                  "Status:&nbsp;&nbsp;&nbsp; <i>ready</i>")),
+            style = "color:white;")
+        )
+      )
+    )
+    
+    show_toast(
+      title = "Download successful",
+      type = "success",
+      position = "bottom-end",
+      timer = 5000
+    )
+    
+    log_print("Download successful")
+    
+    showModal(
+      modalDialog(
+        selectInput(
+          "scheme_db",
+          label = "",
+          choices = if(!is.null(Typing$last_scheme)) {
+            Typing$last_scheme
+          } else {DB$available},
+          selected = if(!is.null(Typing$last_scheme)) {
+            Typing$last_scheme
+          } else {if(!is.null(DB$scheme)) {input$select_cgmlst} else {DB$available[1]}}),
+        title = "Select a local database to load.",
+        footer = tagList(
+          actionButton("load", "Load", class = "btn btn-default")
+        )
+      )
+    )
+  })
+  
+  # Download Target Info (CSV Table)
+  observe({
+    input$download_cgMLST
+    
+    scheme_overview <- read_html(Scheme$link_scheme) %>%
+      html_table(header = FALSE) %>%
+      as.data.frame(stringsAsFactors = FALSE)
+    
+    last_scheme_change <- strptime(scheme_overview$X2[scheme_overview$X1 == "Last Change"],
+                                   format = "%B %d, %Y, %H:%M %p")
+    names(scheme_overview) <- NULL
+    
+    last_file_change <- format(
+      file.info(file.path(DB$database,
+                          ".downloaded_schemes",
+                          paste0(Scheme$folder_name, ".zip")))$mtime, "%Y-%m-%d %H:%M %p")
+    
+    output$cgmlst_scheme <- renderTable({scheme_overview})
+    output$scheme_update_info <- renderText({
+      req(last_file_change)
+      if (last_file_change < last_scheme_change) {
+        "(Newer scheme available \u274c)"
+      } else {
+        "(Scheme is up-to-date \u2705)"
+      }
+    })
+  })
+  
+  # _______________________ ####
+  
+  ## Visualization ----
+  
+  # Render placeholder image
+  
+  output$placeholder <- renderImage({
+    # Path to your PNG image with a transparent background
+    image_path <- paste0(getwd(), "/www/PhyloTrace.png")
+    
+    # Use HTML to display the image with the <img> tag
+    list(src = image_path,
+         height = 180)
+  }, deleteFile = FALSE)
+  
+  # Render tree plot fields
+  
+  output$nj_field <- renderUI(
+    fluidRow(
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
+    )
+  )
+  
+  output$mst_field <- renderUI(
+    fluidRow(
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
+    )
+  )
+  
+  output$upgma_field <- renderUI(
+    fluidRow(
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br(),
+      br(), br(), br(), br(), br(), br(), br(), br(), br(), br()
+    )
+  )
+  
+  ### Render Visualization Controls ----
+  
+  #### NJ and UPGMA controls ----
+  
+  # Control enable/disable of variable mapping inputs
+  observe({
+    shinyjs::toggleState(id = "nj_color_mapping", condition = isTRUE(input$nj_mapping_show))
+    shinyjs::toggleState(id = "nj_tiplab_scale", condition = isTRUE(input$nj_mapping_show))
+    shinyjs::toggleState(id = "upgma_color_mapping", condition = isTRUE(input$upgma_mapping_show))
+    shinyjs::toggleState(id = "upgma_tiplab_scale", condition = isTRUE(input$upgma_mapping_show))
+    
+    shinyjs::toggleState(id = "nj_tipcolor_mapping", condition = isTRUE(input$nj_tipcolor_mapping_show))
+    shinyjs::toggleState(id = "nj_tippoint_scale", condition = isTRUE(input$nj_tipcolor_mapping_show))
+    shinyjs::toggleState(id = "upgma_tipcolor_mapping", condition = isTRUE(input$upgma_tipcolor_mapping_show))
+    shinyjs::toggleState(id = "upgma_tippoint_scale", condition = isTRUE(input$upgma_tipcolor_mapping_show))
+    
+    shinyjs::toggleState(id = "nj_tipshape_mapping", condition = isTRUE(input$nj_tipshape_mapping_show))
+    shinyjs::toggleState(id = "upgma_tipshape_mapping", condition = isTRUE(input$upgma_tipshape_mapping_show))
+    
+    shinyjs::toggleState(id = "nj_fruit_variable", condition = isTRUE(input$nj_tiles_show_1))
+    shinyjs::toggleState(id = "upgma_fruit_variable", condition = isTRUE(input$upgma_tiles_show_1))
+    shinyjs::toggleState(id = "nj_fruit_variable_2", condition = isTRUE(input$nj_tiles_show_2))
+    shinyjs::toggleState(id = "upgma_fruit_variable_2", condition = isTRUE(input$upgma_tiles_show_2))
+    shinyjs::toggleState(id = "nj_fruit_variable_3", condition = isTRUE(input$nj_tiles_show_3))
+    shinyjs::toggleState(id = "upgma_fruit_variable_3", condition = isTRUE(input$upgma_tiles_show_3))
+    shinyjs::toggleState(id = "nj_fruit_variable_4", condition = isTRUE(input$nj_tiles_show_4))
+    shinyjs::toggleState(id = "upgma_fruit_variable_4", condition = isTRUE(input$upgma_tiles_show_4))
+    shinyjs::toggleState(id = "nj_fruit_variable_5", condition = isTRUE(input$nj_tiles_show_5))
+    shinyjs::toggleState(id = "upgma_fruit_variable_5", condition = isTRUE(input$upgma_tiles_show_5))
+    shinyjs::toggleState(id = "nj_tiles_scale_1", condition = isTRUE(input$nj_tiles_show_1))
+    shinyjs::toggleState(id = "upgma_tiles_scale_1", condition = isTRUE(input$upgma_tiles_show_1))
+    shinyjs::toggleState(id = "nj_tiles_scale_2", condition = isTRUE(input$nj_tiles_show_2))
+    shinyjs::toggleState(id = "upgma_tiles_scale_2", condition = isTRUE(input$upgma_tiles_show_2))
+    shinyjs::toggleState(id = "nj_tiles_scale_3", condition = isTRUE(input$nj_tiles_show_3))
+    shinyjs::toggleState(id = "upgma_tiles_scale_3", condition = isTRUE(input$upgma_tiles_show_3))
+    shinyjs::toggleState(id = "nj_tiles_scale_4", condition = isTRUE(input$nj_tiles_show_4))
+    shinyjs::toggleState(id = "upgma_tiles_scale_4", condition = isTRUE(input$upgma_tiles_show_4))
+    shinyjs::toggleState(id = "nj_tiles_scale_5", condition = isTRUE(input$nj_tiles_show_5))
+    shinyjs::toggleState(id = "upgma_tiles_scale_5", condition = isTRUE(input$upgma_tiles_show_5))
+    
+    shinyjs::toggleState(id = "nj_heatmap_sel", condition = isTRUE(input$nj_heatmap_show))
+    shinyjs::toggleState(id = "nj_heatmap_scale", condition = isTRUE(input$nj_heatmap_show))
+    shinyjs::toggleState(id = "upgma_heatmap_sel", condition = isTRUE(input$upgma_heatmap_show))
+    shinyjs::toggleState(id = "upgma_heatmap_scale", condition = isTRUE(input$upgma_heatmap_show))
+  })
+  
+  # Size scaling NJ
+  observe({
+    req(input$nj_ratio)
+    if(input$nj_ratio == "1.6") {
+      updateSliderInput(session, "nj_scale",
+                        step = 5, value = 800, min = 500, max = 1200)
+    } else if(input$nj_ratio == "1.77777777777778") {
+      updateSliderInput(session, "nj_scale",
+                        step = 9, value = 801, min = 504, max = 1197)
+    } else if(input$nj_ratio == "1.33333333333333"){
+      updateSliderInput(session, "nj_scale",
+                        step = 3, value = 801, min = 501, max = 1200)
+    }
+  })
+  
+  # Size scaling UPGMA
+  observe({
+    req(input$upgma_ratio)
+    if(input$upgma_ratio == "1.6") {
+      updateSliderInput(session, "upgma_scale",
+                        step = 5, value = 800, min = 500, max = 1200)
+    } else if(input$upgma_ratio == "1.77777777777778") {
+      updateSliderInput(session, "upgma_scale",
+                        step = 9, value = 801, min = 504, max = 1197)
+    } else if(input$upgma_ratio == "1.33333333333333"){
+      updateSliderInput(session, "upgma_scale",
+                        step = 3, value = 801, min = 501, max = 1200)
+    }
+  })
+  
+  # Size scaling MST
+  observe({
+    req(input$mst_ratio)
+    if(input$mst_ratio == "1.6") {
+      updateSliderInput(session, "mst_scale",
+                        step = 5, value = 800, min = 500, max = 1200)
+    } else if(input$mst_ratio == "1.77777777777778") {
+      updateSliderInput(session, "mst_scale",
+                        step = 9, value = 801, min = 504, max = 1197)
+    } else if(input$mst_ratio == "1.33333333333333"){
+      updateSliderInput(session, "mst_scale",
+                        step = 3, value = 801, min = 501, max = 1200)
+    }
+  })
+  
+  # Custom Labels
+  
+  # Add custom label
+  observeEvent(input$nj_add_new_label, {
+    
+    if(nchar(input$nj_new_label_name) > 0) {
+      if(!(input$nj_new_label_name %in% Vis$custom_label_nj)) {
+        Vis$custom_label_nj <- rbind(Vis$custom_label_nj, input$nj_new_label_name) 
+        if(!(nrow(Vis$custom_label_nj) == 1)) {
+          updateSelectInput(session, "nj_custom_label_sel", selected = input$nj_new_label_name)
+        }
+      } else {
+        show_toast(
+          title = "Label already exists",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+      }
+    } else {
+      show_toast(
+        title = "Min. 1 character",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    }
+  })
+  
+  observeEvent(input$upgma_add_new_label, {
+    
+    if(nchar(input$upgma_new_label_name) > 0) {
+      if(!(input$upgma_new_label_name %in% Vis$custom_label_upgma)) {
+        Vis$custom_label_upgma <- rbind(Vis$custom_label_upgma, input$upgma_new_label_name) 
+        if(!(nrow(Vis$custom_label_upgma) == 1)) {
+          updateSelectInput(session, "upgma_custom_label_sel", selected = input$upgma_new_label_name)
+        }
+      } else {
+        show_toast(
+          title = "Label already exists",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+      }
+    } else {
+      show_toast(
+        title = "Min. 1 character",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    }
+  })
+  
+  # Delete custom label
+  observeEvent(input$nj_del_label, {
+    
+    if(nrow(Vis$custom_label_nj) > 1) {
+      Vis$custom_label_nj <- Vis$custom_label_nj[-which(Vis$custom_label_nj[,1] == input$nj_custom_label_sel), , drop = FALSE]
+    } else if (nrow(Vis$custom_label_nj) == 1) {
+      Vis$nj_label_pos_x <- list()
+      Vis$nj_label_pos_y <- list()
+      Vis$nj_label_size <- list()
+      Vis$custom_label_nj <- data.frame()
+    }
+  })
+  
+  observeEvent(input$upgma_del_label, {
+    
+    if(nrow(Vis$custom_label_upgma) > 1) {
+      Vis$custom_label_upgma <- Vis$custom_label_upgma[-which(Vis$custom_label_upgma[,1] == input$upgma_custom_label_sel), , drop = FALSE]
+    } else if (nrow(Vis$custom_label_upgma) == 1) {
+      Vis$upgma_label_pos_x <- list()
+      Vis$upgma_label_pos_y <- list()
+      Vis$upgma_label_size <- list()
+      Vis$custom_label_upgma <- data.frame()
+    }
+  })
+  
+  # Select custom labels
+  output$nj_custom_label_select <- renderUI({
+    if(nrow(Vis$custom_label_nj) > 0) {
+      selectInput(
+        "nj_custom_label_sel",
+        "",
+        choices = Vis$custom_label_nj[,1]
+      )
+    }
+  })
+  
+  output$upgma_custom_label_select <- renderUI({
+    if(nrow(Vis$custom_label_upgma) > 0) {
+      selectInput(
+        "upgma_custom_label_sel",
+        "",
+        choices = Vis$custom_label_upgma[,1]
+      )
+    }
+  })
+  
+  # Select custom labels
+  output$nj_cust_label_save <- renderUI({
+    if(nrow(Vis$custom_label_nj) > 0) {
+      actionButton(
+        "nj_cust_label_save",
+        "Apply"
+      )
+    } else {
+      column(
+        width = 12,
+        br(), br(), br(), br(), br(), br(),
+        h5("test", style = "color: transparent; margin-bottom: 3px")
+      )
+    }
+  })
+  
+  output$upgma_cust_label_save <- renderUI({
+    if(nrow(Vis$custom_label_upgma) > 0) {
+      actionButton(
+        "upgma_cust_label_save",
+        "Apply"
+      )
+    } else {
+      column(
+        width = 12,
+        br(), br(), br(), br(), br(), br(),
+        h5("test", style = "color: transparent; margin-bottom: 3px")
+      )
+    }
+  })
+  
+  # Custom Label Size
+  output$nj_custom_labelsize <- renderUI({
+    if(length(Vis$custom_label_nj) > 0) {
+      if(!is.null(Vis$nj_label_size[[input$nj_custom_label_sel]])) {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_size"),
+                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
+                    min = 0, max = 10, step = 0.5, ticks = F,
+                    value = Vis$nj_label_size[[input$nj_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_size"),
+                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
+                    min = 0, max = 10, step = 0.5, ticks = F, value = 5,
+                    width = "150px")
+      }
+    } 
+  })
+  
+  output$upgma_custom_labelsize <- renderUI({
+    if(length(Vis$custom_label_upgma) > 0) {
+      if(!is.null(Vis$upgma_label_size[[input$upgma_custom_label_sel]])) {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_size"),
+                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
+                    min = 0, max = 10, step = 0.5, ticks = F,
+                    value = Vis$upgma_label_size[[input$upgma_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_size"),
+                    label = h5("Size", style = "color: white; margin-bottom: 0px;"),
+                    min = 0, max = 10, step = 0.5, ticks = F, value = 5,
+                    width = "150px")
+      }
+    } 
+  })
+  
+  # Render slider input based on selected label
+  output$nj_sliderInput_y <- renderUI({
+    if(length(Vis$custom_label_nj) > 0) {
+      if(!is.null(Vis$nj_label_pos_y[[input$nj_custom_label_sel]])) {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_y"),
+                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = 50, step = 1, ticks = F,
+                    value = Vis$nj_label_pos_y[[input$nj_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_y"),
+                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = sum(DB$data$Include), step = 1, ticks = F, 
+                    value = sum(DB$data$Include) / 2,
+                    width = "150px")
+      }
+    } 
+  })
+  
+  output$upgma_sliderInput_y <- renderUI({
+    if(length(Vis$custom_label_upgma) > 0) {
+      if(!is.null(Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]])) {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_y"),
+                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = 50, step = 1, ticks = F,
+                    value = Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_y"),
+                    label = h5("Vertical", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = sum(DB$data$Include), step = 1, ticks = F, 
+                    value = sum(DB$data$Include) / 2,
+                    width = "150px")
+      }
+    } 
+  })
+  
+  output$nj_sliderInput_x <- renderUI({
+    if(length(Vis$custom_label_nj) > 0) {
+      if(!is.null(Vis$nj_label_pos_x[[input$nj_custom_label_sel]])) {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_x"),
+                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = 50, step = 1, ticks = F,
+                    value = Vis$nj_label_pos_x[[input$nj_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("nj_slider_", input$nj_custom_label_sel, "_x"),
+                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = round(Vis$nj_max_x, 0), step = 1, ticks = F, 
+                    value = round(Vis$nj_max_x / 2, 0),
+                    width = "150px")
+      }
+    }
+  })
+  
+  output$upgma_sliderInput_x <- renderUI({
+    if(length(Vis$custom_label_upgma) > 0) {
+      if(!is.null(Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]])) {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_x"),
+                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = 50, step = 1, ticks = F,
+                    value = Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]],
+                    width = "150px")
+      } else {
+        sliderInput(inputId = paste0("upgma_slider_", input$upgma_custom_label_sel, "_x"),
+                    label = h5("Horizontal", style = "color: white; margin-bottom: 5px;"),
+                    min = 0, max = round(Vis$upgma_max_x, 0), step = 1, ticks = F, 
+                    value = round(Vis$upgma_max_x / 2, 0),
+                    width = "150px")
+      }
+    }
+  })
+  
+  # Apply custom label changes
+  observeEvent(input$nj_cust_label_save, {
+    
+    if(!is.null(Vis$nj_label_pos_y) &
+       !is.null(Vis$nj_label_pos_x) &
+       !is.null(Vis$nj_label_size) &
+       !is.null(input$nj_custom_label_sel)) {
+      Vis$nj_label_pos_y[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_y")]]
+      Vis$nj_label_pos_x[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_x")]]
+      Vis$nj_label_size[[input$nj_custom_label_sel]] <- input[[paste0("nj_slider_", input$nj_custom_label_sel, "_size")]]
+    }
+  })
+  
+  observeEvent(input$upgma_cust_label_save, {
+    
+    if(!is.null(Vis$upgma_label_pos_y) &
+       !is.null(Vis$upgma_label_pos_x) &
+       !is.null(Vis$upgma_label_size) &
+       !is.null(input$upgma_custom_label_sel)) {
+      Vis$upgma_label_pos_y[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_y")]]
+      Vis$upgma_label_pos_x[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_x")]]
+      Vis$upgma_label_size[[input$upgma_custom_label_sel]] <- input[[paste0("upgma_slider_", input$upgma_custom_label_sel, "_size")]]
+    }
+  })
+  
+  # Show delete custom label button if custam label added
+  output$nj_del_label <- renderUI({
+    if(nrow(Vis$custom_label_nj) > 0) {
+      actionButton(
+        "nj_del_label",
+        "",
+        icon = icon("minus")
+      )
+    } else {NULL}
+  })
+  
+  output$upgma_del_label <- renderUI({
+    if(nrow(Vis$custom_label_upgma) > 0) {
+      actionButton(
+        "upgma_del_label",
+        "",
+        icon = icon("minus")
+      )
+    } else {NULL}
+  })
+  
+  # Mapping value number information
+  output$nj_tiplab_mapping_info <- renderUI({
+    if(!is.null(input$nj_color_mapping) & (!is.null(Vis$meta_nj))) {
+      if(is.numeric(unlist(Vis$meta_nj[input$nj_color_mapping]))) {
+        if(input$nj_tiplab_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+          column(
+            width = 3,
+            fluidRow(
+              column(
+                width = 4,
+                h5("Midpoint", style = "color: white; margin-top: 22px;")
+              ),
+              column(
+                width = 8,
+                div(
+                  class = "divmid-sel1",
+                  selectInput(
+                    "nj_color_mapping_div_mid",
+                    label = "",
+                    choices = c("Zero", "Mean", "Median"),
+                    selected = "Mean"
+                  )
+                )
+              )
+            )
+          )
+        } else {
+          column(
+            width = 3,
+            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
+          ) 
+        }
+      } else {
+        if(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))) > 7) {
+          column(
+            width = 3,
+            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$upgma_tiplab_mapping_info <- renderUI({
+    if(!is.null(input$upgma_color_mapping) & (!is.null(Vis$meta_upgma))) {
+      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) {
+        if(input$upgma_tiplab_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+          column(
+            width = 3,
+            fluidRow(
+              column(
+                width = 4,
+                h5("Midpoint", style = "color: white; margin-top: 22px;")
+              ),
+              column(
+                width = 8,
+                div(
+                  class = "divmid-sel1",
+                  selectInput(
+                    "upgma_color_mapping_div_mid",
+                    label = "",
+                    choices = c("Zero", "Mean", "Median"),
+                    selected = "Mean"
+                  )
+                )
+              )
+            )
+          )
+        } else {
+          column(
+            width = 3,
+            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
+          ) 
+        }
+      } else {
+        if(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) > 7) {
+          column(
+            width = 3,
+            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$nj_tipcolor_mapping_info <- renderUI({
+    if(!is.null(input$nj_tipcolor_mapping) & (!is.null(Vis$meta_nj))) {
+      if(is.numeric(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) {
+        if(input$nj_tippoint_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+          column(
+            width = 3,
+            fluidRow(
+              column(
+                width = 4,
+                h5("Midpoint", style = "color: white; margin-top: 22px;")
+              ),
+              column(
+                width = 8,
+                div(
+                  class = "divmid-sel1",
+                  selectInput(
+                    "nj_tipcolor_mapping_div_mid",
+                    label = "",
+                    choices = c("Zero", "Mean", "Median"),
+                    selected = "Mean"
+                  )
+                )
+              )
+            )
+          )
+        } else {
+          column(
+            width = 3,
+            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+          ) 
+        }
+      } else {
+        if(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) > 7) {
+          column(
+            width = 3,
+            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$upgma_tipcolor_mapping_info <- renderUI({
+    if(!is.null(input$upgma_tipcolor_mapping) & (!is.null(Vis$meta_upgma))) {
+      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) {
+        if(input$upgma_tippoint_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+          column(
+            width = 3,
+            fluidRow(
+              column(
+                width = 4,
+                h5("Midpoint", style = "color: white; margin-top: 22px;")
+              ),
+              column(
+                width = 8,
+                div(
+                  class = "divmid-sel1",
+                  selectInput(
+                    "upgma_tipcolor_mapping_div_mid",
+                    label = "",
+                    choices = c("Zero", "Mean", "Median"),
+                    selected = "Mean"
+                  )
+                )
+              )
+            )
+          )
+        } else {
+          column(
+            width = 3,
+            h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+          ) 
+        }
+      } else {
+        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) > 7) {
+          column(
+            width = 3,
+            h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$nj_tipshape_mapping_info <- renderUI({
+    if(!is.null(input$nj_tipshape_mapping) & (!is.null(Vis$meta_nj))) {
+      if(is.numeric(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))) {
+        column(
+          width = 3,
+          h5("Mapping continous variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
+        )
+      } else {
+        if(length(unique(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))) > 6) {
+          column(
+            width = 3,
+            h5("Mapping > 6 variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_tipshape_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )    
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$upgma_tipshape_mapping_info <- renderUI({
+    if(!is.null(input$upgma_tipshape_mapping) & (!is.null(Vis$meta_upgma))) {
+      if(is.numeric(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))) {
+        column(
+          width = 3,
+          h5("Mapping continous variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
+        )
+      } else {
+        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))) > 6) {
+          column(
+            width = 3,
+            h5("Mapping > 6 variables to shape not possible", style = "color: #E18B00; font-style: italic; font-size: 12px; margin-top: 15px;  margin-left: 40px")        
+          )
+        } else {
+          column(
+            width = 3,
+            h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_tipshape_mapping]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+          )    
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$nj_fruit_mapping_info <- renderUI({
+    if(input$nj_tile_num == 1) {
+      if(!is.null(input$nj_fruit_variable) & (!is.null(Vis$meta_nj))) {
+        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable]))) {
+          if(input$nj_tiles_scale_1 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_tiles_mapping_div_mid_1",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$nj_tile_num == 2) {
+      if(!is.null(input$nj_fruit_variable_2) & (!is.null(Vis$meta_nj))) {
+        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) {
+          if(input$nj_tiles_scale_2 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_tiles_mapping_div_mid_2",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$nj_tile_num == 3) {
+      if(!is.null(input$nj_fruit_variable_3) & (!is.null(Vis$meta_nj))) {
+        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) {
+          if(input$nj_tiles_scale_3 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_tiles_mapping_div_mid_3",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$nj_tile_num == 4) {
+      if(!is.null(input$nj_fruit_variable_4) & (!is.null(Vis$meta_nj))) {
+        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) {
+          if(input$nj_tiles_scale_4 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_tiles_mapping_div_mid_4",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$nj_tile_num == 5) {
+      if(!is.null(input$nj_fruit_variable_5) & (!is.null(Vis$meta_nj))) {
+        if(is.numeric(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) {
+          if(input$nj_tiles_scale_5 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_tiles_mapping_div_mid_5",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  output$upgma_fruit_mapping_info <- renderUI({
+    if(input$upgma_tile_num == 1) {
+      if(!is.null(input$upgma_fruit_variable) & (!is.null(Vis$meta_upgma))) {
+        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) {
+          if(input$upgma_tiles_scale_1 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_tiles_mapping_div_mid_1",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$upgma_tile_num == 2) {
+      if(!is.null(input$upgma_fruit_variable_2) & (!is.null(Vis$meta_upgma))) {
+        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) {
+          if(input$upgma_tiles_scale_2 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_tiles_mapping_div_mid_2",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$upgma_tile_num == 3) {
+      if(!is.null(input$upgma_fruit_variable_3) & (!is.null(Vis$meta_upgma))) {
+        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) {
+          if(input$upgma_tiles_scale_3 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_tiles_mapping_div_mid_3",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$upgma_tile_num == 4) {
+      if(!is.null(input$upgma_fruit_variable_4) & (!is.null(Vis$meta_upgma))) {
+        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) {
+          if(input$upgma_tiles_scale_4 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_tiles_mapping_div_mid_4",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    } else if (input$upgma_tile_num == 5) {
+      if(!is.null(input$upgma_fruit_variable_5) & (!is.null(Vis$meta_upgma))) {
+        if(is.numeric(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) {
+          if(input$upgma_tiles_scale_5 %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_tiles_mapping_div_mid_5",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 20px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 (", length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))), ") categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5(paste0(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))), paste0(" categorical values")), style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  output$nj_heatmap_mapping_info <- renderUI({
+    if(!is.null(input$nj_heatmap_select) & (!is.null(Vis$meta_nj))) {
+      if (any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)) & 
+          any(!sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric))) {
+        column(
+          width = 3,
+          h5("Heatmap with categorical and continous values not possible", 
+             style = "color: #E18B00; font-size: 12px; font-style: italic; margin-top: 15px;  margin-left: 40px")
+        ) 
+      } else {
+        if(any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric))) {
+          if(input$nj_heatmap_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "nj_heatmap_div_mid",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_nj[input$nj_heatmap_select]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Categorical values", style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      }
+    } else {NULL}
+  })
+  
+  output$upgma_heatmap_mapping_info <- renderUI({
+    if(!is.null(input$upgma_heatmap_select) & (!is.null(Vis$meta_upgma))) {
+      if (any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)) & 
+          any(!sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric))) {
+        column(
+          width = 3,
+          h5("Heatmap with categorical and continous values not possible", 
+             style = "color: #E18B00; font-size: 12px; font-style: italic; margin-top: 15px;  margin-left: 40px")
+        ) 
+      } else {
+        if(any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric))) {
+          if(input$upgma_heatmap_scale %in% c('Spectral', 'RdYlGn', 'RdYlBu', 'RdGy', 'RdBu', 'PuOr', 'PRGn', 'PiYG', 'BrBG')) {
+            column(
+              width = 3,
+              fluidRow(
+                column(
+                  width = 4,
+                  h5("Midpoint", style = "color: white; margin-top: 22px;")
+                ),
+                column(
+                  width = 8,
+                  div(
+                    class = "divmid-sel1",
+                    selectInput(
+                      "upgma_heatmap_div_mid",
+                      label = "",
+                      choices = c("Zero", "Mean", "Median"),
+                      selected = "Mean"
+                    )
+                  )
+                )
+              )
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Continous values", style = "color: white; font-size: 14px; margin-top: 23px; margin-left: 40px")
+            ) 
+          }
+        } else {
+          if(length(unique(unlist(Vis$meta_upgma[input$upgma_heatmap_select]))) > 7) {
+            column(
+              width = 3,
+              h5(paste0("> 7 categorical values"), style = "color: #E18B00; font-size: 12px; margin-top: 23px;  margin-left: 40px")        
+            )
+          } else {
+            column(
+              width = 3,
+              h5("Categorical values", style = "color: white; font-size: 14px; margin-top: 20px;  margin-left: 40px")        
+            )
+          }
+        }
+      }
+    } else {NULL}
+  })
+  
+  # Tiles offset
+  output$nj_fruit_offset_circ <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "nj_fruit_offset_circ",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_fruit_offset_circ",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_fruit_offset_circ <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        offset <- 0.15
+        step <- 0.1
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.05
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "upgma_fruit_offset_circ",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_fruit_offset_circ",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.05,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$nj_fruit_offset_circ_2 <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "nj_fruit_offset_circ_2",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_fruit_offset_circ_2",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_fruit_offset_circ_2 <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "upgma_fruit_offset_circ_2",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_fruit_offset_circ_2",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$nj_fruit_offset_circ_3 <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "nj_fruit_offset_circ_3",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_fruit_offset_circ_3",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_fruit_offset_circ_3 <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "upgma_fruit_offset_circ_3",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_fruit_offset_circ_3",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$nj_fruit_offset_circ_4 <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "nj_fruit_offset_circ_4",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_fruit_offset_circ_4",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_fruit_offset_circ_4 <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "upgma_fruit_offset_circ_4",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_fruit_offset_circ_4",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$nj_fruit_offset_circ_5 <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "nj_fruit_offset_circ_5",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_fruit_offset_circ_5",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_fruit_offset_circ_5 <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        offset <- 0.15
+        step <- 0.03
+        min <- -0.6
+        max <- 0.6
+      } else {
+        offset <- 0.05
+        step <- 0.01
+        min <- -0.2
+        max <- 0.2
+      }
+      
+      sliderInput(
+        "upgma_fruit_offset_circ_5",
+        label = "",
+        min = min,
+        max = max,
+        step= step,
+        value = offset,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_fruit_offset_circ_5",
+        label = "",
+        min = -0.2,
+        max = 0.2,
+        step= 0.01,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  # For Layout change update tiles offset position
+  observeEvent(input$nj_layout, {
+    
+    if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+      offset <- 0.05
+      step <- 0.01
+      min <- -0.2
+      max <- 0.2
+    } else {
+      offset <- 0.15
+      step <- 0.03
+      min <- -0.6
+      max <- 0.6
+    }
+    
+    updateSliderInput(session, "nj_fruit_offset_circ", min = min, step = step, max = max)
+    updateSliderInput(session, "nj_fruit_offset_circ_2", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "nj_fruit_offset_circ_3", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "nj_fruit_offset_circ_4", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "nj_fruit_offset_circ_5", min = min, step = step, max = max, value = offset) 
+  })
+  
+  observeEvent(input$upgma_layout, {
+    
+    if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+      offset <- 0.05
+      step <- 0.01
+      min <- -0.2
+      max <- 0.2
+    } else {
+      offset <- 0.15
+      step <- 0.03
+      min <- -0.6
+      max <- 0.6
+    }
+    
+    updateSliderInput(session, "upgma_fruit_offset_circ", min = min, step = step, max = max)
+    updateSliderInput(session, "upgma_fruit_offset_circ_2", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "upgma_fruit_offset_circ_3", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "upgma_fruit_offset_circ_4", min = min, step = step, max = max, value = offset)
+    updateSliderInput(session, "upgma_fruit_offset_circ_5", min = min, step = step, max = max, value = offset) 
+  })
+  
+  # Heatmap width
+  output$nj_heatmap_width <- renderUI({
+    if(!is.null(input$nj_heatmap_select)) {
+      length_input <- length(input$nj_heatmap_select)
+      if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
+        if(length_input < 3) {
+          width <- 0.1
+        } else {
+          if (length_input >= 3 && length_input <= 50) {
+            width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+          } else {
+            width <- 1.5
+          }   
+        }
+      } else {
+        if(length_input < 3) {
+          width <- 0.3
+        } else if (length_input >= 3 && length_input <= 27) {
+          width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 3
+        }
+      }
+      
+      sliderInput(
+        "nj_heatmap_width",
+        label = "",
+        min = 0.05,
+        max = 1.5,
+        value = width,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_heatmap_width",
+        label = "",
+        min = 0.05,
+        max = 1.5,
+        value = 0.1,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_heatmap_width <- renderUI({
+    if(!is.null(input$upgma_heatmap_select)) {
+      length_input <- length(input$upgma_heatmap_select)
+      if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
+        if(length_input < 3) {
+          width <- 0.1
+        } else {
+          if (length_input >= 3 && length_input <= 50) {
+            width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+          } else {
+            width <- 1.5
+          }   
+        }
+      } else {
+        if(length_input < 3) {
+          width <- 0.3
+        } else if (length_input >= 3 && length_input <= 27) {
+          width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 3
+        }
+      }
+      
+      sliderInput(
+        "upgma_heatmap_width",
+        label = "",
+        min = 0.05,
+        max = 1.5,
+        value = width,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_heatmap_width",
+        label = "",
+        min = 0.05,
+        max = 1.5,
+        value = 0.1,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  # Update value if new variables added
+  observeEvent(input$nj_heatmap_select, {
+    
+    length_input <- length(input$nj_heatmap_select)
+    if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
+      if(length_input < 3) {
+        width <- 0.1
+      } else {
+        if (length_input >= 3 && length_input <= 50) {
+          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 1.5
+        }   
+      }
+    } else {
+      if(length_input < 3) {
+        width <- 0.3
+      } else if (length_input >= 3 && length_input <= 27) {
+        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+      } else {
+        width <- 3
+      }
+    }
+    updateSliderInput(session, "nj_heatmap_width", value = width)
+  })
+  
+  observeEvent(input$upgma_heatmap_select, {
+    
+    length_input <- length(input$upgma_heatmap_select)
+    if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
+      if(length_input < 3) {
+        width <- 0.1
+      } else {
+        if (length_input >= 3 && length_input <= 50) {
+          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 1.5
+        }   
+      }
+    } else {
+      if(length_input < 3) {
+        width <- 0.3
+      } else if (length_input >= 3 && length_input <= 27) {
+        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+      } else {
+        width <- 3
+      }
+    }
+    updateSliderInput(session, "upgma_heatmap_width", value = width)
+  })
+  
+  # Update value if layout changed
+  observeEvent(input$nj_layout, {
+    length_input <- length(input$nj_heatmap_select)
+    if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
+      if(length_input < 3) {
+        width <- 0.1
+      } else {
+        if (length_input >= 3 && length_input <= 50) {
+          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 1.5
+        }   
+      }
+    } else {
+      if(length_input < 3) {
+        width <- 0.3
+      } else if (length_input >= 3 && length_input <= 27) {
+        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+      } else {
+        width <- 3
+      }
+    }
+    updateSliderInput(session, "nj_heatmap_width", value = width)
+  })
+  
+  observeEvent(input$upgma_layout, {
+    length_input <- length(input$upgma_heatmap_select)
+    if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
+      if(length_input < 3) {
+        width <- 0.1
+      } else {
+        if (length_input >= 3 && length_input <= 50) {
+          width <- min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          width <- 1.5
+        }   
+      }
+    } else {
+      if(length_input < 3) {
+        width <- 0.3
+      } else if (length_input >= 3 && length_input <= 27) {
+        width <- min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+      } else {
+        width <- 3
+      }
+    }
+    updateSliderInput(session, "upgma_heatmap_width", value = width)
+  })
+  
+  # Heatmap column titles position
+  observeEvent(input$nj_layout, {
+    if(!(input$nj_layout == "inward" | input$nj_layout == "circular")) {
+      updateSliderInput(session, "nj_colnames_y", value = -1)
+    } else {
+      updateSliderInput(session, "nj_colnames_y", value = 0)
+    }
+  })
+  
+  observeEvent(input$upgma_layout, {
+    if(!(input$upgma_layout == "inward" | input$upgma_layout == "circular")) {
+      updateSliderInput(session, "upgma_colnames_y", value = -1)
+    } else {
+      updateSliderInput(session, "upgma_colnames_y", value = 0)
+    }
+  })
+  
+  output$nj_colnames_y <- renderUI({
+    if(!is.null(sum(DB$data$Include))) {
+      if(input$nj_layout == "inward" | input$nj_layout == "circular") {
+        min <- 0
+        val <- 0
+      } else {
+        val <- -1
+        if((sum(DB$data$Include) * -0.1) > -2) {
+          min <- -2
+        } else {
+          min <- round(sum(DB$data$Include) * -0.1, 0)
+        }
+      }
+      sliderInput(
+        "nj_colnames_y",
+        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
+        min = min,
+        max = sum(DB$data$Include),
+        value = val,
+        step = 1,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_colnames_y",
+        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
+        min = -10,
+        max = 10,
+        value = 0,
+        step = 1,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_colnames_y <- renderUI({
+    if(!is.null(sum(DB$data$Include))) {
+      if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
+        min <- 0
+        val <- 0
+      } else {
+        val <- -1
+        if((sum(DB$data$Include) * -0.1) > -2) {
+          min <- -2
+        } else {
+          min <- round(sum(DB$data$Include) * -0.1, 0)
+        }
+      }
+      sliderInput(
+        "upgma_colnames_y",
+        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
+        min = min,
+        max = sum(DB$data$Include),
+        value = val,
+        step = 1,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_colnames_y",
+        label = h5("Names Y-Position", style = "color:white; margin-bottom: 0px"),
+        min = -10,
+        max = 10,
+        value = 0,
+        step = 1,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  # Heatmap column titles angle
+  output$nj_colnames_angle <- renderUI({
+    if(!is.null(input$nj_layout)) {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        angle <- 90
+      } else {angle <- -90}
+      sliderInput(
+        "nj_colnames_angle",
+        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
+        min = -90,
+        max = 90,
+        value = angle,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_colnames_angle",
+        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
+        min = -90,
+        max = 90,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_colnames_angle <- renderUI({
+    if(!is.null(input$upgma_layout)) {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        angle <- 90
+      } else {angle <- -90}
+      sliderInput(
+        "upgma_colnames_angle",
+        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
+        min = -90,
+        max = 90,
+        value = angle,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_colnames_angle",
+        label = h5("Names Angle", style = "color:white; margin-bottom: 0px"),
+        min = -90,
+        max = 90,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  # Change heatmap column titles angle and label align when switching layout
+  observeEvent(input$nj_layout, {
+    if(input$nj_layout == "circular" | input$nj_layout == "inward"){
+      angle <- 90
+      val <- TRUE
+    } else {
+      angle <- -90
+      val <- FALSE
+    }
+    updateSwitchInput(session, "nj_align", value = val)
+    updateSliderInput(session, "nj_colnames_angle", value = angle)
+  })
+  
+  observeEvent(input$upgma_layout, {
+    if(input$upgma_layout == "circular" | input$upgma_layout == "inward"){
+      angle <- 90
+      val <- TRUE
+    } else {
+      angle <- -90
+      val <- FALSE
+    }
+    updateSwitchInput(session, "upgma_align", value = val)
+    updateSliderInput(session, "upgma_colnames_angle", value = angle)
+  })
+  
+  # Tile number selector update each other
+  observeEvent(input$nj_tile_num, {
+    updateSelectInput(session, "nj_tile_number", selected = input$nj_tile_num)
+  })
+  
+  observeEvent(input$nj_tile_number, {
+    updateSelectInput(session, "nj_tile_num", selected = input$nj_tile_number)
+  })
+  
+  observeEvent(input$upgma_tile_num, {
+    updateSelectInput(session, "upgma_tile_number", selected = input$upgma_tile_num)
+  })
+  
+  observeEvent(input$upgma_tile_number, {
+    updateSelectInput(session, "upgma_tile_num", selected = input$upgma_tile_number)
+  })
+  
+  # Clade coloring
+  output$nj_clade_scale <- renderUI({
+    if(length(input$nj_parentnode) <= 1) {
+      fluidRow(
+        column(
+          width = 5,
+          h5("Color", style = "color:white; position: relative; right: -15px; margin-top: 30px")
+        ),
+        column(
+          width = 7,
+          align = "center",
+          colorPickr(
+            inputId = "nj_clade_scale",
+            selected = "#D0F221",
+            label = "",
+            update = "changestop",
+            interaction = list(clear = FALSE,
+                               save = FALSE),
+            position = "right-start",
+            width = "100%"
+          )
+        )
+      )
+    } else {
+      fluidRow(
+        column(
+          width = 5,
+          h5("Scale", style = "color:white; position: relative; right: -15px; margin-top: 30px")
+        ),
+        column(
+          width = 7,
+          align = "center",
+          div(
+            class = "sel-clade-scale",
+            selectInput(
+              "nj_clade_scale",
+              "",
+              choices = list(
+                Qualitative = list(
+                  "Set1",
+                  "Set2",
+                  "Set3",
+                  "Pastel1",
+                  "Pastel2",
+                  "Paired",
+                  "Dark2",
+                  "Accent"
+                ),
+                Sequential = list(
+                  "YlOrRd",
+                  "YlOrBr",
+                  "YlGnBu",
+                  "YlGn",
+                  "Reds",
+                  "RdPu",
+                  "Purples",
+                  "PuRd",
+                  "PuBuGn",
+                  "PuBu",
+                  "OrRd",
+                  "Oranges",
+                  "Greys",
+                  "Greens",
+                  "GnBu",
+                  "BuPu",
+                  "BuGn",
+                  "Blues"
+                )
+              )
+            )
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_clade_scale <- renderUI({
+    if(length(input$upgma_parentnode) <= 1) {
+      fluidRow(
+        column(
+          width = 5,
+          h5("Color", style = "color:white; position: relative; right: -15px; margin-top: 30px")
+        ),
+        column(
+          width = 7,
+          align = "center",
+          colorPickr(
+            inputId = "upgma_clade_scale",
+            selected = "#D0F221",
+            label = "",
+            update = "changestop",
+            interaction = list(clear = FALSE,
+                               save = FALSE),
+            position = "right-start",
+            width = "100%"
+          )
+        )
+      )
+    } else {
+      fluidRow(
+        column(
+          width = 5,
+          h5("Scale", style = "color:white; position: relative; right: -15px; margin-top: 30px")
+        ),
+        column(
+          width = 7,
+          align = "center",
+          div(
+            class = "sel-clade-scale",
+            selectInput(
+              "upgma_clade_scale",
+              "",
+              choices = list(
+                Qualitative = list(
+                  "Set1",
+                  "Set2",
+                  "Set3",
+                  "Pastel1",
+                  "Pastel2",
+                  "Paired",
+                  "Dark2",
+                  "Accent"
+                ),
+                Sequential = list(
+                  "YlOrRd",
+                  "YlOrBr",
+                  "YlGnBu",
+                  "YlGn",
+                  "Reds",
+                  "RdPu",
+                  "Purples",
+                  "PuRd",
+                  "PuBuGn",
+                  "PuBu",
+                  "OrRd",
+                  "Oranges",
+                  "Greys",
+                  "Greens",
+                  "GnBu",
+                  "BuPu",
+                  "BuGn",
+                  "Blues"
+                )
+              )
+            )
+          )
+        )
+      )
+    }
+  })
+  
+  # Heatmap variable color scale
+  output$nj_heatmap_scale <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_heatmap_select])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_heatmap_scale",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_heatmap_select]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_heatmap_scale",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_heatmap_scale",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Paired"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_heatmap_scale <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_heatmap_select])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_heatmap_scale",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_heatmap_select]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_heatmap_scale",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_heatmap_scale",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Paired"
+          )
+        )
+      }
+    }
+  })
+  
+  # Tiles variable color scale
+  output$nj_tiles_scale_1 <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiles_scale_1",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_1",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_1",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiles_scale_1 <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiles_scale_1",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_1",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_1",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$nj_tiles_scale_2 <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_2])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiles_scale_2",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_2]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_2",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_2",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiles_scale_2 <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiles_scale_2",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_2",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_2",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$nj_tiles_scale_3 <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_3])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiles_scale_3",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_3]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_3",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_3",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiles_scale_3 <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiles_scale_3",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_3",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_3",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$nj_tiles_scale_4 <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_4])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiles_scale_4",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_4]))) > 7) {
+        shinyjs::disabled(selectInput(
+          "nj_tiles_scale_4",
+          "",
+          choices = list(
+            Gradient = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            )
+          ),
+          selected = "turbo"
+        ))
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_4",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiles_scale_4 <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiles_scale_4",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_4]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_4",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_4",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$nj_tiles_scale_5 <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_5])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiles_scale_5",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_fruit_variable_5]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_5",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiles_scale_5",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiles_scale_5 <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiles_scale_5",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_5",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiles_scale_5",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            ),
+            selected = "Accent"
+          )
+        )
+      }
+    }
+  })
+  
+  # Tip Labels Variable Color Scale
+  output$nj_tiplab_scale <- renderUI({
+    if(class(unlist(Vis$meta_nj[input$nj_color_mapping])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tiplab_scale",
+          "",
+          selectize = FALSE,
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_nj[input$nj_color_mapping]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiplab_scale",
+            "",
+            selectize = FALSE,
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tiplab_scale",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            )
+          )
+        )
+      }
+    }
+  })
+  
+  output$upgma_tiplab_scale <- renderUI({
+    if(class(unlist(Vis$meta_upgma[input$upgma_color_mapping])) == "numeric") {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tiplab_scale",
+          "",
+          choices = list(
+            Continous = list(
+              "Magma" = "magma",
+              "Inferno" = "inferno",
+              "Plasma" = "plasma",
+              "Viridis" = "viridis",
+              "Cividis" = "cividis",
+              "Rocket" = "rocket",
+              "Mako" = "mako",
+              "Turbo" = "turbo"
+            ),
+            Diverging = list(
+              "Spectral",
+              "RdYlGn",
+              "RdYlBu",
+              "RdGy",
+              "RdBu",
+              "PuOr",
+              "PRGn",
+              "PiYG",
+              "BrBG"
+            )
+          )
+        )
+      )
+    } else {
+      if(length(unique(unlist(Vis$meta_upgma[input$upgma_color_mapping]))) > 7) {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiplab_scale",
+            "",
+            choices = list(
+              Gradient = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              )
+            ),
+            selected = "turbo"
+          )
+        )
+      } else {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tiplab_scale",
+            "",
+            choices = list(
+              Qualitative = list(
+                "Set1",
+                "Set2",
+                "Set3",
+                "Pastel1",
+                "Pastel2",
+                "Paired",
+                "Dark2",
+                "Accent"
+              ),
+              Sequential = list(
+                "YlOrRd",
+                "YlOrBr",
+                "YlGnBu",
+                "YlGn",
+                "Reds",
+                "RdPu",
+                "Purples",
+                "PuRd",
+                "PuBuGn",
+                "PuBu",
+                "OrRd",
+                "Oranges",
+                "Greys",
+                "Greens",
+                "GnBu",
+                "BuPu",
+                "BuGn",
+                "Blues"
+              )
+            )
+          )
+        )
+      }
+    }
+  })
+  
+  # Tippoint Scale
+  output$nj_tippoint_scale <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      if(class(unlist(Vis$meta_nj[input$nj_tipcolor_mapping])) == "numeric") {
+        shinyjs::disabled(
+          selectInput(
+            "nj_tippoint_scale",
+            "",
+            choices = list(
+              Continous = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              ),
+              Diverging = list(
+                "Spectral",
+                "RdYlGn",
+                "RdYlBu",
+                "RdGy",
+                "RdBu",
+                "PuOr",
+                "PRGn",
+                "PiYG",
+                "BrBG"
+              )
+            )
+          )
+        )
+      } else {
+        if(length(unique(unlist(Vis$meta_nj[input$nj_tipcolor_mapping]))) > 7) {
+          shinyjs::disabled(
+            selectInput(
+              "nj_tippoint_scale",
+              "",
+              choices = list(
+                Gradient = list(
+                  "Magma" = "magma",
+                  "Inferno" = "inferno",
+                  "Plasma" = "plasma",
+                  "Viridis" = "viridis",
+                  "Cividis" = "cividis",
+                  "Rocket" = "rocket",
+                  "Mako" = "mako",
+                  "Turbo" = "turbo"
+                )
+              ),
+              selected = "turbo"
+            )
+          )
+        } else {
+          shinyjs::disabled(
+            selectInput(
+              "nj_tippoint_scale",
+              "",
+              choices = list(
+                Qualitative = list(
+                  "Set1",
+                  "Set2",
+                  "Set3",
+                  "Pastel1",
+                  "Pastel2",
+                  "Paired",
+                  "Dark2",
+                  "Accent"
+                ),
+                Sequential = list(
+                  "YlOrRd",
+                  "YlOrBr",
+                  "YlGnBu",
+                  "YlGn",
+                  "Reds",
+                  "RdPu",
+                  "Purples",
+                  "PuRd",
+                  "PuBuGn",
+                  "PuBu",
+                  "OrRd",
+                  "Oranges",
+                  "Greys",
+                  "Greens",
+                  "GnBu",
+                  "BuPu",
+                  "BuGn",
+                  "Blues"
+                )
+              ),
+              selected = "Set2"
+            )
+          )
+        }
+      }
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tippoint_scale",
+          "",
+          choices = list(
+            Qualitative = list(
+              "Set1",
+              "Set2",
+              "Set3",
+              "Pastel1",
+              "Pastel2",
+              "Paired",
+              "Dark2",
+              "Accent"
+            ),
+            Sequential = list(
+              "YlOrRd",
+              "YlOrBr",
+              "YlGnBu",
+              "YlGn",
+              "Reds",
+              "RdPu",
+              "Purples",
+              "PuRd",
+              "PuBuGn",
+              "PuBu",
+              "OrRd",
+              "Oranges",
+              "Greys",
+              "Greens",
+              "GnBu",
+              "BuPu",
+              "BuGn",
+              "Blues"
+            )
+          ),
+          selected = "Set2"
+        )
+      )
+    }
+  })
+  
+  output$upgma_tippoint_scale <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      if(class(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping])) == "numeric") {
+        shinyjs::disabled(
+          selectInput(
+            "upgma_tippoint_scale",
+            "",
+            choices = list(
+              Continous = list(
+                "Magma" = "magma",
+                "Inferno" = "inferno",
+                "Plasma" = "plasma",
+                "Viridis" = "viridis",
+                "Cividis" = "cividis",
+                "Rocket" = "rocket",
+                "Mako" = "mako",
+                "Turbo" = "turbo"
+              ),
+              Diverging = list(
+                "Spectral",
+                "RdYlGn",
+                "RdYlBu",
+                "RdGy",
+                "RdBu",
+                "PuOr",
+                "PRGn",
+                "PiYG",
+                "BrBG"
+              )
+            ),
+            selected = c("Viridis" = "viridis")
+          )
+        )
+      } else {
+        if(length(unique(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping]))) > 7) {
+          shinyjs::disabled(
+            selectInput(
+              "upgma_tippoint_scale",
+              "",
+              choices = list(
+                Gradient = list(
+                  "Magma" = "magma",
+                  "Inferno" = "inferno",
+                  "Plasma" = "plasma",
+                  "Viridis" = "viridis",
+                  "Cividis" = "cividis",
+                  "Rocket" = "rocket",
+                  "Mako" = "mako",
+                  "Turbo" = "turbo"
+                )
+              ),
+              selected = "turbo"
+            )
+          )
+        } else {
+          shinyjs::disabled(
+            selectInput(
+              "upgma_tippoint_scale",
+              "",
+              choices = list(
+                Qualitative = list(
+                  "Set1",
+                  "Set2",
+                  "Set3",
+                  "Pastel1",
+                  "Pastel2",
+                  "Paired",
+                  "Dark2",
+                  "Accent"
+                ),
+                Sequential = list(
+                  "YlOrRd",
+                  "YlOrBr",
+                  "YlGnBu",
+                  "YlGn",
+                  "Reds",
+                  "RdPu",
+                  "Purples",
+                  "PuRd",
+                  "PuBuGn",
+                  "PuBu",
+                  "OrRd",
+                  "Oranges",
+                  "Greys",
+                  "Greens",
+                  "GnBu",
+                  "BuPu",
+                  "BuGn",
+                  "Blues"
+                )
+              ),
+              selected = "Set2"
+            )
+          )
+        }
+      }
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tippoint_scale",
+          "",
+          choices = list(
+            Qualitative = list(
+              "Set1",
+              "Set2",
+              "Set3",
+              "Pastel1",
+              "Pastel2",
+              "Paired",
+              "Dark2",
+              "Accent"
+            ),
+            Sequential = list(
+              "YlOrRd",
+              "YlOrBr",
+              "YlGnBu",
+              "YlGn",
+              "Reds",
+              "RdPu",
+              "Purples",
+              "PuRd",
+              "PuBuGn",
+              "PuBu",
+              "OrRd",
+              "Oranges",
+              "Greys",
+              "Greens",
+              "GnBu",
+              "BuPu",
+              "BuGn",
+              "Blues"
+            )
+          ),
+          selected = "Set2"
+        )
+      )
+    }
+  })
+  
+  # Clade Highlights
+  output$nj_parentnode <- renderUI({
+    if(!is.null(Vis$nj_parentnodes)) {
+      pickerInput(
+        "nj_parentnode",
+        label = "",
+        choices = sort(unique(as.numeric(Vis$nj_parentnodes))),
+        multiple = TRUE,
+        options = list(
+          `live-search` = TRUE,
+          size = 10,
+          style = "background-color: white; border-radius: 5px;"
+        ),
+        width = "99%"
+      )
+    } else {
+      pickerInput(
+        "nj_parentnode",
+        label = "",
+        choices = c(),
+        multiple = TRUE,
+        options = list(
+          `live-search` = TRUE,
+          size = 10,
+          style = "background-color: white; border-radius: 5px;"
+        ),
+        width = "99%"
+      )
+    }
+  })
+  
+  output$upgma_parentnode <- renderUI({
+    if(!is.null(Vis$upgma_parentnodes)) {
+      pickerInput(
+        "upgma_parentnode",
+        label = "",
+        choices = sort(unique(as.numeric(Vis$upgma_parentnodes))),
+        multiple = TRUE,
+        options = list(
+          `live-search` = TRUE,
+          size = 10,
+          style = "background-color: white; border-radius: 5px;"
+        ),
+        width = "99%"
+      )
+    } else {
+      pickerInput(
+        "upgma_parentnode",
+        label = "",
+        choices = c(),
+        multiple = TRUE,
+        options = list(
+          `live-search` = TRUE,
+          size = 10,
+          style = "background-color: white; border-radius: 5px;"
+        ),
+        width = "99%"
+      )
+    }
+  })
+  
+  # Branch label size
+  output$nj_branch_size <- renderUI(
+    numericInput(
+      "nj_branch_size",
+      label = h5("Size", style = "color:white; margin-bottom: 0px"),
+      min = 2,
+      max = 10,
+      step = 0.5,
+      value = Vis$branch_size_nj,
+      width = "80px"
+    )
+  )
+  
+  output$upgma_branch_size <- renderUI(
+    numericInput(
+      "upgma_branch_size",
+      label = h5("Size", style = "color:white; margin-bottom: 0px"),
+      min = 2,
+      max = 10,
+      step = 0.5,
+      value = Vis$branch_size_upgma,
+      width = "80px"
+    )
+  )
+  
+  # Tippanel size
+  output$nj_tiplab_padding <- renderUI(
+    if(!is.null(Vis$tiplab_padding_nj)) {
+      sliderInput(
+        inputId = "nj_tiplab_padding",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 0.05,
+        max = 1,
+        value = Vis$tiplab_padding_nj,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "nj_tiplab_padding",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 0.05,
+        max = 1,
+        value = 0.2,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  output$upgma_tiplab_padding <- renderUI(
+    if(!is.null(Vis$tiplab_padding_upgma)) {
+      sliderInput(
+        inputId = "upgma_tiplab_padding",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 0.05,
+        max = 1,
+        value = Vis$tiplab_padding_upgma,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "upgma_tiplab_padding",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 0.05,
+        max = 1,
+        value = 0.2,
+        step = 0.05,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  # Nodepoint size
+  output$nj_nodepoint_size <- renderUI(
+    if(!is.null(Vis$nodepointsize_nj)) {
+      sliderInput(
+        inputId = "nj_nodepoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        value = Vis$nodepointsize_nj,
+        step = 0.5,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "nj_nodepoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        value = 2.5,
+        step = 0.5,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  output$upgma_nodepoint_size <- renderUI(
+    if(!is.null(Vis$nodepointsize_upgma)) {
+      sliderInput(
+        inputId = "upgma_nodepoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        value = Vis$nodepointsize_upgma,
+        step = 0.5,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "upgma_nodepoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        value = 2.5,
+        step = 0.5,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  # Tippoint size 
+  output$nj_tippoint_size <- renderUI(
+    if(!is.null(Vis$tippointsize_nj)) {
+      sliderInput(
+        inputId = "nj_tippoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        step = 0.5,
+        value = Vis$tippointsize_nj,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "nj_tippoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        step = 0.5,
+        value = 4,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  output$upgma_tippoint_size <- renderUI(
+    if(!is.null(Vis$tippointsize_upgma)) {
+      sliderInput(
+        inputId = "upgma_tippoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        step = 0.5,
+        value = Vis$tippointsize_upgma,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        inputId = "upgma_tippoint_size",
+        label = h5("Size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 20,
+        step = 0.5,
+        value = 4,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  )
+  
+  # Tiplabel size
+  output$nj_tiplab_size <- renderUI(
+    if(!is.null(Vis$labelsize_nj)) {
+      numericInput(
+        "nj_tiplab_size",
+        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        step = 0.5,
+        value = Vis$labelsize_nj,
+        width = "80px"
+      )
+    } else {
+      numericInput(
+        "nj_tiplab_size",
+        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        step = 0.5,
+        value = 4,
+        width = "80px"
+      )
+    }
+  )
+  
+  output$upgma_tiplab_size <- renderUI(
+    if(!is.null(Vis$labelsize_upgma)) {
+      numericInput(
+        "upgma_tiplab_size",
+        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        step = 0.5,
+        value = Vis$labelsize_upgma,
+        width = "80px"
+      )
+    } else {
+      numericInput(
+        "upgma_tiplab_size",
+        label = h5("Label size", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        step = 0.5,
+        value = 4,
+        width = "80px"
+      )
+    }
+  )
+  
+  # Rootedge length 
+  output$nj_rootedge_length <- renderUI({
+    if(!is.null(Vis$nj_max_x)) {
+      if(round(ceiling(Vis$nj_max_x) * 0.02, 0) < 1) {
+        min <- 1
+      } else {
+        min <- round(ceiling(Vis$nj_max_x) * 0.02, 0)  
+      }
+      max <- round(ceiling(Vis$nj_max_x) * 0.2, 0)
+      sliderInput(
+        "nj_rootedge_length",
+        label = h5("Rootedge Length", style = "color:white; margin-bottom: 0px"),
+        min = min,
+        max = max,
+        value = round(ceiling(Vis$nj_max_x) * 0.05, 0),
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_rootedge_length",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        value = 2,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_rootedge_length <- renderUI({
+    if(!is.null(Vis$upgma_max_x)) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.02, 0) < 1) {
+        min <- 1
+      } else {
+        min <- round(ceiling(Vis$upgma_max_x) * 0.02, 0)  
+      }
+      max <- round(ceiling(Vis$upgma_max_x) * 0.2, 0)
+      sliderInput(
+        "upgma_rootedge_length",
+        label = h5("Rootedge Length", style = "color:white; margin-bottom: 0px"),
+        min = min,
+        max = max,
+        value = round(ceiling(Vis$upgma_max_x) * 0.05, 0),
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_rootedge_length",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        value = 2,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  # Treescale 
+  output$nj_treescale_width <- renderUI({
+    if(!is.null(Vis$nj_max_x)) {
+      numericInput(
+        "nj_treescale_width",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        value = round(ceiling(Vis$nj_max_x) * 0.1, 0),
+        min = 1,
+        max = round(floor(Vis$nj_max_x) * 0.5, 0),
+        step = 1,
+        width = "80px"
+      )
+    } else {
+      numericInput(
+        "nj_treescale_width",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        value = 2,
+        min = 1,
+        max = 10,
+        step = 1,
+        width = "80px"
+      )
+    }
+  })
+  
+  output$upgma_treescale_width <- renderUI({
+    if(!is.null(Vis$upgma_max_x)) {
+      numericInput(
+        "upgma_treescale_width",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        value = round(ceiling(Vis$upgma_max_x) * 0.1, 0),
+        min = 1,
+        max = round(floor(Vis$upgma_max_x) * 0.5, 0),
+        step = 1,
+        width = "80px"
+      )
+    } else {
+      numericInput(
+        "upgma_treescale_width",
+        label = h5("Length", style = "color:white; margin-bottom: 0px"),
+        value = 2,
+        min = 1,
+        max = 10,
+        step = 1,
+        width = "80px"
+      )
+    }
+  })
+  
+  output$nj_treescale_x <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(ceiling(Vis$nj_min_x) < 1) {
+        floor <- 1
+      } else {
+        floor <- ceiling(Vis$nj_min_x)
+      }
+      sliderInput(
+        "nj_treescale_x",
+        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+        min = floor,
+        max = round(floor(Vis$nj_max_x)),
+        value = round(ceiling(Vis$nj_max_x) * 0.2, 0),
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_treescale_x",
+        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        value = 2,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_treescale_x <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(ceiling(Vis$upgma_min_x) < 1) {
+        floor <- 1
+      } else {
+        floor <- ceiling(Vis$upgma_min_x)
+      }
+      sliderInput(
+        "upgma_treescale_x",
+        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+        min = floor,
+        max = round(floor(Vis$upgma_max_x)),
+        value = round(ceiling(Vis$upgma_max_x) * 0.2, 0),
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_treescale_x",
+        label = h5("X Position", style = "color:white; margin-bottom: 0px"),
+        min = 1,
+        max = 10,
+        value = 2,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$nj_treescale_y <- renderUI({
+    if(!is.null(sum(DB$data$Include))) {
+      sliderInput(
+        "nj_treescale_y",
+        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+        min = 0,
+        max = sum(DB$data$Include),
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_treescale_y",
+        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+        min = 0,
+        max = 10,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_treescale_y <- renderUI({
+    if(!is.null(sum(DB$data$Include))) {
+      sliderInput(
+        "upgma_treescale_y",
+        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+        min = 0,
+        max = sum(DB$data$Include),
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_treescale_y",
+        label = h5("Y Position", style = "color:white; margin-bottom: 0px"),
+        min = 0,
+        max = 10,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  ### Heatmap 
+  # Heatmap picker
+  output$nj_heatmap_sel <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      meta <- select(Vis$meta_nj, -c(taxa, Index, `Assembly ID`, `Assembly Name`,
+                                     Scheme, `Typing Date`, Successes, Errors))
+      
+      # Identify numeric columns
+      numeric_columns <- sapply(meta, is.numeric)
+      
+      numeric_column_names <- names(meta[numeric_columns])
+      
+      non_numeric_column_names <- names(meta)[!numeric_columns]
+      
+      choices <- list()
+      
+      # Add Continuous list only if there are numeric columns
+      if (length(numeric_column_names) > 0) {
+        choices$Continuous <- as.list(setNames(numeric_column_names, numeric_column_names))
+      }
+      
+      # Add Diverging list
+      choices$Categorical <- as.list(setNames(non_numeric_column_names, non_numeric_column_names))
+      
+      div(
+        class = "heatmap-picker",
+        shinyjs::disabled(
+          pickerInput(
+            inputId = "nj_heatmap_select",
+            label = "",
+            width = "100%",
+            choices = if(ncol(Vis$meta_nj) == 11) {
+              c(
+                `Isolation Date` = "Isolation Date",
+                Host = "Host",
+                Country = "Country",
+                City = "City"
+              )
+            } else {choices},
+            options = list(
+              `dropdown-align-center` = TRUE,
+              size = 10,
+              style = "background-color: white; border-radius: 5px;"
+            ),
+            multiple = TRUE
+          )
+        )
+      )
+    } else {
+      div(
+        class = "heatmap-picker",
+        shinyjs::disabled(
+          pickerInput(
+            inputId = "nj_heatmap_select",
+            label = "",
+            width = "100%",
+            choices = c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            ),
+            multiple = TRUE
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_heatmap_sel <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      meta <- select(Vis$meta_upgma, -c(taxa, Index, `Assembly ID`, `Assembly Name`,
+                                        Scheme, `Typing Date`, Successes, Errors))
+      
+      # Identify numeric columns
+      numeric_columns <- sapply(meta, is.numeric)
+      
+      numeric_column_names <- names(meta[numeric_columns])
+      
+      non_numeric_column_names <- names(meta)[!numeric_columns]
+      
+      choices <- list()
+      
+      # Add Continuous list only if there are numeric columns
+      if (length(numeric_column_names) > 0) {
+        choices$Continuous <- as.list(setNames(numeric_column_names, numeric_column_names))
+      }
+      
+      # Add Diverging list
+      choices$Categorical <- as.list(setNames(non_numeric_column_names, non_numeric_column_names))
+      
+      div(
+        class = "heatmap-picker",
+        shinyjs::disabled(
+          pickerInput(
+            inputId = "upgma_heatmap_select",
+            label = "",
+            width = "100%",
+            choices = if(ncol(Vis$meta_upgma) == 11) {
+              c(
+                `Isolation Date` = "Isolation Date",
+                Host = "Host",
+                Country = "Country",
+                City = "City"
+              )
+            } else {choices},
+            options = list(
+              `dropdown-align-center` = TRUE,
+              size = 10,
+              style = "background-color: white; border-radius: 5px;"
+            ),
+            multiple = TRUE
+          )
+        )
+      )
+    } else {
+      div(
+        class = "heatmap-picker",
+        shinyjs::disabled(
+          pickerInput(
+            inputId = "upgma_heatmap_select",
+            label = "",
+            width = "100%",
+            choices = c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            ),
+            multiple = TRUE
+          )
+        )
+      )
+    }
+  })
+  
+  # Heatmap offset
+  output$nj_heatmap_offset <- renderUI({
+    if(!is.null(Vis$nj_max_x)) {
+      sliderInput(
+        "nj_heatmap_offset",
+        label = "",
+        min = 0,
+        max = round(ceiling(Vis$nj_max_x)*1.5, 0),
+        step = 1,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "nj_heatmap_offset",
+        label = "",
+        min = 0,
+        max = 10,
+        step = 1,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  output$upgma_heatmap_offset <- renderUI({
+    if(!is.null(Vis$upgma_max_x)) {
+      sliderInput(
+        "upgma_heatmap_offset",
+        label = "",
+        min = 0,
+        max = round(ceiling(Vis$upgma_max_x)*1.5, 0),
+        step = 1,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      sliderInput(
+        "upgma_heatmap_offset",
+        label = "",
+        min = 0,
+        max = 10,
+        step = 1,
+        value = 0,
+        width = "150px",
+        ticks = FALSE
+      )
+    }
+  })
+  
+  ### Tiling 
+  # Geom Fruit select Variable
+  output$nj_fruit_variable <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$nj_fruit_variable2 <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_2",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_2",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$nj_fruit_variable3 <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_3",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_3",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$nj_fruit_variable4 <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_4",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_4",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$nj_fruit_variable5 <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_5",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_fruit_variable_5",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_fruit_variable <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_fruit_variable2 <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_2",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_2",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_fruit_variable3 <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(selectInput(
+        "upgma_fruit_variable_3",
+        "",
+        choices = if(ncol(Vis$meta_upgma) == 11) {
+          c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        } else {
+          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+        },
+        selected = c(`Isolation Date` = "Isolation Date"),
+        width = "100%"
+      ))
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_3",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_fruit_variable4 <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_4",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_4",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  output$upgma_fruit_variable5 <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_5",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(`Isolation Date` = "Isolation Date"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_fruit_variable_5",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        )
+      )
+    }
+  })
+  
+  # Geom Fruit Width
+  output$nj_fruit_width <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "nj_fruit_width_circ",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        sliderInput(
+          "nj_fruit_width_circ",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "nj_fruit_width_circ",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$nj_fruit_width2 <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "nj_fruit_width_circ_2",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        sliderInput(
+          "nj_fruit_width_circ_2",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "nj_fruit_width_circ_2",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$nj_fruit_width3 <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "nj_fruit_width_circ_3",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        sliderInput(
+          "nj_fruit_width_circ_3",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "nj_fruit_width_circ_3",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$nj_fruit_width4 <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "nj_fruit_width_circ_4",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        sliderInput(
+          "nj_fruit_width_circ_4",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "nj_fruit_width_circ_4",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$nj_fruit_width5 <- renderUI({
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "nj_fruit_width_circ_5",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$nj_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+        sliderInput(
+          "nj_fruit_width_circ_5",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "nj_fruit_width_circ_5",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$upgma_fruit_width <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "upgma_fruit_width_circ",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        sliderInput(
+          "upgma_fruit_width_circ",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "upgma_fruit_width_circ",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$upgma_fruit_width2 <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "upgma_fruit_width_circ_2",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        sliderInput(
+          "upgma_fruit_width_circ_2",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "upgma_fruit_width_circ_2",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$upgma_fruit_width3 <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "upgma_fruit_width_circ_3",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        sliderInput(
+          "upgma_fruit_width_circ_3",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "upgma_fruit_width_circ_3",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$upgma_fruit_width4 <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "upgma_fruit_width_circ_4",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        sliderInput(
+          "upgma_fruit_width_circ_4",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "upgma_fruit_width_circ_4",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  output$upgma_fruit_width5 <- renderUI({
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+          if(width_calc < 1) {width <- 1}
+        } else {
+          width_calc <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          if(width_calc < 1) {width <- 1}
+        }
+      }
+      sliderInput(
+        "upgma_fruit_width_circ_5",
+        label = "",
+        min = 1,
+        max = round(ceiling(Vis$upgma_max_x) * 0.5, 0),
+        value = width,
+        width = "150px",
+        ticks = FALSE
+      )
+    } else {
+      if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+        sliderInput(
+          "upgma_fruit_width_circ_5",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 3,
+          width = "150px",
+          ticks = FALSE
+        )
+      } else {
+        sliderInput(
+          "upgma_fruit_width_circ_5",
+          label = "",
+          min = 1,
+          max = 10,
+          value = 1,
+          width = "150px",
+          ticks = FALSE
+        )
+      }
+    }
+  })
+  
+  # For Layout change update tiles 
+  observeEvent(input$nj_layout, {
+    if((!is.null(Vis$nj_min_x)) & (!is.null(Vis$nj_max_x))) {
+      if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          width <- round(ceiling(Vis$nj_max_x) * 0.033, 0) * 3
+        } else {
+          width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+        }
+      }
+      
+      updateSliderInput(session, "nj_fruit_width_circ", value = width)
+      updateSliderInput(session, "nj_fruit_width_circ_2", value = width)
+      updateSliderInput(session, "nj_fruit_width_circ_3", value = width)
+      updateSliderInput(session, "nj_fruit_width_circ_4", value = width)
+      updateSliderInput(session, "nj_fruit_width_circ_5", value = width) 
+    }
+  })
+  
+  observeEvent(input$upgma_layout, {
+    if((!is.null(Vis$upgma_min_x)) & (!is.null(Vis$upgma_max_x))) {
+      if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- 3
+        } else {
+          width <- 1
+        }
+      } else {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0) * 3
+        } else {
+          width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+        }
+      }
+      
+      updateSliderInput(session, "upgma_fruit_width_circ", value = width)
+      updateSliderInput(session, "upgma_fruit_width_circ_2", value = width)
+      updateSliderInput(session, "upgma_fruit_width_circ_3", value = width)
+      updateSliderInput(session, "upgma_fruit_width_circ_4", value = width)
+      updateSliderInput(session, "upgma_fruit_width_circ_5", value = width) 
+    }
+  })
+  
+  # Tip color mapping 
+  output$nj_tipcolor_mapping <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tipcolor_mapping",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Assembly Name` = "Assembly Name",
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Assembly Name` = "Assembly Name", `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(City = "City"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tipcolor_mapping",
+          "",
+          choices = c(
+            `Assembly Name` = "Assembly Name",
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c(City = "City")
+        )
+      )
+    }
+  })
+  
+  output$upgma_tipcolor_mapping <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tipcolor_mapping",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Assembly Name` = "Assembly Name",
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Assembly Name` = "Assembly Name", `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(City = "City"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tipcolor_mapping",
+          "",
+          choices = c(
+            `Assembly Name` = "Assembly Name",
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c(City = "City")
+        )
+      )
+    }
+  })
+  
+  # Tip shape Mapping 
+  output$nj_tipshape_mapping <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tipshape_mapping",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c("Host" = "Host"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_tipshape_mapping",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c("Host" = "Host"),
+          width = "100%"
+        )
+      )
+    }
+  })
+  
+  output$upgma_tipshape_mapping <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tipshape_mapping",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c("Host" = "Host"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_tipshape_mapping",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c("Host" = "Host"),
+          width = "100%"
+        )
+      )
+    }
+  })
+  
+  # Branch label 
+  output$nj_branch_label <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      selectInput(
+        "nj_branch_label",
+        "",
+        choices = if(ncol(Vis$meta_nj) == 11) {
+          c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        } else {
+          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                 names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+        },
+        selected = c("Host" = "Host"),
+        width = "100%"
+      )
+    } else {
+      selectInput(
+        "nj_branch_label",
+        "",
+        choices = c(
+          `Isolation Date` = "Isolation Date",
+          Host = "Host",
+          Country = "Country",
+          City = "City"
+        ),
+        selected = c("Host" = "Host"),
+        width = "100%"
+      )
+    }
+  })
+  
+  output$upgma_branch_label <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      selectInput(
+        "upgma_branch_label",
+        "",
+        choices = if(ncol(Vis$meta_upgma) == 11) {
+          c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        } else {
+          append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+        },
+        selected = c("Host" = "Host"),
+        width = "100%"
+      )
+    } else {
+      selectInput(
+        "upgma_branch_label",
+        "",
+        choices = c(
+          `Isolation Date` = "Isolation Date",
+          Host = "Host",
+          Country = "Country",
+          City = "City"
+        ),
+        selected = c("Host" = "Host"),
+        width = "100%"
+      )
+    }
+  })
+  
+  # Color mapping 
+  output$nj_color_mapping <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      shinyjs::disabled(
+        selectInput(
+          "nj_color_mapping",
+          "",
+          choices = if(ncol(Vis$meta_nj) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+          },
+          selected = c(Country = "Country"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "nj_color_mapping",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c(Country = "Country"),
+          width = "100%"
+        )
+      )
+    }
+  })
+  
+  output$upgma_color_mapping <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_color_mapping",
+          "",
+          choices = if(ncol(Vis$meta_upgma) == 11) {
+            c(
+              `Isolation Date` = "Isolation Date",
+              Host = "Host",
+              Country = "Country",
+              City = "City"
+            )
+          } else {
+            append(c(`Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                   names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+          },
+          selected = c(Country = "Country"),
+          width = "100%"
+        )
+      )
+    } else {
+      shinyjs::disabled(
+        selectInput(
+          "upgma_color_mapping",
+          "",
+          choices = c(
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          ),
+          selected = c(Country = "Country"),
+          width = "100%"
+        )
+      )
+    }
+  })
+  
+  # Tip labels 
+  output$nj_tiplab <- renderUI({
+    if(!is.null(Vis$meta_nj)) {
+      selectInput(
+        "nj_tiplab",
+        label = "",
+        choices = if(ncol(Vis$meta_nj) == 11) {
+          c(
+            Index = "Index",
+            `Assembly ID` = "Assembly ID",
+            `Assembly Name` = "Assembly Name",
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        } else {
+          append(c(Index = "Index", `Assembly ID` = "Assembly ID", `Assembly Name` = "Assembly Name",
+                   `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                 names(Vis$meta_nj)[13:ncol(Vis$meta_nj)])
+        },
+        selected = c(`Assembly Name` = "Assembly Name"),
+        width = "100%"
+      )
+    } else {
+      selectInput(
+        "nj_tiplab",
+        label = "",
+        choices = c(
+          Index = "Index",
+          `Assembly ID` = "Assembly ID",
+          `Assembly Name` = "Assembly Name",
+          `Isolation Date` = "Isolation Date",
+          Host = "Host",
+          Country = "Country",
+          City = "City"
+        ),
+        selected = c(`Assembly Name` = "Assembly Name"),
+        width = "100%"
+      )
+    }
+  })
+  
+  output$upgma_tiplab <- renderUI({
+    if(!is.null(Vis$meta_upgma)) {
+      selectInput(
+        "upgma_tiplab",
+        label = "",
+        choices = if(ncol(Vis$meta_upgma) == 11) {
+          c(
+            Index = "Index",
+            `Assembly ID` = "Assembly ID",
+            `Assembly Name` = "Assembly Name",
+            `Isolation Date` = "Isolation Date",
+            Host = "Host",
+            Country = "Country",
+            City = "City"
+          )
+        } else {
+          append(c(Index = "Index", `Assembly ID` = "Assembly ID", `Assembly Name` = "Assembly Name",
+                   `Isolation Date` = "Isolation Date", Host = "Host", Country = "Country", City = "City"),
+                 names(Vis$meta_upgma)[13:ncol(Vis$meta_upgma)])
+        },
+        selected = c(`Assembly Name` = "Assembly Name"),
+        width = "100%"
+      )
+    } else {
+      selectInput(
+        "upgma_tiplab",
+        label = "",
+        choices = c(
+          Index = "Index",
+          `Assembly ID` = "Assembly ID",
+          `Assembly Name` = "Assembly Name",
+          `Isolation Date` = "Isolation Date",
+          Host = "Host",
+          Country = "Country",
+          City = "City"
+        ),
+        selected = c(`Assembly Name` = "Assembly Name"),
+        width = "100%"
+      )
+    }
+  })
+  
+  #### MST controls ----
+  
+  # Clustering UI
+  output$mst_cluster <- renderUI({
+    req(DB$schemeinfo)
+    numericInput(
+      inputId = "mst_cluster_threshold",
+      label = NULL,
+      value = as.numeric(DB$schemeinfo[7, 2]),
+      min = 1,
+      max = 99
+    )
+  })
+  
+  # MST color mapping
+  output$mst_color_mapping <- renderUI({
+    if(input$mst_color_var == FALSE) {
+      fluidRow(
+        column(
+          width = 7,
+          div(
+            class = "node_color",
+            colorPickr(
+              inputId = "mst_color_node",
+              width = "100%",
+              selected = "#B2FACA",
+              label = "",
+              update = "changestop",
+              interaction = list(clear = FALSE,
+                                 save = FALSE),
+              position = "right-start"
+            )
+          )
+        ),
+        column(
+          width = 5,
+          dropMenu(
+            actionBttn(
+              "mst_node_menu",
+              label = "",
+              color = "default",
+              size = "sm",
+              style = "material-flat",
+              icon = icon("sliders")
+            ),
+            placement = "top-start",
+            theme = "translucent",
+            width = 5,
+            numericInput(
+              "node_opacity",
+              label = h5("Opacity", style = "color:white; margin-bottom: 0px;"),
+              value = 1,
+              step = 0.1,
+              min = 0,
+              max = 1,
+              width = "80px"
+            )
+          )
+        )
+      ) 
+    } else {
+      fluidRow(
+        column(
+          width = 9,
+          div(
+            class = "mst_col_sel",
+            selectInput(
+              "mst_col_var",
+              label = "",
+              choices = if(any(DB$cust_var[DB$cust_var$Variable[which(DB$cust_var$Variable %in% c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)]))],]$Type != "categ")) {
+                selection <- c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)])
+                cust_vars <- DB$cust_var$Variable[which(DB$cust_var$Variable %in% selection)]
+                selection[-which(selection == cust_vars[DB$cust_var[cust_vars,]$Type != "categ"])]
+              } else {c("Isolation Date", names(DB$meta)[-c(1, 2, 3, 4, 5, 6, 10, 11, 12)])},
+              width = "100%"
+            )
+          )
+        ),
+        column(
+          width = 3,
+          dropMenu(
+            actionBttn(
+              "mst_col_menu",
+              label = "",
+              color = "default",
+              size = "sm",
+              style = "material-flat",
+              icon = icon("sliders")
+            ),
+            placement = "top-start",
+            theme = "translucent",
+            width = 5,
+            selectInput(
+              "mst_col_scale",
+              label = h5("Color Scale", style = "color:white; margin-bottom: 0px;"),
+              choices = c("Viridis", "Rainbow"),
+              width = "150px"
+            ),
+            br(), br(), br(), br()
+          )
+        )
+      ) 
+    }
+  })
+  
+  observeEvent(input$mst_color_var, {
+    
+    if(input$mst_color_var == TRUE) {
+      updateSelectizeInput(session, inputId = "mst_node_shape", choices = c("Pie Nodes" = "custom"))
+      updateSelectizeInput(session, inputId = "mst_node_label", choices = c("Assembly Name"))
+    } else {
+      updateSelectizeInput(session, inputId = "mst_node_shape", 
+                           choices = list(`Label inside` = c("Circle" = "circle", "Box" = "box", "Text" = "text"),
+                                          `Label outside` = c("Diamond" = "diamond", "Hexagon" = "hexagon","Dot" = "dot", "Square" = "square")),
+                           selected = c("Dot" = "dot"))
+      updateSelectizeInput(session, inputId = "mst_node_label",
+                           choices = names(DB$meta)[c(1, 3, 4, 6, 7, 8, 9)],
+                           selected = "Assembly Name")
+    }
+  })
+  
+  # MST node labels 
+  output$mst_node_label <- renderUI({
+    selectInput(
+      "mst_node_label",
+      label = "",
+      choices = names(DB$meta)[c(1, 3, 4, 6, 7, 8, 9)],
+      selected = "Assembly Name",
+      width = "100%"
+    )
+  })
+  
+  ### Plot Reactives ----
+  
+  #### MST ----
+  
+  mst_tree <- reactive({
+    data <- toVisNetworkData(Vis$ggraph_1)
+    data$nodes <- mutate(data$nodes, 
+                                label = label_mst(),
+                                value = mst_node_scaling(),
+                                opacity = node_opacity())
+    
+    ctxRendererJS <- htmlwidgets::JS("({ctx, id, x, y, state: { selected, hover }, style, font, label, metadata}) => {
+                            var pieData = JSON.parse(metadata);
+                            var radius = style.size;
+                            var centerX = x;
+                            var centerY = y;
+                            var total = pieData.reduce((sum, slice) => sum + slice.value, 0)
+                            var startAngle = 0;
+
+                            const drawNode = () => {
+                                // Set shadow properties
+                                if (style.shadow) {
+                                  var shadowSize = style.shadowSize;
+                                  ctx.shadowColor = style.shadowColor;
+                                  ctx.shadowBlur = style.shadowSize;
+                                  ctx.shadowOffsetX = style.shadowX;
+                                  ctx.shadowOffsetY = style.shadowY;
+                                  
+                                  ctx.beginPath();
+                                  ctx.arc(centerX, centerY, radius, 0, 2 * Math.PI);
+                                  ctx.fill();
+                                  
+                                  ctx.shadowColor = 'transparent';
+                                  ctx.shadowBlur = 0;
+                                  ctx.shadowOffsetX = 0;
+                                  ctx.shadowOffsetY = 0;
+                                }
+
+                                pieData.forEach(slice => {
+                                    var sliceAngle = 2 * Math.PI * (slice.value / total);
+                                    ctx.beginPath();
+                                    ctx.moveTo(centerX, centerY);
+                                    ctx.arc(centerX, centerY, radius, startAngle, startAngle + sliceAngle);
+                                    ctx.closePath();
+                                    ctx.fillStyle = slice.color;
+                                    ctx.fill();
+                                     if (pieData.length > 1) {
+                ctx.strokeStyle = 'black';
+                ctx.lineWidth = 1;
+                ctx.stroke();
+            }
+                                    startAngle += sliceAngle;
+                                });
+                    
+                                // Draw a border
+                                ctx.beginPath();
+                                ctx.arc(centerX, centerY, radius, 0, 2 * Math.PI);
+                                ctx.strokeStyle = 'black';
+                                ctx.lineWidth = 1;
+                                ctx.stroke();
+                            };
+                            drawLabel = () => {
+                              //Draw the label
+                              var lines = label.split(`\n`);
+                              var lineHeight = font.size;
+                              ctx.font = `${font.size}px ${font.face}`;
+                              ctx.fillStyle = font.color;
+                              ctx.textAlign = 'center';
+                              ctx.textBaseline = 'middle';
+                              lines.forEach((line, index) => {
+                                ctx.fillText(line, centerX, 
+                                centerY + radius + (index + 1) * lineHeight);
+                              })
+                            }
+                            
+                            return {
+                                drawNode,
+                                drawExternalLabel: drawLabel,
+                                nodeDimensions: { width: 2 * radius, height: 2 * radius },
+                            };
+                        }")
+    
+    Vis$var_cols <- NULL
+    
+    # Generate pie charts as nodes
+    if(input$mst_color_var == TRUE & (!is.null(input$mst_col_var))) {
+      
+      group <- character(nrow(data$nodes))
+      for (i in 1:length(unique(Vis$meta_mst[[input$mst_col_var]]))) {
+        group[i] <- unique(Vis$meta_mst[[input$mst_col_var]])[i]
+      }
+      
+      data$nodes <- cbind(data$nodes, data.frame(metadata = character(nrow(data$nodes))))
+      
+      if(length(which(data$nodes$group == "")) != 0) {
+        data$nodes$group[which(data$nodes$group == "")] <- data$nodes$group[1]
+      }
+      
+      if(is.null(input$mst_col_scale)) {
+        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
+                                      color = viridis(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
+      } else if (input$mst_col_scale == "Rainbow") {
+        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
+                                      color = rainbow(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
+      } else if (input$mst_col_scale == "Viridis") {
+        Vis$var_cols <- data.frame(value = unique(Vis$meta_mst[[input$mst_col_var]]),
+                                      color = viridis(length(unique(Vis$meta_mst[[input$mst_col_var]]))))
+      }
+      
+      for(i in 1:nrow(data$nodes)) {
+        
+        iso_subset <- strsplit(data$nodes$label[i], split = "\n")[[1]]
+        variable <- Vis$meta_mst[[input$mst_col_var]]
+        values <- variable[which(Vis$meta_mst$`Assembly Name` %in% iso_subset)]
+        
+        for(j in 1:length(unique(values))) {
+          
+          share <- sum(unique(values)[j] == values) / length(values) * 100
+          color <- Vis$var_cols$color[Vis$var_cols$value == unique(values)[j]]
+          
+          if(j == 1) {
+            pie_vec <- paste0('{"value":', share,',"color":"', color,'"}')
+          } else {
+            pie_vec <- paste0(pie_vec, ',{"value":', share,',"color":"', color,'"}')
+          }
+        }
+        
+        data$nodes$metadata[i] <- paste0('[', pie_vec, ']')
+      }
+    }
+    
+    data$edges <- mutate(data$edges,
+                                length = if(input$mst_scale_edges == FALSE) {
+                                  input$mst_edge_length
+                                } else {
+                                  data$edges$weight * input$mst_edge_length_scale
+                                },
+                                label = as.character(data$edges$weight),
+                                opacity = input$mst_edge_opacity)
+    
+    if (input$mst_show_clusters) {
+      clusters <- compute_clusters(data$nodes, data$edges, input$mst_cluster_threshold)
+      if (input$mst_cluster_type == "Area") {
+        data$nodes$group <- clusters$group
+      }
+    }
+    
+    visNetwork_graph <- visNetwork(data$nodes, data$edges,
+                                   main = mst_title(),
+                                   background = mst_background_color(),
+                                   submain = mst_subtitle()) %>%
+      visNodes(size = mst_node_size(),
+               shape = input$mst_node_shape,
+               shadow = input$mst_shadow,
+               color = mst_color_node(),
+               ctxRenderer = ctxRendererJS,
+               scaling = list(min = mst_node_size_min(),
+                              max = mst_node_size_max()),
+               font = list(color = node_font_color(),
+                           size = input$node_label_fontsize)) %>%
+      visEdges(color = mst_color_edge(),
+               font = list(color = mst_edge_font_color(),
+                           size = mst_edge_font_size(),
+                           strokeWidth = 4)) %>%
+      visOptions(collapse = TRUE) %>%
+      visInteraction(hover = TRUE) %>%
+      visLayout(randomSeed = 1) %>%
+      visLegend(useGroups = FALSE,
+                zoom = TRUE,
+                width = legend_width(),
+                position = input$mst_legend_ori,
+                ncol = legend_col(),
+                addNodes = mst_legend())
+    
+    if (input$mst_show_clusters) {
+      if (input$mst_cluster_col_scale == "Viridis") {
+        color_palette <- viridis(length(unique(data$nodes$group)))
+      } else {
+        color_palette <- rainbow(length(unique(data$nodes$group)))
+      }
+      
+      if (input$mst_cluster_type == "Area") {
+        for (i in 1:length(unique(data$nodes$group))) {
+          visNetwork_graph <- visNetwork_graph %>% 
+            visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
+        }
+      } else {
+        thin_edges <- data$edges
+        thin_edges$width <- 1
+        thin_edges$color <- "black"
+        
+        thick_edges <- data$edges
+        thick_edges$width <- 24
+        
+        thick_edges$color <- rep("rgba(0, 0, 0, 0)", length(data$edges$from))
+        color_palette <- rainbow(length(unique(clusters$edges)))
+        for (i in 1:length(unique(clusters$edges))) {
+          print(clusters$edges)
+          if (unique(clusters$edges)[i] != "0") {
+            edge_color <- paste(col2rgb(color_palette[i]), collapse=", ")
+            thick_edges$color[clusters$edges == unique(clusters$edges)[i]] <- paste0("rgba(", edge_color, ", 0.5)")
+          }
+        }
+        merged_edges <- rbind(thick_edges, thin_edges)
+        data$edges <- merged_edges
+        visNetwork_graph <- visNetwork(data$nodes, data$edges,
+                                       main = mst_title(),
+                                       background = mst_background_color(),
+                                       submain = mst_subtitle()) %>%
+          visNodes(size = mst_node_size(),
+                   shape = input$mst_node_shape,
+                   shadow = input$mst_shadow,
+                   color = mst_color_node(),
+                   ctxRenderer = ctxRendererJS,
+                   scaling = list(min = mst_node_size_min(),
+                                  max = mst_node_size_max()),
+                   font = list(color = node_font_color(),
+                               size = input$node_label_fontsize)) %>%
+          visEdges(color = mst_color_edge(),
+                   font = list(color = mst_edge_font_color(),
+                               size = mst_edge_font_size(),
+                               strokeWidth = 4),
+                   smooth = FALSE,
+                   physics = FALSE) %>%
+          visOptions(collapse = TRUE) %>%
+          visInteraction(hover = TRUE) %>%
+          visLayout(randomSeed = 1) %>%
+          visLegend(useGroups = FALSE,
+                    zoom = TRUE,
+                    width = legend_width(),
+                    position = input$mst_legend_ori,
+                    ncol = legend_col(),
+                    addNodes = mst_legend())
+      }
+    }
+    visNetwork_graph
+  })
+  
+  # MST legend
+  legend_col <- reactive({
+    if(!is.null(Vis$var_cols)) {
+      if(nrow(Vis$var_cols) > 10) {
+        3
+      } else if(nrow(Vis$var_cols) > 5) {
+        2
+      } else {
+        1
+      }
+    } else {1}
+  })
+  
+  mst_legend <- reactive({
+    if(is.null(Vis$var_cols)) {
+      NULL
+    } else {
+      legend <- Vis$var_cols
+      names(legend)[1] <- "label"
+      mutate(legend, shape = "dot",
+             font.color = input$mst_legend_color,
+             size = input$mst_symbol_size,
+             font.size = input$mst_font_size)
+    }
+  })
+  
+  # Set MST legend width
+  legend_width <- reactive({
+    0.2
+  })
+  
+  # Set MST node shape
+  mst_node_shape <- reactive({
+    if(input$mst_node_shape == "Pie Nodes"){
+      "dot"
+    } else if(input$mst_node_shape %in% c("circle", "database", "box", "text")) {
+      shinyjs::disable('scale_nodes') 
+      updateCheckboxInput(session, "scale_nodes", value = FALSE)
+      shinyjs::disable('mst_node_size') 
+      shinyjs::disable('mst_node_scale')
+      input$mst_node_shape
+    } else {
+      shinyjs::enable('scale_nodes') 
+      shinyjs::enable('mst_node_size') 
+      shinyjs::enable('mst_node_scale')
+      input$mst_node_shape
+    }
+  })
+  
+  # Set MST label
+  label_mst <- reactive({
+    Vis$unique_meta[, colnames(Vis$unique_meta) %in% input$mst_node_label]
+  })
+  
+  # Set node color
+  mst_color_node <- reactive({
+    input$mst_color_node
+  })
+  
+  # Node Label Color
+  node_font_color <- reactive({
+    input$node_font_color
+  })
+  
+  
+  # Node Size Scaling
+  mst_node_scaling <- reactive({
+    if(input$scale_nodes == TRUE){
+      Vis$unique_meta$size
+    } else {NULL}
+  })
+  
+  # Node Size Min/May
+  mst_node_size_min <- reactive({
+    input$mst_node_scale[1]
+  })
+  
+  mst_node_size_max <- reactive({
+    input$mst_node_scale[2]
+  })
+  
+  # Node Size
+  mst_node_size <- reactive({
+    input$mst_node_size
+  })
+  
+  # Node Alpha/Opacity
+  node_opacity <- reactive({
+    input$node_opacity
+  })
+  
+  # Set Title
+  mst_title <- reactive({
+    if(!is.null(input$mst_title)) {
+      if(nchar(input$mst_title) < 1) {
+        list(text = "title",
+             style = paste0(
+               "font-family:Georgia, Times New Roman, Times, serif;",
+               "text-align:center;",
+               "font-size: ", as.character(input$mst_title_size), "px", 
+               "; color: ", as.character(mst_background_color()))
+        )
+      } else {
+        list(text = input$mst_title,
+             style = paste0(
+               "font-family:Georgia, Times New Roman, Times, serif;",
+               "text-align:center;",
+               "font-size: ", as.character(input$mst_title_size), "px", 
+               "; color: ", as.character(input$mst_title_color))
+        )
+      }
+    } else {
+      list(text = "title",
+           style = paste0(
+             "font-family:Georgia, Times New Roman, Times, serif;",
+             "text-align:center;",
+             "font-size: ", as.character(input$mst_title_size), "px", 
+             "; color: ", as.character(mst_background_color()))
+      )
+    }
+  })
+  
+  # Set Subtitle
+  mst_subtitle <- reactive({
+    list(text = input$mst_subtitle,
+         style = paste0(
+           "font-family:Georgia, Times New Roman, Times, serif;",
+           "text-align:center;",
+           "font-size: ", as.character(input$mst_subtitle_size), "px", 
+           "; color: ", as.character(input$mst_subtitle_color))
+    )
+  })
+  
+  # Background color
+  
+  mst_background_color <- reactive({
+    if(input$mst_background_transparent == TRUE) {
+      'rgba(0, 0, 0, 0)'
+    } else{
+      input$mst_background_color
+    }
+  })
+  
+  # Edge font color
+  mst_edge_font_color <- reactive({
+    input$mst_edge_font_color
+  })
+  
+  # Edge color
+  mst_color_edge <- reactive({
+    input$mst_color_edge
+  })
+  
+  # Edge font size
+  mst_edge_font_size <- reactive({
+    input$mst_edge_font_size
+  })
+  
+  #### NJ ----
+  
+  nj_tree <- reactive({
+    
+    # Convert negative edges 
+    Vis$nj[["edge.length"]] <- abs(Vis$nj[["edge.length"]])
+    
+    if(input$nj_nodelabel_show == TRUE) {
+      ggtree(Vis$nj, alpha = 0.2, layout = layout_nj()) + 
+        geom_nodelab(aes(label = node), color = "#29303A", size = nj_tiplab_size() + 1, hjust = 0.7) +
+        nj_limit() +
+        nj_inward() 
+    } else {
+      tree <- 
+        ggtree(Vis$nj, 
+               color = input$nj_color,
+               layout = layout_nj(),
+               ladderize = input$nj_ladder) %<+% Vis$meta_nj +
+        nj_clades() +
+        nj_tiplab() +
+        nj_tiplab_scale() + 
+        new_scale_color() +
+        nj_limit() +
+        nj_inward() +
+        nj_label_branch() +
+        nj_treescale() +
+        nj_nodepoint() +
+        nj_tippoint() +
+        nj_tippoint_scale() + 
+        new_scale_color() +
+        nj_clip_label() +
+        nj_rootedge() +
+        ggtitle(label = input$nj_title,
+                subtitle = input$nj_subtitle) +
+        theme_tree(bgcolor = input$nj_bg) +
+        theme(plot.title = element_text(colour = input$nj_title_color,
+                                        size = input$nj_title_size),
+              plot.subtitle = element_text(colour = input$nj_title_color,
+                                           size = input$nj_subtitle_size),
+              legend.background = element_rect(fill = input$nj_bg),
+              legend.direction = input$nj_legend_orientation,
+              legend.title = element_text(color = input$nj_color,
+                                          size = input$nj_legend_size*1.2),
+              legend.title.align = 0.5,
+              legend.position = nj_legend_pos(),
+              legend.text = element_text(color = input$nj_color, 
+                                         size = input$nj_legend_size),
+              legend.key = element_rect(fill = input$nj_bg),
+              legend.box.spacing = unit(1.5, "cm"),
+              legend.key.size = unit(0.05*input$nj_legend_size, 'cm'),
+              plot.background = element_rect(fill = input$nj_bg, color = input$nj_bg)) +
+        new_scale_fill() +
+        nj_fruit() +
+        nj_gradient() +
+        new_scale_fill() +
+        nj_fruit2() +
+        nj_gradient2() +
+        new_scale_fill() +
+        nj_fruit3() +
+        nj_gradient3() +
+        new_scale_fill() +
+        nj_fruit4() +
+        nj_gradient4() +
+        new_scale_fill() +
+        nj_fruit5() +
+        nj_gradient5() +
+        new_scale_fill() 
+      
+      # Add custom labels
+      if(length(Vis$custom_label_nj) > 0) {
+        
+        for(i in Vis$custom_label_nj[,1]) {
+          
+          if(!is.null(Vis$nj_label_pos_x[[i]])) {
+            x_pos <- Vis$nj_label_pos_x[[i]]
+          } else {
+            x_pos <- round(Vis$nj_max_x / 2, 0)
+          }
+          
+          if(!is.null(Vis$nj_label_pos_y[[i]])) {
+            y_pos <- Vis$nj_label_pos_y[[i]]
+          } else {
+            y_pos <- sum(DB$data$Include) / 2
+          }
+          
+          if(!is.null(Vis$nj_label_size[[i]])) {
+            size <- Vis$nj_label_size[[i]]
+          } else {
+            size <- 5
+          }
+          
+          tree <- tree + annotate("text",
+                                  x = x_pos,
+                                  y = y_pos, 
+                                  label = i,
+                                  size = size)
+        }
+      }
+      
+      # Add heatmap
+      if(input$nj_heatmap_show == TRUE & length(input$nj_heatmap_select) > 0) {
+        if (!(any(sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)) & 
+              any(!sapply(Vis$meta_nj[input$nj_heatmap_select], is.numeric)))) {
+          tree <- gheatmap.mod(tree, 
+                               data = select(Vis$meta_nj, input$nj_heatmap_select),
+                               offset = nj_heatmap_offset(),
+                               width = nj_heatmap_width(),
+                               legend_title = input$nj_heatmap_title,
+                               colnames_angle = -nj_colnames_angle(),
+                               colnames_offset_y = nj_colnames_y(),
+                               colnames_color = input$nj_color) +
+            nj_heatmap_scale()
+        }
+      } 
+      
+      # Sizing control
+      Vis$nj_plot <- ggplotify::as.ggplot(tree, 
+                                          scale = input$nj_zoom,
+                                          hjust = input$nj_h,
+                                          vjust = input$nj_v)  
+      
+      Vis$nj_true <- TRUE
+      
+      # Correct background color if zoomed out
+      cowplot::ggdraw(Vis$nj_plot) + 
+        theme(plot.background = element_rect(fill = input$nj_bg, color = input$nj_bg))
+    }
+  })
+  
+  # Heatmap width
+  nj_heatmap_width <- reactive({
+    if(!is.null(input$nj_heatmap_width)) {
+      input$nj_heatmap_width
+    } else {
+      length_input <- length(input$nj_heatmap_select)
+      if((!(input$nj_layout == "circular")) & (!(input$nj_layout == "inward"))) {
+        if(length_input < 3) {
+          0.1
+        } else {
+          if (length_input >= 3 && length_input <= 50) {
+            min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+          } else {
+            1.5
+          }   
+        }
+      } else {
+        if(length_input < 3) {
+          0.3
+        } else if (length_input >= 3 && length_input <= 27) {
+          min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          3
+        }
+      }
+    }
+  })
+  
+  # Heatmap column titles position
+  nj_colnames_y <- reactive({
+    if(!is.null(input$nj_colnames_y)) {
+      input$nj_colnames_y
+    } else {
+      if(input$nj_layout == "inward" | input$nj_layout == "circular") {
+        0
+      } else {-1}
+    }
+  })
+  
+  # Heatmap column titles angle
+  nj_colnames_angle <- reactive({
+    if(!is.null(input$nj_colnames_angle)) {
+      input$nj_colnames_angle
+    } else {
+      if(!is.null(input$nj_layout)) {
+        if(input$nj_layout == "inward" | input$nj_layout == "circular") {
+          90
+        } else {-90}
+      } else {-90}
+    }
+  })
+  
+  # Heatmap scale
+  nj_heatmap_scale <- reactive({
+    if(!is.null(input$nj_heatmap_scale) & !is.null(input$nj_heatmap_div_mid)) {
+      if(input$nj_heatmap_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$nj_heatmap_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$nj_heatmap_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_heatmap_select]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_heatmap_select]), na.rm = TRUE)
+        }
+        scale_fill_gradient2(low = brewer.pal(3, input$nj_heatmap_scale)[1],
+                             mid = brewer.pal(3, input$nj_heatmap_scale)[2],
+                             high = brewer.pal(3, input$nj_heatmap_scale)[3],
+                             midpoint = midpoint,
+                             name = input$nj_heatmap_title)
+      } else {
+        if(input$nj_heatmap_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_nj[input$nj_heatmap_select])) == "numeric") {
+            if(input$nj_heatmap_scale == "magma") {
+              scale_fill_viridis(option = "A",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "inferno") {
+              scale_fill_viridis(option = "B",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "plasma") {
+              scale_fill_viridis(option = "C",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "viridis") {
+              scale_fill_viridis(option = "D",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "cividis") {
+              scale_fill_viridis(option = "E",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "rocket") {
+              scale_fill_viridis(option = "F",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "mako") {
+              scale_fill_viridis(option = "G",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "turbo") {
+              scale_fill_viridis(option = "H",
+                                 name = input$nj_heatmap_title)
+            } 
+          } else {
+            if(input$nj_heatmap_scale == "magma") {
+              scale_fill_viridis(discrete = TRUE, option = "A",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "inferno") {
+              scale_fill_viridis(discrete = TRUE, option = "B",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "plasma") {
+              scale_fill_viridis(discrete = TRUE, option = "C",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "viridis") {
+              scale_fill_viridis(discrete = TRUE, option = "D",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "cividis") {
+              scale_fill_viridis(discrete = TRUE, option = "E",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "rocket") {
+              scale_fill_viridis(discrete = TRUE, option = "F",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "mako") {
+              scale_fill_viridis(discrete = TRUE, option = "G",
+                                 name = input$nj_heatmap_title)
+            } else if(input$nj_heatmap_scale == "turbo") {
+              scale_fill_viridis(discrete = TRUE, option = "H",
+                                 name = input$nj_heatmap_title)
+            } 
+          }
+        } else {
+          scale_fill_brewer(palette = input$nj_heatmap_scale,
+                            name = input$nj_heatmap_title)
+        }
+      }
+    }
+  })
+  
+  # Tippoint Scale
+  nj_tippoint_scale <- reactive({
+    if(!is.null(input$nj_tippoint_scale) & !is.null(input$nj_tipcolor_mapping_div_mid)) {
+      if(input$nj_tippoint_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$nj_tipcolor_mapping_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$nj_tipcolor_mapping_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_tipcolor_mapping]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_tipcolor_mapping]), na.rm = TRUE)
+        }
+        scale_color_gradient2(low = brewer.pal(3, input$nj_tippoint_scale)[1],
+                              mid = brewer.pal(3, input$nj_tippoint_scale)[2],
+                              high = brewer.pal(3, input$nj_tippoint_scale)[3],
+                              midpoint = midpoint)
+      } else {
+        if(input$nj_tippoint_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_nj[input$nj_tipcolor_mapping])) == "numeric") {
+            if(input$nj_tippoint_scale == "magma") {
+              scale_color_viridis(option = "A")
+            } else if(input$nj_tippoint_scale == "inferno") {
+              scale_color_viridis(option = "B")
+            } else if(input$nj_tippoint_scale == "plasma") {
+              scale_color_viridis(option = "C")
+            } else if(input$nj_tippoint_scale == "viridis") {
+              scale_color_viridis(option = "D")
+            } else if(input$nj_tippoint_scale == "cividis") {
+              scale_color_viridis(option = "E")
+            } else if(input$nj_tippoint_scale == "rocket") {
+              scale_color_viridis(option = "F")
+            } else if(input$nj_tippoint_scale == "mako") {
+              scale_color_viridis(option = "G")
+            } else if(input$nj_tippoint_scale == "turbo") {
+              scale_color_viridis(option = "H")
+            } 
+          } else {
+            if(input$nj_tippoint_scale == "magma") {
+              scale_color_viridis(discrete = TRUE, option = "A")
+            } else if(input$nj_tippoint_scale == "inferno") {
+              scale_color_viridis(discrete = TRUE, option = "B")
+            } else if(input$nj_tippoint_scale == "plasma") {
+              scale_color_viridis(discrete = TRUE, option = "C")
+            } else if(input$nj_tippoint_scale == "viridis") {
+              scale_color_viridis(discrete = TRUE, option = "D")
+            } else if(input$nj_tippoint_scale == "cividis") {
+              scale_color_viridis(discrete = TRUE, option = "E")
+            } else if(input$nj_tippoint_scale == "rocket") {
+              scale_color_viridis(discrete = TRUE, option = "F")
+            } else if(input$nj_tippoint_scale == "mako") {
+              scale_color_viridis(discrete = TRUE, option = "G")
+            } else if(input$nj_tippoint_scale == "turbo") {
+              scale_color_viridis(discrete = TRUE, option = "H")
+            } 
+          }
+        } else {
+          scale_color_brewer(palette = input$nj_tippoint_scale)
+        }
+      }
+    }
+  })
+  
+  # Tiplab Scale
+  nj_tiplab_scale <- reactive({
+    if(!is.null(input$nj_tiplab_scale) & !is.null(input$nj_color_mapping_div_mid)) {
+      if(input$nj_tiplab_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$nj_color_mapping_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$nj_color_mapping_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_color_mapping]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_nj[input$nj_color_mapping]), na.rm = TRUE)
+        }
+        scale_color_gradient2(low = brewer.pal(3, input$nj_tiplab_scale)[1],
+                              mid = brewer.pal(3, input$nj_tiplab_scale)[2],
+                              high = brewer.pal(3, input$nj_tiplab_scale)[3],
+                              midpoint = midpoint)
+      } else {
+        if(input$nj_tiplab_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_nj[input$nj_color_mapping])) == "numeric") {
+            if(input$nj_tiplab_scale == "magma") {
+              scale_color_viridis(option = "A")
+            } else if(input$nj_tiplab_scale == "inferno") {
+              scale_color_viridis(option = "B")
+            } else if(input$nj_tiplab_scale == "plasma") {
+              scale_color_viridis(option = "C")
+            } else if(input$nj_tiplab_scale == "viridis") {
+              scale_color_viridis(option = "D")
+            } else if(input$nj_tiplab_scale == "cividis") {
+              scale_color_viridis(option = "E")
+            } else if(input$nj_tiplab_scale == "rocket") {
+              scale_color_viridis(option = "F")
+            } else if(input$nj_tiplab_scale == "mako") {
+              scale_color_viridis(option = "G")
+            } else if(input$nj_tiplab_scale == "turbo") {
+              scale_color_viridis(option = "H")
+            } 
+          } else {
+            if(input$nj_tiplab_scale == "magma") {
+              scale_color_viridis(discrete = TRUE, option = "A")
+            } else if(input$nj_tiplab_scale == "inferno") {
+              scale_color_viridis(discrete = TRUE, option = "B")
+            } else if(input$nj_tiplab_scale == "plasma") {
+              scale_color_viridis(discrete = TRUE, option = "C")
+            } else if(input$nj_tiplab_scale == "viridis") {
+              scale_color_viridis(discrete = TRUE, option = "D")
+            } else if(input$nj_tiplab_scale == "cividis") {
+              scale_color_viridis(discrete = TRUE, option = "E")
+            } else if(input$nj_tiplab_scale == "rocket") {
+              scale_color_viridis(discrete = TRUE, option = "F")
+            } else if(input$nj_tiplab_scale == "mako") {
+              scale_color_viridis(discrete = TRUE, option = "G")
+            } else if(input$nj_tiplab_scale == "turbo") {
+              scale_color_viridis(discrete = TRUE, option = "H")
+            } 
+          }
+        } else {
+          scale_color_brewer(palette = input$nj_tiplab_scale)
+        }
+      }
+    }
+  })
+  
+  # Clade Highlight
+  nj_clades <- reactive({
+    if(!is.null(input$nj_parentnode)) {
+      if(!length(input$nj_parentnode) == 0) {
+        if(length(input$nj_parentnode) == 1) {
+          fill <- input$nj_clade_scale
+        } else if (length(input$nj_parentnode) == 2) {
+          if(startsWith(input$nj_clade_scale, "#")) {
+            fill <- brewer.pal(3, "Set1")[1:2]
+          } else {
+            fill <- brewer.pal(3, input$nj_clade_scale)[1:2]
+          }
+        } else {
+          fill <- brewer.pal(length(input$nj_parentnode), input$nj_clade_scale)
+        }
+        geom_hilight(node = as.numeric(input$nj_parentnode),
+                     fill = fill,
+                     type = input$nj_clade_type,
+                     to.bottom = TRUE
+        )
+      } else {NULL}
+    }
+  })
+  
+  # Legend Position
+  nj_legend_pos <- reactive({
+    if(!is.null(input$nj_legend_x) & !is.null(input$nj_legend_y)) {
+      c(input$nj_legend_x, input$nj_legend_y)
+    } else {
+      c(0.1, 1)
+    }
+  })
+  
+  # Heatmap offset
+  nj_heatmap_offset <- reactive({
+    if(is.null(input$nj_heatmap_offset)) {
+      0
+    } else {input$nj_heatmap_offset}
+  })
+  
+  # Tiles fill color gradient
+  nj_gradient <- reactive({
+    if(!is.null(input$nj_tiles_show_1) & 
+       !is.null(input$nj_fruit_variable) & 
+       !is.null(input$nj_tiles_scale_1) & 
+       !is.null(input$nj_tiles_mapping_div_mid_1)) {
+      if(input$nj_tiles_show_1 == TRUE) {
+        if(input$nj_tiles_scale_1 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$nj_tiles_mapping_div_mid_1 == "Zero") {
+            midpoint <- 0
+          } else if(input$nj_tiles_mapping_div_mid_1 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable]), na.rm = TRUE)
+          }
+          scale_fill_gradient2(low = brewer.pal(3, input$nj_tiles_scale_1)[1],
+                               mid = brewer.pal(3, input$nj_tiles_scale_1)[2],
+                               high = brewer.pal(3, input$nj_tiles_scale_1)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$nj_tiles_scale_1 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
+              if(input$nj_tiles_scale_1 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$nj_tiles_scale_1 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$nj_tiles_scale_1 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$nj_tiles_scale_1 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$nj_tiles_scale_1 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$nj_tiles_scale_1 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$nj_tiles_scale_1 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$nj_tiles_scale_1 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$nj_tiles_scale_1 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$nj_tiles_scale_1 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$nj_tiles_scale_1 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$nj_tiles_scale_1 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$nj_tiles_scale_1 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$nj_tiles_scale_1 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$nj_tiles_scale_1 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$nj_tiles_scale_1 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$nj_tiles_scale_1)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_gradient2 <- reactive({
+    if(!is.null(input$nj_tiles_show_2) & 
+       !is.null(input$nj_fruit_variable_2) & 
+       !is.null(input$nj_tiles_scale_2) & 
+       !is.null(input$nj_tiles_mapping_div_mid_2)) {
+      if(input$nj_tiles_show_2 == TRUE) {
+        if(input$nj_tiles_scale_2 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$nj_tiles_mapping_div_mid_2 == "Zero") {
+            midpoint <- 0
+          } else if(input$nj_tiles_mapping_div_mid_2 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_2]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_2]), na.rm = TRUE)
+          }
+          scale_fill_gradient2(low = brewer.pal(3, input$nj_tiles_scale_2)[1],
+                               mid = brewer.pal(3, input$nj_tiles_scale_2)[2],
+                               high = brewer.pal(3, input$nj_tiles_scale_2)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$nj_tiles_scale_2 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_2])) == "numeric") {
+              if(input$nj_tiles_scale_2 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$nj_tiles_scale_2 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$nj_tiles_scale_2 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$nj_tiles_scale_2 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$nj_tiles_scale_2 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$nj_tiles_scale_2 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$nj_tiles_scale_2 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$nj_tiles_scale_2 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$nj_tiles_scale_2 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$nj_tiles_scale_2 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$nj_tiles_scale_2 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$nj_tiles_scale_2 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$nj_tiles_scale_2 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$nj_tiles_scale_2 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$nj_tiles_scale_2 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$nj_tiles_scale_2 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$nj_tiles_scale_2)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_gradient3 <- reactive({
+    if(!is.null(input$nj_tiles_show_3) & 
+       !is.null(input$nj_fruit_variable_3) & 
+       !is.null(input$nj_tiles_scale_3 & 
+                !is.null(input$nj_tiles_mapping_div_mid_3))) {
+      if(input$nj_tiles_show_3 == TRUE) {
+        if(input$nj_tiles_scale_3 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$nj_tiles_mapping_div_mid_3 == "Zero") {
+            midpoint <- 0
+          } else if(input$nj_tiles_mapping_div_mid_3 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_3]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_3]), na.rm = TRUE)
+          }
+          scale_fill_gradient3(low = brewer.pal(3, input$nj_tiles_scale_3)[1],
+                               mid = brewer.pal(3, input$nj_tiles_scale_3)[2],
+                               high = brewer.pal(3, input$nj_tiles_scale_3)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$nj_tiles_scale_3 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_3])) == "numeric") {
+              if(input$nj_tiles_scale_3 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$nj_tiles_scale_3 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$nj_tiles_scale_3 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$nj_tiles_scale_3 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$nj_tiles_scale_3 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$nj_tiles_scale_3 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$nj_tiles_scale_3 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$nj_tiles_scale_3 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$nj_tiles_scale_3 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$nj_tiles_scale_3 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$nj_tiles_scale_3 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$nj_tiles_scale_3 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$nj_tiles_scale_3 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$nj_tiles_scale_3 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$nj_tiles_scale_3 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$nj_tiles_scale_3 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$nj_tiles_scale_3)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_gradient4 <- reactive({
+    if(!is.null(input$nj_tiles_show_4) & 
+       !is.null(input$nj_fruit_variable_4) & 
+       !is.null(input$nj_tiles_scale_4) & 
+       !is.null(input$nj_tiles_mapping_div_mid_4)) {
+      if(input$nj_tiles_show_4 == TRUE) {
+        if(input$nj_tiles_scale_4 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$nj_tiles_mapping_div_mid_4 == "Zero") {
+            midpoint <- 0
+          } else if(input$nj_tiles_mapping_div_mid_4 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_4]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_4]), na.rm = TRUE)
+          }
+          scale_fill_gradient4(low = brewer.pal(3, input$nj_tiles_scale_4)[1],
+                               mid = brewer.pal(3, input$nj_tiles_scale_4)[2],
+                               high = brewer.pal(3, input$nj_tiles_scale_4)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$nj_tiles_scale_4 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable])) == "numeric") {
+              if(input$nj_tiles_scale_4 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$nj_tiles_scale_4 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$nj_tiles_scale_4 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$nj_tiles_scale_4 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$nj_tiles_scale_4 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$nj_tiles_scale_4 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$nj_tiles_scale_4 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$nj_tiles_scale_4 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$nj_tiles_scale_4 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$nj_tiles_scale_4 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$nj_tiles_scale_4 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$nj_tiles_scale_4 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$nj_tiles_scale_4 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$nj_tiles_scale_4 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$nj_tiles_scale_4 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$nj_tiles_scale_4 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$nj_tiles_scale_4)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_gradient5 <- reactive({
+    if(!is.null(input$nj_tiles_show_5) & 
+       !is.null(input$nj_fruit_variable_5) & 
+       !is.null(input$nj_tiles_scale_5) & 
+       !is.null(input$nj_tiles_mapping_div_mid_5)) {
+      if(input$nj_tiles_show_5 == TRUE) {
+        if(input$nj_tiles_scale_5 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$nj_tiles_mapping_div_mid_5 == "Zero") {
+            midpoint <- 0
+          } else if(input$nj_tiles_mapping_div_mid_5 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_nj[input$nj_fruit_variable_5]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_nj[input$nj_fruit_variable_5]), na.rm = TRUE)
+          }
+          scale_fill_gradient5(low = brewer.pal(3, input$nj_tiles_scale_5)[1],
+                               mid = brewer.pal(3, input$nj_tiles_scale_5)[2],
+                               high = brewer.pal(3, input$nj_tiles_scale_5)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$nj_tiles_scale_5 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_nj[input$nj_fruit_variable_5])) == "numeric") {
+              if(input$nj_tiles_scale_5 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$nj_tiles_scale_5 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$nj_tiles_scale_5 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$nj_tiles_scale_5 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$nj_tiles_scale_5 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$nj_tiles_scale_5 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$nj_tiles_scale_5 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$nj_tiles_scale_5 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$nj_tiles_scale_5 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$nj_tiles_scale_5 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$nj_tiles_scale_5 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$nj_tiles_scale_5 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$nj_tiles_scale_5 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$nj_tiles_scale_5 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$nj_tiles_scale_5 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$nj_tiles_scale_5 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$nj_tiles_scale_5)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  # No label clip off for linear NJ tree
+  nj_clip_label <- reactive({
+    if(!(input$nj_layout == "circular" | input$nj_layout == "inward")) {
+      coord_cartesian(clip = "off")
+    } else {NULL}
+  })
+  
+  # Geom Fruit
+  nj_fruit <- reactive({
+    if((!is.null(input$nj_tiles_show_1)) & 
+       (!is.null(input$nj_fruit_variable)) & 
+       (!is.null(input$nj_layout)) & 
+       (!is.null(input$nj_fruit_offset_circ)) & 
+       (!is.null(input$nj_fruit_width_circ)) & 
+       (!is.null(input$nj_fruit_alpha))) {
+      if(input$nj_tiles_show_1 == TRUE) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
+            offset = input$nj_fruit_offset_circ,
+            width = input$nj_fruit_width_circ,
+            alpha = input$nj_fruit_alpha
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
+            offset = input$nj_fruit_offset_circ,
+            width = input$nj_fruit_width_circ,
+            alpha = input$nj_fruit_alpha
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$nj_tiles_show_1 == TRUE) {
+        if(!is.null(Vis$nj_max_x)) {
+          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
+            offset = 0,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable)),
+            offset = 0,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  # Geom Fruit
+  nj_fruit2 <- reactive({
+    if((!is.null(input$nj_tiles_show_2)) & 
+       (!is.null(input$nj_fruit_variable_2)) & 
+       (!is.null(input$nj_layout)) & 
+       (!is.null(input$nj_fruit_offset_circ_2)) & 
+       (!is.null(input$nj_fruit_width_circ_2)) & 
+       (!is.null(input$nj_fruit_alpha_2))) {
+      if(input$nj_tiles_show_2 == TRUE) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_2)),
+            offset = input$nj_fruit_offset_circ_2,
+            width = input$nj_fruit_width_circ_2,
+            alpha = input$nj_fruit_alpha_2
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_2)),
+            offset = input$nj_fruit_offset_circ_2,
+            width = input$nj_fruit_width_circ_2,
+            alpha = input$nj_fruit_alpha_2
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$nj_tiles_show_2 == TRUE) {
+        if(!is.null(Vis$nj_max_x)) {
+          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_2)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_2)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_fruit3 <- reactive({
+    if((!is.null(input$nj_tiles_show_3)) & 
+       (!is.null(input$nj_fruit_variable_3)) & 
+       (!is.null(input$nj_layout)) & 
+       (!is.null(input$nj_fruit_offset_circ_3)) & 
+       (!is.null(input$nj_fruit_width_circ_3)) & 
+       (!is.null(input$nj_fruit_alpha_3))) {
+      if(input$nj_tiles_show_3 == TRUE) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_3)),
+            offset = input$nj_fruit_offset_circ_3,
+            width = input$nj_fruit_width_circ_3,
+            alpha = input$nj_fruit_alpha_3
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_3)),
+            offset = input$nj_fruit_offset_circ_3,
+            width = input$nj_fruit_width_circ_3,
+            alpha = input$nj_fruit_alpha_3
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$nj_tiles_show_3 == TRUE) {
+        if(!is.null(Vis$nj_max_x)) {
+          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_3)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_3)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  nj_fruit4 <- reactive({
+    if((!is.null(input$nj_tiles_show_4)) & 
+       (!is.null(input$nj_fruit_variable_4)) & 
+       (!is.null(input$nj_layout)) & 
+       (!is.null(input$nj_fruit_offset_circ_4)) & 
+       (!is.null(input$nj_fruit_width_circ_4)) & 
+       (!is.null(input$nj_fruit_alpha_4))) {
+      if(input$nj_tiles_show_4 == TRUE) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_4)),
+            offset = input$nj_fruit_offset_circ_4,
+            width = input$nj_fruit_width_circ_4,
+            alpha = input$nj_fruit_alpha_4
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_4)),
+            offset = input$nj_fruit_offset_circ_4,
+            width = input$nj_fruit_width_circ_4,
+            alpha = input$nj_fruit_alpha_4
+          )
+        }
+      } else {
+        if(input$nj_tiles_show_4 == TRUE) {
+          if(!is.null(Vis$nj_max_x)) {
+            if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+              width <- 1
+            } else {
+              width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+            }
+          } else {
+            width <- 2
+          }
+          if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+            geom_fruit(
+              geom = geom_tile,
+              mapping = aes(fill= !!sym(input$nj_fruit_variable_4)),
+              offset = 0.15,
+              width = width * 3,
+              alpha = 1
+            )
+          } else {
+            geom_fruit(
+              geom = geom_tile,
+              mapping = aes(fill= !!sym(input$nj_fruit_variable_4)),
+              offset = 0.05,
+              width = width,
+              alpha = 1
+            )
+          }
+        } else {NULL}
+      }
+    }
+  })
+  
+  nj_fruit5 <- reactive({
+    if((!is.null(input$nj_tiles_show_5)) & 
+       (!is.null(input$nj_fruit_variable_5)) & 
+       (!is.null(input$nj_layout)) & 
+       (!is.null(input$nj_fruit_offset_circ_5)) & 
+       (!is.null(input$nj_fruit_width_circ_5)) & 
+       (!is.null(input$nj_fruit_alpha_5))) {
+      if(input$nj_tiles_show_5 == TRUE) {
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_5)),
+            offset = input$nj_fruit_offset_circ_5,
+            width = input$nj_fruit_width_circ_5,
+            alpha = input$nj_fruit_alpha_5
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$nj_fruit_variable_5)),
+            offset = input$nj_fruit_offset_circ_5,
+            width = input$nj_fruit_width_circ_5,
+            alpha = input$nj_fruit_alpha_5
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$nj_tiles_show_5 == TRUE) {
+        if(!is.null(Vis$nj_max_x)) {
+          if(round(ceiling(Vis$nj_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$nj_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_5)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$nj_fruit_variable_5)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  # Xlim
+  nj_limit <- reactive({
+    if(input$nj_layout == "circular") {
+      xlim(input$nj_xlim, NA)
+    } else {NULL}
+  })
+  
+  # Treescale
+  nj_treescale <- reactive({
+    if(!input$nj_layout == "circular") {
+      if(input$nj_treescale_show == TRUE) {
+        geom_treescale(x = nj_treescale_x(),
+                       y = nj_treescale_y(),
+                       width = nj_treescale_width(),
+                       color = input$nj_color,
+                       fontsize = 4)
+      } else {NULL}
+    } else {NULL}
+  }) 
+  
+  # Treescale Y Position
+  nj_treescale_y <- reactive({
+    if(is.null(input$nj_treescale_y)) {
+      0
+    } else {input$nj_treescale_y}
+  })
+  
+  # Treescale X Position
+  nj_treescale_x <- reactive({
+    if(is.null(input$nj_treescale_x)) {
+      round(ceiling(Vis$nj_max_x) * 0.2, 0)
+    } else {input$nj_treescale_x}
+  })
+  
+  # Treescale width
+  nj_treescale_width <- reactive({
+    if(!is.null(input$nj_treescale_width)) {
+      input$nj_treescale_width
+    } else {
+      round(ceiling(Vis$nj_max_x) * 0.1, 0)
+    }
+  })
+  
+  # Label branches
+  nj_label_branch <- reactive({
+    if(!input$nj_layout == "circular" | !input$nj_layout == "inward") {
+      if(input$nj_show_branch_label == TRUE) {
+        geom_label(
+          aes(
+            x=!!sym("branch"), 
+            label= !!sym(input$nj_branch_label)),
+          fill = input$nj_branch_label_color,
+          size = nj_branch_size(),
+          label.r = unit(input$nj_branch_labelradius, "lines"),
+          nudge_x = input$nj_branch_x,
+          nudge_y = input$nj_branch_y,
+          fontface = input$nj_branchlab_fontface,
+          alpha = input$nj_branchlab_alpha
+        )
+      } else {NULL}
+    } else {NULL}
+  })
+  
+  # Branch label size
+  nj_branch_size <- reactive({
+    if(!is.null(input$nj_branch_size)) {
+      input$nj_branch_size
+    } else {
+      Vis$branch_size_nj
+    }
+  })
+  
+  # Rootedge
+  nj_rootedge <- reactive({
+    if(input$nj_rootedge_show == TRUE) {
+      if(is.null(input$nj_rootedge_length)) {
+        geom_rootedge(rootedge = round(ceiling(Vis$nj_max_x) * 0.05, 0),
+                      linetype = input$nj_rootedge_line)
+      } else {
+        geom_rootedge(rootedge = input$nj_rootedge_length,
+                      linetype = input$nj_rootedge_line)
+      }
+    } else {NULL}
+  })
+  
+  # Tippoints
+  nj_tippoint <- reactive({
+    if(input$nj_tippoint_show == TRUE | input$nj_tipcolor_mapping_show == TRUE | input$nj_tipshape_mapping_show == TRUE) {
+      if(input$nj_tipcolor_mapping_show == TRUE & input$nj_tipshape_mapping_show == FALSE) {
+        geom_tippoint(
+          aes(color = !!sym(input$nj_tipcolor_mapping)),
+          alpha = input$nj_tippoint_alpha,
+          shape = input$nj_tippoint_shape,
+          size = nj_tippoint_size()
+        )
+      } else if (input$nj_tipcolor_mapping_show == FALSE & input$nj_tipshape_mapping_show == TRUE) {
+        geom_tippoint(
+          aes(shape = !!sym(input$nj_tipshape_mapping)),
+          alpha = input$nj_tippoint_alpha,
+          color = input$nj_tippoint_color,
+          size = nj_tippoint_size()
+        )
+      } else if (input$nj_tipcolor_mapping_show == TRUE & input$nj_tipshape_mapping_show == TRUE) {
+        geom_tippoint(
+          aes(shape = !!sym(input$nj_tipshape_mapping),
+              color = !!sym(input$nj_tipcolor_mapping)),
+          alpha = input$nj_tippoint_alpha,
+          size = nj_tippoint_size()
+        )
+      } else {
+        geom_tippoint(
+          alpha = input$nj_tippoint_alpha,
+          colour = input$nj_tippoint_color,
+          fill = input$nj_tippoint_color,
+          shape = input$nj_tippoint_shape,
+          size = nj_tippoint_size()
+        )
+      } 
+    } else {NULL}
+  })
+  
+  # Nodepoints
+  nj_nodepoint <- reactive({
+    if(input$nj_nodepoint_show == TRUE) {
+      geom_nodepoint(
+        alpha = input$nj_nodepoint_alpha,
+        color = input$nj_nodepoint_color,
+        shape = input$nj_nodepoint_shape,
+        size = nj_nodepoint_size()
+      )
+    } else {NULL}
+  })
+  
+  # Nodepoint size
+  nj_nodepoint_size <- reactive({
+    if(!is.null(input$nj_nodepoint_size)) {
+      input$nj_nodepoint_size
+    } else {
+      Vis$nodepointsize_nj
+    }
+  })
+  
+  # NJ circular or not
+  nj_tiplab <- reactive({
+    if(input$nj_tiplab_show == TRUE) {
+      if(input$nj_layout == "circular") {
+        if(input$nj_mapping_show == TRUE) {
+          geom_tiplab(
+            nj_mapping_tiplab(), 
+            geom = "text",
+            size = nj_tiplab_size(),
+            alpha = input$nj_tiplab_alpha,
+            fontface = input$nj_tiplab_fontface,
+            align = as.logical(input$nj_align),
+            hjust = as.numeric(input$nj_tiplab_position),
+            check.overlap = input$nj_tiplab_overlap
+          )
+        } else {
+          geom_tiplab(
+            nj_mapping_tiplab(),
+            color = input$nj_tiplab_color,
+            geom = "text",
+            size = nj_tiplab_size(),
+            alpha = input$nj_tiplab_alpha,
+            fontface = input$nj_tiplab_fontface,
+            align = as.logical(input$nj_align),
+            hjust = as.numeric(input$nj_tiplab_position),
+            check.overlap = input$nj_tiplab_overlap
+          )
+        }
+      } else if (input$nj_layout == "inward") {
+        if(input$nj_mapping_show == TRUE) {
+          geom_tiplab(
+            nj_mapping_tiplab(), 
+            geom = "text",
+            size = nj_tiplab_size(),
+            alpha = input$nj_tiplab_alpha,
+            fontface = input$nj_tiplab_fontface,
+            align = as.logical(input$nj_align),
+            hjust = as.numeric(input$nj_tiplab_position_inw),
+            check.overlap = input$nj_tiplab_overlap
+          )
+        } else {
+          geom_tiplab(
+            nj_mapping_tiplab(),
+            color = input$nj_tiplab_color,
+            geom = "text",
+            size = nj_tiplab_size(),
+            alpha = input$nj_tiplab_alpha,
+            fontface = input$nj_tiplab_fontface,
+            align = as.logical(input$nj_align),
+            hjust = as.numeric(input$nj_tiplab_position_inw),
+            check.overlap = input$nj_tiplab_overlap
+          )
+        }
+      } else {
+        if(input$nj_mapping_show == TRUE) {
+          if(input$nj_geom == TRUE) {
+            geom_tiplab(
+              nj_mapping_tiplab(), 
+              geom = nj_geom(),
+              angle = input$nj_tiplab_angle,
+              size = nj_tiplab_size(),
+              alpha = input$nj_tiplab_alpha,
+              fontface = input$nj_tiplab_fontface,
+              align = as.logical(input$nj_align),
+              nudge_x = input$nj_tiplab_nudge_x,
+              check.overlap = input$nj_tiplab_overlap,
+              label.padding = unit(nj_tiplab_padding(), "lines"),
+              label.r = unit(input$nj_tiplab_labelradius, "lines"), 
+              fill = input$nj_tiplab_fill
+            )
+          } else {
+            geom_tiplab(
+              nj_mapping_tiplab(), 
+              geom = nj_geom(),
+              angle = input$nj_tiplab_angle,
+              size = nj_tiplab_size(),
+              alpha = input$nj_tiplab_alpha,
+              fontface = input$nj_tiplab_fontface,
+              align = as.logical(input$nj_align),
+              nudge_x = input$nj_tiplab_nudge_x,
+              check.overlap = input$nj_tiplab_overlap
+            )
+          }
+        } else {
+          if(input$nj_geom == TRUE) {
+            geom_tiplab(
+              nj_mapping_tiplab(), 
+              geom = nj_geom(),
+              color = input$nj_tiplab_color,
+              angle = input$nj_tiplab_angle,
+              size = nj_tiplab_size(),
+              alpha = input$nj_tiplab_alpha,
+              fontface = input$nj_tiplab_fontface,
+              align = as.logical(input$nj_align),
+              nudge_x = input$nj_tiplab_nudge_x,
+              check.overlap = input$nj_tiplab_overlap,
+              label.padding = unit(nj_tiplab_padding(), "lines"),
+              label.r = unit(input$nj_tiplab_labelradius, "lines"), 
+              fill = input$nj_tiplab_fill
+            )
+          } else {
+            geom_tiplab(
+              nj_mapping_tiplab(), 
+              geom = nj_geom(),
+              color = input$nj_tiplab_color,
+              angle = input$nj_tiplab_angle,
+              size = nj_tiplab_size(),
+              alpha = input$nj_tiplab_alpha,
+              fontface = input$nj_tiplab_fontface,
+              align = as.logical(input$nj_align),
+              nudge_x = input$nj_tiplab_nudge_x,
+              check.overlap = input$nj_tiplab_overlap
+            )
+          }
+        }
+      }
+    } else {NULL}
+  })
+  
+  # Tip panel size
+  nj_tiplab_padding <- reactive({
+    if(!is.null(input$nj_tiplab_padding)) {
+      input$nj_tiplab_padding
+    } else {
+      Vis$tiplab_padding_nj
+    }
+  })
+  
+  # Tiplab size
+  nj_tiplab_size <- reactive({
+    if(!is.null(input$nj_tiplab_size)) {
+      input$nj_tiplab_size
+    } else {
+      Vis$labelsize_nj
+    }
+  })
+  
+  # Tippoint size
+  nj_tippoint_size <- reactive({
+    if(!is.null(input$nj_tippoint_size)) {
+      input$nj_tippoint_size
+    } else {
+      Vis$tippointsize_nj
+    }
+  })
+  
+  # Show Label Panels?
+  nj_geom <- reactive({
+    if(input$nj_geom == TRUE) {
+      "label"
+    } else {"text"}
+  })
+  
+  # NJ Tiplab color
+  nj_mapping_tiplab <- reactive({
+    if(input$nj_mapping_show == TRUE) {
+      if(!is.null(input$nj_tiplab)) {
+        aes(label = !!sym(input$nj_tiplab),
+            color = !!sym(input$nj_color_mapping))
+      } else {
+        aes(label = !!sym("Assembly Name"),
+            color = !!sym(input$nj_color_mapping))
+      }
+    } else {
+      if(!is.null(input$nj_tiplab)) {
+        aes(label = !!sym(input$nj_tiplab))
+      } else {
+        aes(label = !!sym("Assembly Name"))
+      }
+    }
+  })
+  
+  # NJ Tree Layout
+  layout_nj <- reactive({
+    if(input$nj_layout == "inward") {
+      "circular"
+    } else {input$nj_layout}
+  })
+  
+  # NJ inward circular
+  nj_inward <- reactive({
+    if (input$nj_layout == "inward") {
+      layout_inward_circular(xlim = input$nj_inward_xlim)
+    } else {
+      NULL
+    }
+  })
+  
+  #### UPGMA ----
+  
+  upgma_tree <- reactive({
+    if(input$upgma_nodelabel_show == TRUE) {
+      ggtree(Vis$upgma, alpha = 0.2, layout = layout_upgma()) + 
+        geom_nodelab(aes(label = node), color = "#29303A", size = upgma_tiplab_size() + 1, hjust = 0.7) +
+        upgma_limit() +
+        upgma_inward() 
+    } else {
+      tree <-
+        ggtree(Vis$upgma, 
+               color = input$upgma_color,
+               layout = layout_upgma(),
+               ladderize = input$upgma_ladder) %<+% Vis$meta_upgma +
+        upgma_tiplab() +
+        upgma_tiplab_scale() + 
+        new_scale_color() +
+        upgma_limit() +
+        upgma_inward() +
+        upgma_label_branch() +
+        upgma_treescale() +
+        upgma_nodepoint() +
+        upgma_tippoint() +
+        upgma_tippoint_scale() + 
+        new_scale_color() +
+        upgma_clip_label() +
+        upgma_rootedge() +
+        upgma_clades() +
+        ggtitle(label = input$upgma_title,
+                subtitle = input$upgma_subtitle) +
+        theme_tree(bgcolor = input$upgma_bg) +
+        theme(plot.title = element_text(colour = input$upgma_title_color,
+                                        size = input$upgma_title_size),
+              plot.subtitle = element_text(colour = input$upgma_title_color,
+                                           size = input$upgma_subtitle_size),
+              legend.background = element_rect(fill = input$upgma_bg),
+              legend.direction = input$upgma_legend_orientation,
+              legend.title = element_text(color = input$upgma_color,
+                                          size = input$upgma_legend_size*1.2),
+              legend.title.align = 0.5,
+              legend.position = upgma_legend_pos(),
+              legend.text = element_text(color = input$upgma_color, 
+                                         size = input$upgma_legend_size),
+              legend.key = element_rect(fill = input$upgma_bg),
+              legend.box.spacing = unit(1.5, "cm"),
+              legend.key.size = unit(0.05*input$upgma_legend_size, 'cm'),
+              plot.background = element_rect(fill = input$upgma_bg, color = input$upgma_bg)) +
+        new_scale_fill() +
+        upgma_fruit() +
+        upgma_gradient() +
+        new_scale_fill() +
+        upgma_fruit2() +
+        upgma_gradient2() +
+        new_scale_fill() +
+        upgma_fruit3() +
+        upgma_gradient3() +
+        new_scale_fill() +
+        upgma_fruit4() +
+        upgma_gradient4() +
+        new_scale_fill() +
+        upgma_fruit5() +
+        upgma_gradient5() +
+        new_scale_fill() 
+      
+      # Add custom labels
+      if(length(Vis$custom_label_upgma) > 0) {
+        
+        for(i in Vis$custom_label_upgma[,1]) {
+          
+          if(!is.null(Vis$upgma_label_pos_x[[i]])) {
+            x_pos <- Vis$upgma_label_pos_x[[i]]
+          } else {
+            x_pos <- round(Vis$upgma_max_x / 2, 0)
+          }
+          
+          if(!is.null(Vis$upgma_label_pos_y[[i]])) {
+            y_pos <- Vis$upgma_label_pos_y[[i]]
+          } else {
+            y_pos <- sum(DB$data$Include) / 2
+          }
+          
+          if(!is.null(Vis$upgma_label_size[[i]])) {
+            size <- Vis$upgma_label_size[[i]]
+          } else {
+            size <- 5
+          }
+          
+          tree <- tree + annotate("text",
+                                  x = x_pos,
+                                  y = y_pos, 
+                                  label = i,
+                                  size = size)
+        }
+      }
+      
+      # Add heatmap
+      if(input$upgma_heatmap_show == TRUE & length(input$upgma_heatmap_select) > 0) {
+        if (!(any(sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)) & 
+              any(!sapply(Vis$meta_upgma[input$upgma_heatmap_select], is.numeric)))) {
+          tree <- gheatmap.mod(tree, 
+                               data = select(Vis$meta_upgma, input$upgma_heatmap_select),
+                               offset = upgma_heatmap_offset(),
+                               width = upgma_heatmap_width(),
+                               legend_title = input$upgma_heatmap_title,
+                               colnames_angle = -upgma_colnames_angle(),
+                               colnames_offset_y = upgma_colnames_y(),
+                               colnames_color = input$upgma_color) +
+            upgma_heatmap_scale()
+        }
+      } 
+      
+      # Sizing control
+      Vis$upgma_plot <- ggplotify::as.ggplot(tree, 
+                                             scale = input$upgma_zoom,
+                                             hjust = input$upgma_h,
+                                             vjust = input$upgma_v)  
+      
+      # Correct background color if zoomed out
+      cowplot::ggdraw(Vis$upgma_plot) + 
+        theme(plot.background = element_rect(fill = input$upgma_bg, color = input$upgma_bg))
+    }
+  })
+  
+  # Heatmap width
+  upgma_heatmap_width <- reactive({
+    if(!is.null(input$upgma_heatmap_width)) {
+      input$upgma_heatmap_width
+    } else {
+      length_input <- length(input$upgma_heatmap_select)
+      if((!(input$upgma_layout == "circular")) & (!(input$upgma_layout == "inward"))) {
+        if(length_input < 3) {
+          0.1
+        } else {
+          if (length_input >= 3 && length_input <= 50) {
+            min(0.15 + 0.05 * floor((length_input - 3) / 2), 1.5)
+          } else {
+            1.5
+          }   
+        }
+      } else {
+        if(length_input < 3) {
+          0.3
+        } else if (length_input >= 3 && length_input <= 27) {
+          min(0.6 + 0.2 * floor((length_input - 3) / 2), 1.5)
+        } else {
+          3
+        }
+      }
+    }
+  })
+  
+  # Heatmap column titles position
+  upgma_colnames_y <- reactive({
+    if(!is.null(input$upgma_colnames_y)) {
+      input$upgma_colnames_y
+    } else {
+      if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
+        0
+      } else {-1}
+    }
+  })
+  
+  # Heatmap column titles angle
+  upgma_colnames_angle <- reactive({
+    if(!is.null(input$upgma_colnames_angle)) {
+      input$upgma_colnames_angle
+    } else {
+      if(!is.null(input$upgma_layout)) {
+        if(input$upgma_layout == "inward" | input$upgma_layout == "circular") {
+          90
+        } else {-90}
+      } else {-90}
+    }
+  })
+  
+  # Heatmap scale
+  upgma_heatmap_scale <- reactive({
+    if(!is.null(input$upgma_heatmap_scale) & !is.null(input$upgma_heatmap_div_mid)) {
+      if(input$upgma_heatmap_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$upgma_heatmap_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$upgma_heatmap_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_heatmap_select]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_heatmap_select]), na.rm = TRUE)
+        }
+        scale_fill_gradient2(low = brewer.pal(3, input$upgma_heatmap_scale)[1],
+                             mid = brewer.pal(3, input$upgma_heatmap_scale)[2],
+                             high = brewer.pal(3, input$upgma_heatmap_scale)[3],
+                             midpoint = midpoint,
+                             name = input$upgma_heatmap_title)
+      } else {
+        if(input$upgma_heatmap_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_upgma[input$upgma_heatmap_select])) == "numeric") {
+            if(input$upgma_heatmap_scale == "magma") {
+              scale_fill_viridis(option = "A",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "inferno") {
+              scale_fill_viridis(option = "B",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "plasma") {
+              scale_fill_viridis(option = "C",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "viridis") {
+              scale_fill_viridis(option = "D",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "cividis") {
+              scale_fill_viridis(option = "E",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "rocket") {
+              scale_fill_viridis(option = "F",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "mako") {
+              scale_fill_viridis(option = "G",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "turbo") {
+              scale_fill_viridis(option = "H",
+                                 name = input$upgma_heatmap_title)
+            } 
+          } else {
+            if(input$upgma_heatmap_scale == "magma") {
+              scale_fill_viridis(discrete = TRUE, option = "A",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "inferno") {
+              scale_fill_viridis(discrete = TRUE, option = "B",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "plasma") {
+              scale_fill_viridis(discrete = TRUE, option = "C",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "viridis") {
+              scale_fill_viridis(discrete = TRUE, option = "D",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "cividis") {
+              scale_fill_viridis(discrete = TRUE, option = "E",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "rocket") {
+              scale_fill_viridis(discrete = TRUE, option = "F",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "mako") {
+              scale_fill_viridis(discrete = TRUE, option = "G",
+                                 name = input$upgma_heatmap_title)
+            } else if(input$upgma_heatmap_scale == "turbo") {
+              scale_fill_viridis(discrete = TRUE, option = "H",
+                                 name = input$upgma_heatmap_title)
+            } 
+          }
+        } else {
+          scale_fill_brewer(palette = input$upgma_heatmap_scale,
+                            name = input$upgma_heatmap_title)
+        }
+      }
+    }
+  })
+  
+  # Tippoint Scale
+  upgma_tippoint_scale <- reactive({
+    if(!is.null(input$upgma_tippoint_scale) & !is.null(input$upgma_tipcolor_mapping_div_mid)) {
+      if(input$upgma_tippoint_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$upgma_tipcolor_mapping_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$upgma_tipcolor_mapping_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_tipcolor_mapping]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_tipcolor_mapping]), na.rm = TRUE)
+        }
+        scale_color_gradient2(low = brewer.pal(3, input$upgma_tippoint_scale)[1],
+                              mid = brewer.pal(3, input$upgma_tippoint_scale)[2],
+                              high = brewer.pal(3, input$upgma_tippoint_scale)[3],
+                              midpoint = midpoint)
+      } else {
+        if(input$upgma_tippoint_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_upgma[input$upgma_tipcolor_mapping])) == "numeric") {
+            if(input$upgma_tippoint_scale == "magma") {
+              scale_color_viridis(option = "A")
+            } else if(input$upgma_tippoint_scale == "inferno") {
+              scale_color_viridis(option = "B")
+            } else if(input$upgma_tippoint_scale == "plasma") {
+              scale_color_viridis(option = "C")
+            } else if(input$upgma_tippoint_scale == "viridis") {
+              scale_color_viridis(option = "D")
+            } else if(input$upgma_tippoint_scale == "cividis") {
+              scale_color_viridis(option = "E")
+            } else if(input$upgma_tippoint_scale == "rocket") {
+              scale_color_viridis(option = "F")
+            } else if(input$upgma_tippoint_scale == "mako") {
+              scale_color_viridis(option = "G")
+            } else if(input$upgma_tippoint_scale == "turbo") {
+              scale_color_viridis(option = "H")
+            } 
+          } else {
+            if(input$upgma_tippoint_scale == "magma") {
+              scale_color_viridis(discrete = TRUE, option = "A")
+            } else if(input$upgma_tippoint_scale == "inferno") {
+              scale_color_viridis(discrete = TRUE, option = "B")
+            } else if(input$upgma_tippoint_scale == "plasma") {
+              scale_color_viridis(discrete = TRUE, option = "C")
+            } else if(input$upgma_tippoint_scale == "viridis") {
+              scale_color_viridis(discrete = TRUE, option = "D")
+            } else if(input$upgma_tippoint_scale == "cividis") {
+              scale_color_viridis(discrete = TRUE, option = "E")
+            } else if(input$upgma_tippoint_scale == "rocket") {
+              scale_color_viridis(discrete = TRUE, option = "F")
+            } else if(input$upgma_tippoint_scale == "mako") {
+              scale_color_viridis(discrete = TRUE, option = "G")
+            } else if(input$upgma_tippoint_scale == "turbo") {
+              scale_color_viridis(discrete = TRUE, option = "H")
+            } 
+          }
+        } else {
+          scale_color_brewer(palette = input$upgma_tippoint_scale)
+        }
+      }
+    }
+  })
+  
+  # Tiplab Scale
+  upgma_tiplab_scale <- reactive({
+    if(!is.null(input$upgma_tiplab_scale) & !is.null(input$upgma_color_mapping_div_mid)) {
+      if(input$upgma_tiplab_scale %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+        if(input$upgma_color_mapping_div_mid == "Zero") {
+          midpoint <- 0
+        } else if(input$upgma_color_mapping_div_mid == "Mean") {
+          midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_color_mapping]), na.rm = TRUE)
+        } else {
+          midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_color_mapping]), na.rm = TRUE)
+        }
+        scale_color_gradient2(low = brewer.pal(3, input$upgma_tiplab_scale)[1],
+                              mid = brewer.pal(3, input$upgma_tiplab_scale)[2],
+                              high = brewer.pal(3, input$upgma_tiplab_scale)[3],
+                              midpoint = midpoint)
+      } else {
+        if(input$upgma_tiplab_scale %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+          if(class(unlist(Vis$meta_upgma[input$upgma_color_mapping])) == "numeric") {
+            if(input$upgma_tiplab_scale == "magma") {
+              scale_color_viridis(option = "A")
+            } else if(input$upgma_tiplab_scale == "inferno") {
+              scale_color_viridis(option = "B")
+            } else if(input$upgma_tiplab_scale == "plasma") {
+              scale_color_viridis(option = "C")
+            } else if(input$upgma_tiplab_scale == "viridis") {
+              scale_color_viridis(option = "D")
+            } else if(input$upgma_tiplab_scale == "cividis") {
+              scale_color_viridis(option = "E")
+            } else if(input$upgma_tiplab_scale == "rocket") {
+              scale_color_viridis(option = "F")
+            } else if(input$upgma_tiplab_scale == "mako") {
+              scale_color_viridis(option = "G")
+            } else if(input$upgma_tiplab_scale == "turbo") {
+              scale_color_viridis(option = "H")
+            } 
+          } else {
+            if(input$upgma_tiplab_scale == "magma") {
+              scale_color_viridis(discrete = TRUE, option = "A")
+            } else if(input$upgma_tiplab_scale == "inferno") {
+              scale_color_viridis(discrete = TRUE, option = "B")
+            } else if(input$upgma_tiplab_scale == "plasma") {
+              scale_color_viridis(discrete = TRUE, option = "C")
+            } else if(input$upgma_tiplab_scale == "viridis") {
+              scale_color_viridis(discrete = TRUE, option = "D")
+            } else if(input$upgma_tiplab_scale == "cividis") {
+              scale_color_viridis(discrete = TRUE, option = "E")
+            } else if(input$upgma_tiplab_scale == "rocket") {
+              scale_color_viridis(discrete = TRUE, option = "F")
+            } else if(input$upgma_tiplab_scale == "mako") {
+              scale_color_viridis(discrete = TRUE, option = "G")
+            } else if(input$upgma_tiplab_scale == "turbo") {
+              scale_color_viridis(discrete = TRUE, option = "H")
+            } 
+          }
+        } else {
+          scale_color_brewer(palette = input$upgma_tiplab_scale)
+        }
+      }
+    }
+  })
+  
+  # Clade Highlight
+  upgma_clades <- reactive({
+    if(!is.null(input$upgma_parentnode)) {
+      if(!length(input$upgma_parentnode) == 0) {
+        if(length(input$upgma_parentnode) == 1) {
+          fill <- input$upgma_clade_scale
+        } else if (length(input$upgma_parentnode) == 2) {
+          if(startsWith(input$upgma_clade_scale, "#")) {
+            fill <- brewer.pal(3, "Set1")[1:2]
+          } else {
+            fill <- brewer.pal(3, input$upgma_clade_scale)[1:2]
+          }
+        } else {
+          fill <- brewer.pal(length(input$upgma_parentnode), input$upgma_clade_scale)
+        }
+        geom_hilight(node = as.numeric(input$upgma_parentnode),
+                     fill = fill,
+                     type = input$upgma_clade_type,
+                     to.bottom = TRUE)
+      } else {NULL}
+    }
+  })
+  
+  # Legend Position
+  upgma_legend_pos <- reactive({
+    if(!is.null(input$upgma_legend_x) & !is.null(input$upgma_legend_y)) {
+      c(input$upgma_legend_x, input$upgma_legend_y)
+    } else {
+      c(0.1, 1)
+    }
+  })
+  
+  # Heatmap offset
+  upgma_heatmap_offset <- reactive({
+    if(is.null(input$upgma_heatmap_offset)) {
+      0
+    } else {input$upgma_heatmap_offset}
+  })
+  
+  # Tiles fill color gradient
+  upgma_gradient <- reactive({
+    if(!is.null(input$upgma_tiles_show_1) & 
+       !is.null(input$upgma_fruit_variable) & 
+       !is.null(input$upgma_tiles_scale_1) &
+       !is.null(input$upgma_tiles_mapping_div_mid_1)) {
+      if(input$upgma_tiles_show_1 == TRUE) {
+        if(input$upgma_tiles_scale_1 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$upgma_tiles_mapping_div_mid_1 == "Zero") {
+            midpoint <- 0
+          } else if(input$upgma_tiles_mapping_div_mid_1 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable]), na.rm = TRUE)
+          }
+          scale_fill_gradient2(low = brewer.pal(3, input$upgma_tiles_scale_1)[1],
+                               mid = brewer.pal(3, input$upgma_tiles_scale_1)[2],
+                               high = brewer.pal(3, input$upgma_tiles_scale_1)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$upgma_tiles_scale_1 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
+              if(input$upgma_tiles_scale_1 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$upgma_tiles_scale_1 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$upgma_tiles_scale_1 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$upgma_tiles_scale_1 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$upgma_tiles_scale_1 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$upgma_tiles_scale_1 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$upgma_tiles_scale_1 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$upgma_tiles_scale_1 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$upgma_tiles_scale_1 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$upgma_tiles_scale_1 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$upgma_tiles_scale_1 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$upgma_tiles_scale_1 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$upgma_tiles_scale_1 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$upgma_tiles_scale_1 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$upgma_tiles_scale_1 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$upgma_tiles_scale_1 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$upgma_tiles_scale_1)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_gradient2 <- reactive({
+    if(!is.null(input$upgma_tiles_show_2) & 
+       !is.null(input$upgma_fruit_variable_2) & 
+       !is.null(input$upgma_tiles_scale_2) &
+       !is.null(input$upgma_tiles_mapping_div_mid_2)) {
+      if(input$upgma_tiles_show_2 == TRUE) {
+        if(input$upgma_tiles_scale_2 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$upgma_tiles_mapping_div_mid_2 == "Zero") {
+            midpoint <- 0
+          } else if(input$upgma_tiles_mapping_div_mid_2 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_2]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_2]), na.rm = TRUE)
+          }
+          scale_fill_gradient2(low = brewer.pal(3, input$upgma_tiles_scale_2)[1],
+                               mid = brewer.pal(3, input$upgma_tiles_scale_2)[2],
+                               high = brewer.pal(3, input$upgma_tiles_scale_2)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$upgma_tiles_scale_2 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_2])) == "numeric") {
+              if(input$upgma_tiles_scale_2 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$upgma_tiles_scale_2 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$upgma_tiles_scale_2 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$upgma_tiles_scale_2 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$upgma_tiles_scale_2 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$upgma_tiles_scale_2 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$upgma_tiles_scale_2 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$upgma_tiles_scale_2 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$upgma_tiles_scale_2 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$upgma_tiles_scale_2 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$upgma_tiles_scale_2 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$upgma_tiles_scale_2 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$upgma_tiles_scale_2 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$upgma_tiles_scale_2 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$upgma_tiles_scale_2 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$upgma_tiles_scale_2 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$upgma_tiles_scale_2)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_gradient3 <- reactive({
+    if(!is.null(input$upgma_tiles_show_3) & 
+       !is.null(input$upgma_fruit_variable_3) & 
+       !is.null(input$upgma_tiles_scale_3) &
+       !is.null(input$upgma_tiles_mapping_div_mid_3)) {
+      if(input$upgma_tiles_show_3 == TRUE) {
+        if(input$upgma_tiles_scale_3 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$upgma_tiles_mapping_div_mid_3 == "Zero") {
+            midpoint <- 0
+          } else if(input$upgma_tiles_mapping_div_mid_3 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_3]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_3]), na.rm = TRUE)
+          }
+          scale_fill_gradient3(low = brewer.pal(3, input$upgma_tiles_scale_3)[1],
+                               mid = brewer.pal(3, input$upgma_tiles_scale_3)[2],
+                               high = brewer.pal(3, input$upgma_tiles_scale_3)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$upgma_tiles_scale_3 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_3])) == "numeric") {
+              if(input$upgma_tiles_scale_3 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$upgma_tiles_scale_3 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$upgma_tiles_scale_3 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$upgma_tiles_scale_3 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$upgma_tiles_scale_3 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$upgma_tiles_scale_3 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$upgma_tiles_scale_3 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$upgma_tiles_scale_3 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$upgma_tiles_scale_3 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$upgma_tiles_scale_3 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$upgma_tiles_scale_3 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$upgma_tiles_scale_3 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$upgma_tiles_scale_3 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$upgma_tiles_scale_3 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$upgma_tiles_scale_3 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$upgma_tiles_scale_3 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$upgma_tiles_scale_3)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_gradient4 <- reactive({
+    if(!is.null(input$upgma_tiles_show_4) & 
+       !is.null(input$upgma_fruit_variable_4) & 
+       !is.null(input$upgma_tiles_scale_4) &
+       !is.null(input$upgma_tiles_mapping_div_mid_4)) {
+      if(input$upgma_tiles_show_4 == TRUE) {
+        if(input$upgma_tiles_scale_4 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$upgma_tiles_mapping_div_mid_4 == "Zero") {
+            midpoint <- 0
+          } else if(input$upgma_tiles_mapping_div_mid_4 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_4]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_4]), na.rm = TRUE)
+          }
+          scale_fill_gradient4(low = brewer.pal(3, input$upgma_tiles_scale_4)[1],
+                               mid = brewer.pal(3, input$upgma_tiles_scale_4)[2],
+                               high = brewer.pal(3, input$upgma_tiles_scale_4)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$upgma_tiles_scale_4 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable])) == "numeric") {
+              if(input$upgma_tiles_scale_4 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$upgma_tiles_scale_4 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$upgma_tiles_scale_4 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$upgma_tiles_scale_4 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$upgma_tiles_scale_4 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$upgma_tiles_scale_4 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$upgma_tiles_scale_4 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$upgma_tiles_scale_4 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$upgma_tiles_scale_4 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$upgma_tiles_scale_4 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$upgma_tiles_scale_4 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$upgma_tiles_scale_4 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$upgma_tiles_scale_4 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$upgma_tiles_scale_4 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$upgma_tiles_scale_4 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$upgma_tiles_scale_4 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$upgma_tiles_scale_4)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_gradient5 <- reactive({
+    if(!is.null(input$upgma_tiles_show_5) & 
+       !is.null(input$upgma_fruit_variable_5) & 
+       !is.null(input$upgma_tiles_scale_5) &
+       !is.null(input$upgma_tiles_mapping_div_mid_5)) {
+      if(input$upgma_tiles_show_5 == TRUE) {
+        if(input$upgma_tiles_scale_5 %in% c("Spectral", "RdYlGn", "RdYlBu", "RdGy", "RdBu", "PuOr", "PRGn", "PiYG", "BrBG")) {
+          if(input$upgma_tiles_mapping_div_mid_5 == "Zero") {
+            midpoint <- 0
+          } else if(input$upgma_tiles_mapping_div_mid_5 == "Mean") {
+            midpoint <- mean(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_5]), na.rm = TRUE)
+          } else {
+            midpoint <- median(as.matrix(Vis$meta_upgma[input$upgma_fruit_variable_5]), na.rm = TRUE)
+          }
+          scale_fill_gradient5(low = brewer.pal(3, input$upgma_tiles_scale_5)[1],
+                               mid = brewer.pal(3, input$upgma_tiles_scale_5)[2],
+                               high = brewer.pal(3, input$upgma_tiles_scale_5)[3],
+                               midpoint = midpoint)
+        } else {
+          if(input$upgma_tiles_scale_5 %in% c("magma", "inferno", "plasma", "viridis", "cividis", "rocket", "mako", "turbo")) {
+            if(class(unlist(Vis$meta_upgma[input$upgma_fruit_variable_5])) == "numeric") {
+              if(input$upgma_tiles_scale_5 == "magma") {
+                scale_fill_viridis(option = "A")
+              } else if(input$upgma_tiles_scale_5 == "inferno") {
+                scale_fill_viridis(option = "B")
+              } else if(input$upgma_tiles_scale_5 == "plasma") {
+                scale_fill_viridis(option = "C")
+              } else if(input$upgma_tiles_scale_5 == "viridis") {
+                scale_fill_viridis(option = "D")
+              } else if(input$upgma_tiles_scale_5 == "cividis") {
+                scale_fill_viridis(option = "E")
+              } else if(input$upgma_tiles_scale_5 == "rocket") {
+                scale_fill_viridis(option = "F")
+              } else if(input$upgma_tiles_scale_5 == "mako") {
+                scale_fill_viridis(option = "G")
+              } else if(input$upgma_tiles_scale_5 == "turbo") {
+                scale_fill_viridis(option = "H")
+              } 
+            } else {
+              if(input$upgma_tiles_scale_5 == "magma") {
+                scale_fill_viridis(discrete = TRUE, option = "A")
+              } else if(input$upgma_tiles_scale_5 == "inferno") {
+                scale_fill_viridis(discrete = TRUE, option = "B")
+              } else if(input$upgma_tiles_scale_5 == "plasma") {
+                scale_fill_viridis(discrete = TRUE, option = "C")
+              } else if(input$upgma_tiles_scale_5 == "viridis") {
+                scale_fill_viridis(discrete = TRUE, option = "D")
+              } else if(input$upgma_tiles_scale_5 == "cividis") {
+                scale_fill_viridis(discrete = TRUE, option = "E")
+              } else if(input$upgma_tiles_scale_5 == "rocket") {
+                scale_fill_viridis(discrete = TRUE, option = "F")
+              } else if(input$upgma_tiles_scale_5 == "mako") {
+                scale_fill_viridis(discrete = TRUE, option = "G")
+              } else if(input$upgma_tiles_scale_5 == "turbo") {
+                scale_fill_viridis(discrete = TRUE, option = "H")
+              } 
+            }
+          } else {
+            scale_fill_brewer(palette = input$upgma_tiles_scale_5)
+          }
+        }
+      } else {NULL}
+    }
+  })
+  
+  # No label clip off for linear upgma tree
+  upgma_clip_label <- reactive({
+    if(!(input$upgma_layout == "circular" | input$upgma_layout == "inward")) {
+      coord_cartesian(clip = "off")
+    } else {NULL}
+  })
+  
+  # Geom Fruit
+  upgma_fruit <- reactive({
+    if((!is.null(input$upgma_tiles_show_1)) & 
+       (!is.null(input$upgma_fruit_variable)) & 
+       (!is.null(input$upgma_layout)) & 
+       (!is.null(input$upgma_fruit_offset_circ)) & 
+       (!is.null(input$upgma_fruit_width_circ)) & 
+       (!is.null(input$upgma_fruit_alpha))) {
+      if(input$upgma_tiles_show_1 == TRUE) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
+            offset = input$upgma_fruit_offset_circ,
+            width = input$upgma_fruit_width_circ,
+            alpha = input$upgma_fruit_alpha
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
+            offset = input$upgma_fruit_offset_circ,
+            width = input$upgma_fruit_width_circ,
+            alpha = input$upgma_fruit_alpha
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$upgma_tiles_show_1 == TRUE) {
+        if(!is.null(Vis$upgma_max_x)) {
+          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
+            offset = 0,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable)),
+            offset = 0,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  # Geom Fruit
+  upgma_fruit2 <- reactive({
+    if((!is.null(input$upgma_tiles_show_2)) & 
+       (!is.null(input$upgma_fruit_variable_2)) & 
+       (!is.null(input$upgma_layout)) & 
+       (!is.null(input$upgma_fruit_offset_circ_2)) & 
+       (!is.null(input$upgma_fruit_width_circ_2)) & 
+       (!is.null(input$upgma_fruit_alpha_2))) {
+      if(input$upgma_tiles_show_2 == TRUE) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_2)),
+            offset = input$upgma_fruit_offset_circ_2,
+            width = input$upgma_fruit_width_circ_2,
+            alpha = input$upgma_fruit_alpha_2
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_2)),
+            offset = input$upgma_fruit_offset_circ_2,
+            width = input$upgma_fruit_width_circ_2,
+            alpha = input$upgma_fruit_alpha_2
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$upgma_tiles_show_2 == TRUE) {
+        if(!is.null(Vis$upgma_max_x)) {
+          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_2)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_2)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_fruit3 <- reactive({
+    if((!is.null(input$upgma_tiles_show_3)) & 
+       (!is.null(input$upgma_fruit_variable_3)) & 
+       (!is.null(input$upgma_layout)) & 
+       (!is.null(input$upgma_fruit_offset_circ_3)) & 
+       (!is.null(input$upgma_fruit_width_circ_3)) & 
+       (!is.null(input$upgma_fruit_alpha_3))) {
+      if(input$upgma_tiles_show_3 == TRUE) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_3)),
+            offset = input$upgma_fruit_offset_circ_3,
+            width = input$upgma_fruit_width_circ_3,
+            alpha = input$upgma_fruit_alpha_3
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_3)),
+            offset = input$upgma_fruit_offset_circ_3,
+            width = input$upgma_fruit_width_circ_3,
+            alpha = input$upgma_fruit_alpha_3
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$upgma_tiles_show_3 == TRUE) {
+        if(!is.null(Vis$upgma_max_x)) {
+          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_3)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_3)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  upgma_fruit4 <- reactive({
+    if((!is.null(input$upgma_tiles_show_4)) & 
+       (!is.null(input$upgma_fruit_variable_4)) & 
+       (!is.null(input$upgma_layout)) & 
+       (!is.null(input$upgma_fruit_offset_circ_4)) & 
+       (!is.null(input$upgma_fruit_width_circ_4)) & 
+       (!is.null(input$upgma_fruit_alpha_4))) {
+      if(input$upgma_tiles_show_4 == TRUE) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_4)),
+            offset = input$upgma_fruit_offset_circ_4,
+            width = input$upgma_fruit_width_circ_4,
+            alpha = input$upgma_fruit_alpha_4
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_4)),
+            offset = input$upgma_fruit_offset_circ_4,
+            width = input$upgma_fruit_width_circ_4,
+            alpha = input$upgma_fruit_alpha_4
+          )
+        }
+      } else {
+        if(input$upgma_tiles_show_4 == TRUE) {
+          if(!is.null(Vis$upgma_max_x)) {
+            if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+              width <- 1
+            } else {
+              width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+            }
+          } else {
+            width <- 2
+          }
+          if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+            geom_fruit(
+              geom = geom_tile,
+              mapping = aes(fill= !!sym(input$upgma_fruit_variable_4)),
+              offset = 0.15,
+              width = width * 3,
+              alpha = 1
+            )
+          } else {
+            geom_fruit(
+              geom = geom_tile,
+              mapping = aes(fill= !!sym(input$upgma_fruit_variable_4)),
+              offset = 0.05,
+              width = width,
+              alpha = 1
+            )
+          }
+        } else {NULL}
+      }
+    }
+  })
+  
+  upgma_fruit5 <- reactive({
+    if((!is.null(input$upgma_tiles_show_5)) & 
+       (!is.null(input$upgma_fruit_variable_5)) & 
+       (!is.null(input$upgma_layout)) & 
+       (!is.null(input$upgma_fruit_offset_circ_5)) & 
+       (!is.null(input$upgma_fruit_width_circ_5)) & 
+       (!is.null(input$upgma_fruit_alpha_5))) {
+      if(input$upgma_tiles_show_5 == TRUE) {
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_5)),
+            offset = input$upgma_fruit_offset_circ_5,
+            width = input$upgma_fruit_width_circ_5,
+            alpha = input$upgma_fruit_alpha_5
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill = !!sym(input$upgma_fruit_variable_5)),
+            offset = input$upgma_fruit_offset_circ_5,
+            width = input$upgma_fruit_width_circ_5,
+            alpha = input$upgma_fruit_alpha_5
+          )
+        }
+      } else {NULL}
+    } else {
+      if(input$upgma_tiles_show_5 == TRUE) {
+        if(!is.null(Vis$upgma_max_x)) {
+          if(round(ceiling(Vis$upgma_max_x) * 0.1, 0) < 1) {
+            width <- 1
+          } else {
+            width <- round(ceiling(Vis$upgma_max_x) * 0.033, 0)
+          }
+        } else {
+          width <- 2
+        }
+        if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_5)),
+            offset = 0.15,
+            width = width * 3,
+            alpha = 1
+          )
+        } else {
+          geom_fruit(
+            geom = geom_tile,
+            mapping = aes(fill= !!sym(input$upgma_fruit_variable_5)),
+            offset = 0.05,
+            width = width,
+            alpha = 1
+          )
+        }
+      } else {NULL}
+    }
+  })
+  
+  # Xlim
+  upgma_limit <- reactive({
+    if(input$upgma_layout == "circular") {
+      xlim(input$upgma_xlim, NA)
+    } else {NULL}
+  })
+  
+  # Treescale
+  upgma_treescale <- reactive({
+    if(!input$upgma_layout == "circular") {
+      if(input$upgma_treescale_show == TRUE) {
+        geom_treescale(x = upgma_treescale_x(),
+                       y = upgma_treescale_y(),
+                       width = upgma_treescale_width(),
+                       color = input$upgma_color,
+                       fontsize = 4)
+      } else {NULL}
+    } else {NULL}
+  }) 
+  
+  # Treescale Y Position
+  upgma_treescale_y <- reactive({
+    if(is.null(input$upgma_treescale_y)) {
+      0
+    } else {input$upgma_treescale_y}
+  })
+  
+  # Treescale X Position
+  upgma_treescale_x <- reactive({
+    if(is.null(input$upgma_treescale_x)) {
+      round(ceiling(Vis$upgma_max_x) * 0.2, 0)
+    } else {input$upgma_treescale_x}
+  })
+  
+  # Treescale width
+  upgma_treescale_width <- reactive({
+    if(!is.null(input$upgma_treescale_width)) {
+      input$upgma_treescale_width
+    } else {
+      round(ceiling(Vis$upgma_max_x) * 0.1, 0)
+    }
+  })
+  
+  # Label branches
+  upgma_label_branch <- reactive({
+    if(!input$upgma_layout == "circular" | !input$upgma_layout == "inward") {
+      if(input$upgma_show_branch_label == TRUE) {
+        geom_label(
+          aes(
+            x=!!sym("branch"), 
+            label= !!sym(input$upgma_branch_label)),
+          fill = input$upgma_branch_label_color,
+          size = upgma_branch_size(),
+          label.r = unit(input$upgma_branch_labelradius, "lines"),
+          nudge_x = input$upgma_branch_x,
+          nudge_y = input$upgma_branch_y,
+          fontface = input$upgma_branchlab_fontface,
+          alpha = input$upgma_branchlab_alpha
+        )
+      } else {NULL}
+    } else {NULL}
+  })
+  
+  # Branch label size
+  upgma_branch_size <- reactive({
+    if(!is.null(input$upgma_branch_size)) {
+      input$upgma_branch_size
+    } else {
+      Vis$branch_size_upgma
+    }
+  })
+  
+  # Rootedge
+  upgma_rootedge <- reactive({
+    if(input$upgma_rootedge_show == TRUE) {
+      if(is.null(input$upgma_rootedge_length)) {
+        geom_rootedge(rootedge = round(ceiling(Vis$upgma_max_x) * 0.05, 0),
+                      linetype = input$upgma_rootedge_line)
+      } else {
+        geom_rootedge(rootedge = input$upgma_rootedge_length,
+                      linetype = input$upgma_rootedge_line)
+      }
+    } else {NULL}
+  })
+  
+  # Tippoints
+  upgma_tippoint <- reactive({
+    if(input$upgma_tippoint_show == TRUE | input$upgma_tipcolor_mapping_show == TRUE | input$upgma_tipshape_mapping_show == TRUE) {
+      if(input$upgma_tipcolor_mapping_show == TRUE & input$upgma_tipshape_mapping_show == FALSE) {
+        geom_tippoint(
+          aes(color = !!sym(input$upgma_tipcolor_mapping)),
+          alpha = input$upgma_tippoint_alpha,
+          shape = input$upgma_tippoint_shape,
+          size = upgma_tippoint_size()
+        )
+      } else if (input$upgma_tipcolor_mapping_show == FALSE & input$upgma_tipshape_mapping_show == TRUE) {
+        geom_tippoint(
+          aes(shape = !!sym(input$upgma_tipshape_mapping)),
+          alpha = input$upgma_tippoint_alpha,
+          color = input$upgma_tippoint_color,
+          size = upgma_tippoint_size()
+        )
+      } else if (input$upgma_tipcolor_mapping_show == TRUE & input$upgma_tipshape_mapping_show == TRUE) {
+        geom_tippoint(
+          aes(shape = !!sym(input$upgma_tipshape_mapping),
+              color = !!sym(input$upgma_tipcolor_mapping)),
+          alpha = input$upgma_tippoint_alpha,
+          size = upgma_tippoint_size()
+        )
+      } else {
+        geom_tippoint(
+          alpha = input$upgma_tippoint_alpha,
+          colour = input$upgma_tippoint_color,
+          fill = input$upgma_tippoint_color,
+          shape = input$upgma_tippoint_shape,
+          size = upgma_tippoint_size()
+        )
+      } 
+    } else {NULL}
+  })
+  
+  # Nodepoints
+  upgma_nodepoint <- reactive({
+    if(input$upgma_nodepoint_show == TRUE) {
+      geom_nodepoint(
+        alpha = input$upgma_nodepoint_alpha,
+        color = input$upgma_nodepoint_color,
+        shape = input$upgma_nodepoint_shape,
+        size = upgma_nodepoint_size()
+      )
+    } else {NULL}
+  })
+  
+  # Nodepoint size
+  upgma_nodepoint_size <- reactive({
+    if(!is.null(input$upgma_nodepoint_size)) {
+      input$upgma_nodepoint_size
+    } else {
+      Vis$nodepointsize_upgma
+    }
+  })
+  
+  # upgma circular or not
+  upgma_tiplab <- reactive({
+    if(input$upgma_tiplab_show == TRUE) {
+      if(input$upgma_layout == "circular") {
+        if(input$upgma_mapping_show == TRUE) {
+          geom_tiplab(
+            upgma_mapping_tiplab(), 
+            geom = "text",
+            size = upgma_tiplab_size(),
+            alpha = input$upgma_tiplab_alpha,
+            fontface = input$upgma_tiplab_fontface,
+            align = as.logical(input$upgma_align),
+            hjust = as.numeric(input$upgma_tiplab_position),
+            check.overlap = input$upgma_tiplab_overlap
+          )
+        } else {
+          geom_tiplab(
+            upgma_mapping_tiplab(),
+            color = input$upgma_tiplab_color,
+            geom = "text",
+            size = upgma_tiplab_size(),
+            alpha = input$upgma_tiplab_alpha,
+            fontface = input$upgma_tiplab_fontface,
+            align = as.logical(input$upgma_align),
+            hjust = as.numeric(input$upgma_tiplab_position),
+            check.overlap = input$upgma_tiplab_overlap
+          )
+        }
+      } else if (input$upgma_layout == "inward") {
+        if(input$upgma_mapping_show == TRUE) {
+          geom_tiplab(
+            upgma_mapping_tiplab(), 
+            geom = "text",
+            size = upgma_tiplab_size(),
+            alpha = input$upgma_tiplab_alpha,
+            fontface = input$upgma_tiplab_fontface,
+            align = as.logical(input$upgma_align),
+            hjust = as.numeric(input$upgma_tiplab_position_inw),
+            check.overlap = input$upgma_tiplab_overlap
+          )
+        } else {
+          geom_tiplab(
+            upgma_mapping_tiplab(),
+            color = input$upgma_tiplab_color,
+            geom = "text",
+            size = upgma_tiplab_size(),
+            alpha = input$upgma_tiplab_alpha,
+            fontface = input$upgma_tiplab_fontface,
+            align = as.logical(input$upgma_align),
+            hjust = as.numeric(input$upgma_tiplab_position_inw),
+            check.overlap = input$upgma_tiplab_overlap
+          )
+        }
+      } else {
+        if(input$upgma_mapping_show == TRUE) {
+          if(input$upgma_geom == TRUE) {
+            geom_tiplab(
+              upgma_mapping_tiplab(), 
+              geom = upgma_geom(),
+              angle = input$upgma_tiplab_angle,
+              size = upgma_tiplab_size(),
+              alpha = input$upgma_tiplab_alpha,
+              fontface = input$upgma_tiplab_fontface,
+              align = as.logical(input$upgma_align),
+              nudge_x = input$upgma_tiplab_nudge_x,
+              check.overlap = input$upgma_tiplab_overlap,
+              label.padding = unit(upgma_tiplab_padding(), "lines"),
+              label.r = unit(input$upgma_tiplab_labelradius, "lines"), 
+              fill = input$upgma_tiplab_fill
+            )
+          } else {
+            geom_tiplab(
+              upgma_mapping_tiplab(), 
+              geom = upgma_geom(),
+              angle = input$upgma_tiplab_angle,
+              size = upgma_tiplab_size(),
+              alpha = input$upgma_tiplab_alpha,
+              fontface = input$upgma_tiplab_fontface,
+              align = as.logical(input$upgma_align),
+              nudge_x = input$upgma_tiplab_nudge_x,
+              check.overlap = input$upgma_tiplab_overlap
+            )
+          }
+        } else {
+          if(input$upgma_geom == TRUE) {
+            geom_tiplab(
+              upgma_mapping_tiplab(), 
+              geom = upgma_geom(),
+              color = input$upgma_tiplab_color,
+              angle = input$upgma_tiplab_angle,
+              size = upgma_tiplab_size(),
+              alpha = input$upgma_tiplab_alpha,
+              fontface = input$upgma_tiplab_fontface,
+              align = as.logical(input$upgma_align),
+              nudge_x = input$upgma_tiplab_nudge_x,
+              check.overlap = input$upgma_tiplab_overlap,
+              label.padding = unit(upgma_tiplab_padding(), "lines"),
+              label.r = unit(input$upgma_tiplab_labelradius, "lines"), 
+              fill = input$upgma_tiplab_fill
+            )
+          } else {
+            geom_tiplab(
+              upgma_mapping_tiplab(), 
+              geom = upgma_geom(),
+              color = input$upgma_tiplab_color,
+              angle = input$upgma_tiplab_angle,
+              size = upgma_tiplab_size(),
+              alpha = input$upgma_tiplab_alpha,
+              fontface = input$upgma_tiplab_fontface,
+              align = as.logical(input$upgma_align),
+              nudge_x = input$upgma_tiplab_nudge_x,
+              check.overlap = input$upgma_tiplab_overlap
+            )
+          }
+        }
+      }
+    } else {NULL}
+  })
+  
+  # Tip panel size
+  upgma_tiplab_padding <- reactive({
+    if(!is.null(input$upgma_tiplab_padding)) {
+      input$upgma_tiplab_padding
+    } else {
+      Vis$tiplab_padding_upgma
+    }
+  })
+  
+  # Tiplab size
+  upgma_tiplab_size <- reactive({
+    if(!is.null(input$upgma_tiplab_size)) {
+      input$upgma_tiplab_size
+    } else {
+      Vis$labelsize_upgma
+    }
+  })
+  
+  # Tippoint size
+  upgma_tippoint_size <- reactive({
+    if(!is.null(input$upgma_tippoint_size)) {
+      input$upgma_tippoint_size
+    } else {
+      Vis$tippointsize_upgma
+    }
+  })
+  
+  # Show Label Panels?
+  upgma_geom <- reactive({
+    if(input$upgma_geom == TRUE) {
+      "label"
+    } else {"text"}
+  })
+  
+  # upgma Tiplab color
+  upgma_mapping_tiplab <- reactive({
+    if(input$upgma_mapping_show == TRUE) {
+      if(!is.null(input$upgma_tiplab)) {
+        aes(label = !!sym(input$upgma_tiplab),
+            color = !!sym(input$upgma_color_mapping))
+      } else {
+        aes(label = !!sym("Assembly Name"),
+            color = !!sym(input$upgma_color_mapping))
+      }
+    } else {
+      if(!is.null(input$upgma_tiplab)) {
+        aes(label = !!sym(input$upgma_tiplab))
+      } else {
+        aes(label = !!sym("Assembly Name"))
+      }
+    }
+  })
+  
+  # upgma Tree Layout
+  layout_upgma <- reactive({
+    if(input$upgma_layout == "inward") {
+      "circular"
+    } else {input$upgma_layout}
+  })
+  
+  # upgma inward circular
+  upgma_inward <- reactive({
+    if (input$upgma_layout == "inward") {
+      layout_inward_circular(xlim = input$upgma_inward_xlim)
+    } else {
+      NULL
+    }
+  })
+  
+  ### Save MST Plot ----
+  output$save_plot_html <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save MST;", paste0("MST_", Sys.Date(), ".html")))
+      paste0("MST_", Sys.Date(), ".html")
+    },
+    content = function(file) {
+      mst_tree() %>% visSave(file = file, background = mst_background_color())
+    }
+  )
+  
+  ### Save NJ Plot ----
+  
+  # Define download handler to save the plot
+  
+  output$download_nj <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save NJ;", paste0("NJ_", Sys.Date(), ".", input$filetype_nj)))
+      paste0("NJ_", Sys.Date(), ".", input$filetype_nj)
+    },
+    content = function(file) {
+      if (input$filetype_nj == "png") {
+        png(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale))
+        print(nj_tree())
+        dev.off()
+      } else if (input$filetype_nj == "jpeg") {
+        jpeg(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale), quality = 100)
+        print(nj_tree())
+        dev.off()
+      } else if (input$filetype_nj == "svg") {
+        plot <- print(nj_tree())
+        ggsave(file=file, plot=plot, device = svg(width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio))/96,
+                                                  height = as.numeric(input$nj_scale)/96))
+      } else if (input$filetype_nj == "bmp") {
+        bmp(file, width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale))
+        print(nj_tree())
+        dev.off()
+      }
+    }
+  )
+  
+  ### Save UPGMA Plot ----
+  
+  # Define download handler to save the plot
+  
+  output$download_upgma <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save UPGMA;", paste0("UPGMA_", Sys.Date(), ".", input$filetype_upgma)))
+      paste0("UPGMA_", Sys.Date(), ".", input$filetype_upgma)
+    },
+    content = function(file) {
+      if (input$filetype_upgma == "png") {
+        png(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale))
+        print(upgma_tree())
+        dev.off()
+      } else if (input$filetype_upgma == "jpeg") {
+        jpeg(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale), quality = 100)
+        print(upgma_tree())
+        dev.off()
+      } else if (input$filetype_upgma == "svg") {
+        plot <- print(upgma_tree())
+        ggsave(file=file, plot=plot, device = svg(width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio))/96,
+                                                  height = as.numeric(input$upgma_scale)/96))
+      } else if (input$filetype_upgma == "bmp") {
+        bmp(file, width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale))
+        print(upgma_tree())
+        dev.off()
+      }
+    }
+  )
+  
+  ### Reactive Events ----
+  
+  # MST cluster reset button
+  observeEvent(input$mst_cluster_reset, {
+    if(!is.null(DB$schemeinfo))
+    updateNumericInput(session, "mst_cluster_threshold", value = as.numeric(DB$schemeinfo[7, 2]))
+  })
+  
+  # Shut off "Align Labels" control for UPGMA trees
+  shinyjs::disable('upgma_align')
+  shinyjs::disable('upgma_tiplab_linesize')
+  shinyjs::disable('upgma_tiplab_linetype')
+  
+  # Conditional disabling of control elemenmts
+  observe({
+    
+    # Tiles for inward layout
+    if(input$nj_layout == "inward") {
+      shinyjs::disable('nj_tiles_show') 
+      shinyjs::disable('nj_tiles_show_2')
+      shinyjs::disable('nj_tiles_show_3') 
+      shinyjs::disable('nj_tiles_show_4')
+      shinyjs::disable('nj_tiles_show_5') 
+      shinyjs::disable('nj_fruit_variable')
+      shinyjs::disable('nj_fruit_variable_2')
+      shinyjs::disable('nj_fruit_variable_3')
+      shinyjs::disable('nj_fruit_variable_4')
+      shinyjs::disable('nj_fruit_variable_5')
+      shinyjs::disable('nj_fruit_width')
+      shinyjs::disable('nj_fruit_width_2')
+      shinyjs::disable('nj_fruit_width_3')
+      shinyjs::disable('nj_fruit_width_4')
+      shinyjs::disable('nj_fruit_width_5')
+      shinyjs::disable('nj_fruit_offset')
+      shinyjs::disable('nj_fruit_offset_2')
+      shinyjs::disable('nj_fruit_offset_3')
+      shinyjs::disable('nj_fruit_offset_4')
+      shinyjs::disable('nj_fruit_offset_5')
+    } else {
+      shinyjs::enable('nj_tiles_show') 
+      shinyjs::enable('nj_tiles_show_2')
+      shinyjs::enable('nj_tiles_show_3') 
+      shinyjs::enable('nj_tiles_show_4')
+      shinyjs::enable('nj_tiles_show_5') 
+      shinyjs::enable('nj_fruit_variable')
+      shinyjs::enable('nj_fruit_variable_2')
+      shinyjs::enable('nj_fruit_variable_3')
+      shinyjs::enable('nj_fruit_variable_4')
+      shinyjs::enable('nj_fruit_variable_5')
+      shinyjs::enable('nj_fruit_width')
+      shinyjs::enable('nj_fruit_width_2')
+      shinyjs::enable('nj_fruit_width_3')
+      shinyjs::enable('nj_fruit_width_4')
+      shinyjs::enable('nj_fruit_width_5')
+      shinyjs::enable('nj_fruit_offset')
+      shinyjs::enable('nj_fruit_offset_2')
+      shinyjs::enable('nj_fruit_offset_3')
+      shinyjs::enable('nj_fruit_offset_4')
+      shinyjs::enable('nj_fruit_offset_5')
+    }
+    
+    if(input$upgma_layout == "inward") {
+      shinyjs::disable('upgma_tiles_show') 
+      shinyjs::disable('upgma_tiles_show_2')
+      shinyjs::disable('upgma_tiles_show_3') 
+      shinyjs::disable('upgma_tiles_show_4')
+      shinyjs::disable('upgma_tiles_show_5') 
+      shinyjs::disable('upgma_fruit_variable')
+      shinyjs::disable('upgma_fruit_variable_2')
+      shinyjs::disable('upgma_fruit_variable_3')
+      shinyjs::disable('upgma_fruit_variable_4')
+      shinyjs::disable('upgma_fruit_variable_5')
+      shinyjs::disable('upgma_fruit_width')
+      shinyjs::disable('upgma_fruit_width_2')
+      shinyjs::disable('upgma_fruit_width_3')
+      shinyjs::disable('upgma_fruit_width_4')
+      shinyjs::disable('upgma_fruit_width_5')
+      shinyjs::disable('upgma_fruit_offset')
+      shinyjs::disable('upgma_fruit_offset_2')
+      shinyjs::disable('upgma_fruit_offset_3')
+      shinyjs::disable('upgma_fruit_offset_4')
+      shinyjs::disable('upgma_fruit_offset_5')
+    } else {
+      shinyjs::enable('upgma_tiles_show') 
+      shinyjs::enable('upgma_tiles_show_2')
+      shinyjs::enable('upgma_tiles_show_3') 
+      shinyjs::enable('upgma_tiles_show_4')
+      shinyjs::enable('upgma_tiles_show_5') 
+      shinyjs::enable('upgma_fruit_variable')
+      shinyjs::enable('upgma_fruit_variable_2')
+      shinyjs::enable('upgma_fruit_variable_3')
+      shinyjs::enable('upgma_fruit_variable_4')
+      shinyjs::enable('upgma_fruit_variable_5')
+      shinyjs::enable('upgma_fruit_width')
+      shinyjs::enable('upgma_fruit_width_2')
+      shinyjs::enable('upgma_fruit_width_3')
+      shinyjs::enable('upgma_fruit_width_4')
+      shinyjs::enable('upgma_fruit_width_5')
+      shinyjs::enable('upgma_fruit_offset')
+      shinyjs::enable('upgma_fruit_offset_2')
+      shinyjs::enable('upgma_fruit_offset_3')
+      shinyjs::enable('upgma_fruit_offset_4')
+      shinyjs::enable('upgma_fruit_offset_5')
+    }
+    
+    # Shut off branch labels for NJ and UPGMA plots for circular layout
+    if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+      shinyjs::disable('nj_show_branch_label')
+    } else {
+      shinyjs::enable('nj_show_branch_label')
+    }
+    
+    if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+      shinyjs::disable('upgma_show_branch_label')
+    } else {
+      shinyjs::enable('upgma_show_branch_label')
+    }
+  })
+  
+  #### Generate Plot ----
+  
+  hamming_nj <- reactive({
+    if(anyNA(DB$allelic_profile)) {
+      if(input$na_handling == "omit") {
+        allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
+        
+        allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
+        
+        compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
+        
+      } else if(input$na_handling == "ignore_na"){
+        compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
+        
+      } else {
+        compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
+      } 
+      
+    } else {compute.distMatrix(DB$allelic_profile_true, hamming.dist)}
+  })
+  
+  hamming_mst <- reactive({
+    if(anyNA(DB$allelic_profile)) {
+      if(input$na_handling == "omit") {
+        allelic_profile_noNA <- DB$allelic_profile[, colSums(is.na(DB$allelic_profile)) == 0]
+        
+        allelic_profile_noNA_true <- allelic_profile_noNA[which(DB$data$Include == TRUE),]
+        
+        dist <- compute.distMatrix(allelic_profile_noNA_true, hamming.dist)
+        
+      } else if (input$na_handling == "ignore_na") {
+        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distIgnore)
+      } else {
+        dist <- compute.distMatrix(DB$allelic_profile_true, hamming.distCategory)
+      }
+    } else {
+      dist <- compute.distMatrix(DB$allelic_profile_true, hamming.dist)
+    }
+    
+    # Find indices of pairs with a distance of 0
+    zero_distance_pairs <- as.data.frame(which(as.matrix(dist) == 0, arr.ind = TRUE))
+    
+    zero_distance_pairs <- zero_distance_pairs[zero_distance_pairs$row != zero_distance_pairs$col, ]
+    
+    if(nrow(zero_distance_pairs) > 0) {
+      
+      # Sort each row so that x <= y
+      df_sorted <- t(apply(zero_distance_pairs, 1, function(row) sort(row)))
+      
+      # Remove duplicate rows
+      df_unique <- as.data.frame(unique(df_sorted))
+      
+      colnames(df_unique) <- c("col", "row")
+      
+      # get metadata in df
+      vector_col <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        vector_col[count] <- Vis$meta_mst$`Assembly Name`[i]
+        count <- count + 1
+      }
+      
+      vector_row <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        vector_row[count] <- Vis$meta_mst$`Assembly Name`[i]
+        count <- count + 1
+      }
+      
+      col_id <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_id[count] <- Vis$meta_mst$`Assembly ID`[i]
+        count <- count + 1
+      }
+      
+      row_id <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_id[count] <- Vis$meta_mst$`Assembly ID`[i]
+        count <- count + 1
+      }
+      
+      col_index <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_index[count] <- Vis$meta_mst$Index[i]
+        count <- count + 1
+      }
+      
+      row_index <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_index[count] <- Vis$meta_mst$Index[i]
+        count <- count + 1
+      }
+      
+      col_date <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_date[count] <- Vis$meta_mst$`Isolation Date`[i]
+        count <- count + 1
+      }
+      
+      row_date <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_date[count] <- Vis$meta_mst$`Isolation Date`[i]
+        count <- count + 1
+      }
+      
+      col_host <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_host[count] <- Vis$meta_mst$Host[i]
+        count <- count + 1
+      }
+      
+      row_host <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_host[count] <- Vis$meta_mst$Host[i]
+        count <- count + 1
+      }
+      
+      col_country <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_country[count] <- Vis$meta_mst$Country[i]
+        count <- count + 1
+      }
+      
+      row_country <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_country[count] <- Vis$meta_mst$Country[i]
+        count <- count + 1
+      }
+      
+      col_city <- character(0)
+      count <- 1
+      for (i in df_unique$col) {
+        col_city[count] <- Vis$meta_mst$City[i]
+        count <- count + 1
+      }
+      
+      row_city <- character(0)
+      count <- 1
+      for (i in df_unique$row) {
+        row_city[count] <- Vis$meta_mst$City[i]
+        count <- count + 1
+      }
+      
+      df_unique <- cbind(df_unique, col_name = vector_col, row_name = vector_row, 
+                         col_index = col_index, row_index = row_index, col_id = col_id,
+                         row_id = row_id, col_date = col_date, row_date = row_date,
+                         col_host = col_host, row_host = row_host, col_country = col_country,
+                         row_country = row_country, col_city = col_city, row_city = row_city)
+      
+      # Add groups
+      grouped_df <- df_unique %>%
+        group_by(col) %>%
+        mutate(group_id = cur_group_id())
+      
+      # Merge groups
+      name <- character(0)
+      index <- character(0)
+      id <- character(0)
+      count <- 1
+      for (i in grouped_df$group_id) {
+        name[count] <- paste(unique(append(grouped_df$col_name[which(grouped_df$group_id == i)], 
+                                           grouped_df$row_name[which(grouped_df$group_id == i)])), 
+                             collapse = "\n")
+        
+        id[count] <- paste(unique(append(grouped_df$col_id[which(grouped_df$group_id == i)], 
+                                         grouped_df$row_id[which(grouped_df$group_id == i)])), 
+                           collapse = "\n")
+        
+        index[count] <- paste(unique(append(grouped_df$col_index[which(grouped_df$group_id == i)], 
+                                            grouped_df$row_index[which(grouped_df$group_id == i)])), 
+                              collapse = "\n")
+        
+        count <- count + 1
+      }
+      
+      merged_names <- cbind(grouped_df, "Index" = index, "Assembly Name" = name, "Assembly ID" = id)
+      
+      # remove duplicate groups
+      
+      final <- merged_names[!duplicated(merged_names$group_id), ]
+      
+      final_cleaned <- final[!(final$col_name %in% final$row_name),]
+      
+      final_cleaned <- select(final_cleaned, 3, 17:20)
+      
+      # adapt metadata
+      Date_merged <- character(0)
+      for(j in 1:length(final_cleaned$Index)) {
+        Date <- character(0)
+        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
+          Date <- append(Date, Vis$meta_mst$`Isolation Date`[which(Vis$meta_mst$Index == i)])
+        }
+        Date_merged <- append(Date_merged, paste(Date, collapse = "\n"))
+      }
+      
+      Host_merged <- character(0)
+      for(j in 1:length(final_cleaned$Index)) {
+        Host <- character(0)
+        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
+          Host <- append(Host, Vis$meta_mst$Host[which(Vis$meta_mst$Index == i)])
+        }
+        Host_merged <- append(Host_merged, paste(Host, collapse = "\n"))
+      }
+      
+      Country_merged <- character(0)
+      for(j in 1:length(final_cleaned$Index)) {
+        Country <- character(0)
+        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
+          Country <- append(Country, Vis$meta_mst$Country[which(Vis$meta_mst$Index == i)])
+        }
+        Country_merged <- append(Country_merged, paste(Country, collapse = "\n"))
+      }
+      
+      City_merged <- character(0)
+      for(j in 1:length(final_cleaned$Index)) {
+        City <- character(0)
+        for(i in strsplit(final_cleaned$Index, "\n")[[j]]) {
+          City <- append(City, Vis$meta_mst$City[which(Vis$meta_mst$Index == i)])
+        }
+        City_merged <- append(City_merged, paste(City, collapse = "\n"))
+      }
+      
+      final_meta <- cbind(final_cleaned, "Isolation Date" = Date_merged, 
+                          "Host" = Host_merged, "Country" = Country_merged, "City" = City_merged)
+      
+      
+      # Merging with original data frame / allelic profile
+      
+      allelic_profile_true <- DB$allelic_profile_true
+      meta_true <- Vis$meta_mst
+      
+      rownames(allelic_profile_true) <- Vis$meta_mst$`Assembly Name`
+      rownames(meta_true) <- Vis$meta_mst$`Assembly Name`
+      
+      omit <- unique(append(df_unique$col_name, df_unique$row_name)) %in% final_cleaned$col_name
+      
+      omit_id <- unique(append(df_unique$col_name, df_unique$row_name))[!omit]
+      
+      remove <- !(rownames(allelic_profile_true) %in% omit_id)
+      
+      allelic_profile_clean <- allelic_profile_true[remove, ]
+      
+      meta_clean <- meta_true[remove, ]
+      
+      # substitute meta assembly names with group names
+      
+      count <- 1
+      for(i in which(rownames(meta_clean) %in% final_meta$col_name)) {
+        meta_clean$Index[i] <- final_meta$Index[count]
+        meta_clean$`Assembly Name`[i] <- final_meta$`Assembly Name`[count]
+        meta_clean$`Assembly ID`[i] <- final_meta$`Assembly ID`[count]
+        meta_clean$`Isolation Date`[i] <- final_meta$`Isolation Date`[count]
+        meta_clean$Host[i] <- final_meta$Host[count]
+        meta_clean$Country[i] <- final_meta$Country[count]
+        meta_clean$City[i] <- final_meta$City[count]
+        count <- count + 1
+      }
+      
+      # Metadata completion
+      # get group size
+      
+      size_vector <- numeric(0)
+      for(i in 1:nrow(meta_clean)) {
+        if (str_count(meta_clean$`Assembly Name`[i], "\n") == 0) {
+          size_vector[i] <- 1
+        } else {
+          size_vector[i] <- str_count(meta_clean$`Assembly Name`[i], "\n") +1
+        }
+      }
+      
+      meta_clean <- mutate(meta_clean, size = size_vector)
+      
+      # get font size dependent on group size
+      
+      font_size <- numeric(nrow(meta_clean))
+      
+      for (i in 1:length(font_size)) {
+        if(meta_clean$size[i] < 3) {
+          font_size[i] <- 12
+        } else {
+          font_size[i] <- 11
+        }
+      }
+      
+      # get v-align dependent on group size
+      valign <- numeric(nrow(meta_clean))
+      
+      for (i in 1:length(valign)) {
+        if(meta_clean$size[i] == 1) {
+          valign[i] <- -30
+        } else if(meta_clean$size[i] == 2) {
+          valign[i] <- -38
+        } else if(meta_clean$size[i] == 3) {
+          valign[i] <- -46
+        } else if(meta_clean$size[i] == 4) {
+          valign[i] <- -54
+        } else if(meta_clean$size[i] == 5) {
+          valign[i] <- -62
+        } else if(meta_clean$size[i] > 5) {
+          valign[i] <- -70
+        }
+      }
+      
+      Vis$unique_meta <- meta_clean %>%
+        cbind(font_size = font_size, valign = valign)
+      
+      # final dist calculation
+      
+      if(anyNA(DB$allelic_profile)){
+        if(input$na_handling == "omit") {
+          allelic_profile_clean_noNA_names <- allelic_profile_clean[, colSums(is.na(allelic_profile_clean)) == 0]
+          compute.distMatrix(allelic_profile_clean_noNA_names, hamming.dist)
+        } else if (input$na_handling == "ignore_na") {
+          compute.distMatrix(allelic_profile_clean, hamming.distIgnore)
+        } else {
+          compute.distMatrix(allelic_profile_clean, hamming.distCategory)
+        }
+      } else {compute.distMatrix(allelic_profile_clean, hamming.dist)}
+      
+      
+    } else {
+      font_size <- rep(12, nrow(Vis$meta_mst))
+      valign <- rep(-30, nrow(Vis$meta_mst))
+      size <- rep(1, nrow(Vis$meta_mst))
+      Vis$unique_meta <- Vis$meta_mst %>%
+        cbind(size , font_size, valign)
+      
+      dist
+    }
+    
+  })
+  
+  observeEvent(input$create_tree, {
+    log_print("Input create_tree")
+    
+    if(is.null(DB$data)) {
+      log_print("Missing data")
+      
+      show_toast(
+        title = "Missing data",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if(nrow(DB$allelic_profile_true) < 3) {
+      log_print("Min. of 3 entries required for visualization")
+      
+      show_toast(
+        title = "Min. of 3 entries required for visualization",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      
+      if(any(duplicated(DB$meta$`Assembly Name`)) | any(duplicated(DB$meta$`Assembly ID`))) {
+        log_print("Duplicated assemblies")
+        
+        dup_name <- which(duplicated(DB$meta_true$`Assembly Name`))
+        dup_id <- which(duplicated(DB$meta_true$`Assembly ID`))
+        
+        showModal(
+          modalDialog(
+            if((length(dup_name) + length(dup_id)) == 1) {
+              if(length(dup_name) == 1) {
+                HTML(paste0("Entry #", dup_name,
+                            " contains a duplicated assembly name:", "<br><br>",
+                            DB$meta_true$`Assembly Name`[dup_name]))
+              } else {
+                HTML(paste0("Entry #", dup_id,
+                            " contains a duplicated assembly ID:", "<br><br>",
+                            DB$meta_true$`Assembly ID`[dup_id]))
+              }
+            } else {
+              if(length(dup_name) == 0) {
+                HTML(c("Entries contain duplicated IDs <br><br>",
+                       paste0(unique(DB$meta_true$`Assembly ID`[dup_id]), "<br>")))
+              } else if(length(dup_id) == 0) {
+                HTML(c("Entries contain duplicated names<br><br>",
+                       paste0(unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>")))
+              } else {
+                HTML(c("Entries contain duplicated names and IDs <br><br>",
+                       paste0("Name: ", unique(DB$meta_true$`Assembly Name`[dup_name]), "<br>"),
+                       paste0("ID: ", unique(DB$meta_true$`Assembly ID`[dup_id]), "<br>")))
+              }
+            },
+            title = "Duplicate entries",
+            fade = TRUE,
+            easyClose = TRUE,
+            footer = tagList(
+              modalButton("Cancel"),
+              actionButton("change_entries", "Go to Entry Table", class = "btn btn-default")
+            )
+          )
+        )
+      } else {
+        
+        set.seed(1)
+        
+        if (input$tree_algo == "Neighbour-Joining") {
+          
+          log_print("Rendering NJ tree")
+          
+          output$nj_field <- renderUI({
+            addSpinner(
+              plotOutput("tree_nj", width = paste0(as.character(as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), "px"), height = paste0(as.character(input$nj_scale), "px")),
+              spin = "dots",
+              color = "#ffffff"
+            )
+          })
+          
+          Vis$meta_nj <- select(DB$meta_true, -2)
+          
+          if(length(unique(gsub(" ", "_", colnames(Vis$meta_nj)))) < length(gsub(" ", "_", colnames(Vis$meta_nj)))) {
+            show_toast(
+              title = "Conflicting Custom Variable Names",
+              type = "warning",
+              position = "bottom-end",
+              timer = 6000
+            )
+          } else {
+            
+            # Create phylogenetic tree data
+            Vis$nj <- ape::nj(hamming_nj())
+            
+            # Create phylogenetic tree meta data
+            Vis$meta_nj <- mutate(Vis$meta_nj, taxa = Index) %>%
+              relocate(taxa)
+            
+            # Get number of included entries calculate start values for tree 
+            if(!is.null(input$nj_layout)) {
+              if(input$nj_layout == "circular" | input$nj_layout == "inward") {
+                if(sum(DB$data$Include) < 21) {
+                  Vis$labelsize_nj <- 5.5
+                  Vis$tippointsize_nj <- 5.5
+                  Vis$nodepointsize_nj <- 4
+                  Vis$tiplab_padding_nj <- 0.25
+                  Vis$branch_size_nj <- 4.5
+                } else if (between(sum(DB$data$Include), 21, 40)) {
+                  Vis$labelsize_nj <- 5
+                  Vis$tippointsize_nj <- 5
+                  Vis$nodepointsize_nj <- 3.5
+                  Vis$tiplab_padding_nj <- 0.2
+                  Vis$branch_size_nj <- 4
+                } else if (between(sum(DB$data$Include), 41, 60)) {
+                  Vis$labelsize_nj <- 4.5
+                  Vis$tippointsize_nj <- 4.5
+                  Vis$nodepointsize_nj <- 3
+                  Vis$tiplab_padding_nj <- 0.15
+                  Vis$branch_size_nj <- 3.5
+                } else if (between(sum(DB$data$Include), 61, 80)) {
+                  Vis$labelsize_nj <- 4
+                  Vis$tippointsize_nj <- 4
+                  Vis$nodepointsize_nj <- 2.5
+                  Vis$tiplab_padding_nj <- 0.1
+                  Vis$branch_size_nj <- 3
+                } else if (between(sum(DB$data$Include), 81, 100)) {
+                  Vis$labelsize_nj <- 3.5
+                  Vis$tippointsize_nj <- 3.5
+                  Vis$nodepointsize_nj <- 2
+                  Vis$tiplab_padding_nj <- 0.1
+                  Vis$branch_size_nj <- 2.5
+                } else {
+                  Vis$labelsize_nj <- 3
+                  Vis$tippointsize_nj <- 3
+                  Vis$nodepointsize_nj <- 1.5
+                  Vis$tiplab_padding_nj <- 0.05
+                  Vis$branch_size_nj <- 2
+                }
+              } else {
+                if(sum(DB$data$Include) < 21) {
+                  Vis$labelsize_nj <- 5
+                  Vis$tippointsize_nj <- 5
+                  Vis$nodepointsize_nj <- 4
+                  Vis$tiplab_padding_nj <- 0.25
+                  Vis$branch_size_nj <- 4.5
+                } else if (between(sum(DB$data$Include), 21, 40)) {
+                  Vis$labelsize_nj <- 4.5
+                  Vis$tippointsize_nj <- 4.5
+                  Vis$nodepointsize_nj <- 3.5
+                  Vis$tiplab_padding_nj <- 0.2
+                  Vis$branch_size_nj <- 4
+                } else if (between(sum(DB$data$Include), 41, 60)) {
+                  Vis$labelsize_nj <- 4
+                  Vis$tippointsize_nj <- 4
+                  Vis$nodepointsize_nj <- 3
+                  Vis$tiplab_padding_nj <- 0.15
+                  Vis$branch_size_nj <- 3.5
+                } else if (between(sum(DB$data$Include), 61, 80)) {
+                  Vis$labelsize_nj <- 3.5
+                  Vis$tippointsize_nj <- 3.5
+                  Vis$nodepointsize_nj <- 2.5
+                  Vis$tiplab_padding_nj <- 0.1
+                  Vis$branch_size_nj <- 3
+                } else if (between(sum(DB$data$Include), 81, 100)) {
+                  Vis$labelsize_nj <- 3
+                  Vis$tippointsize_nj <- 3
+                  Vis$nodepointsize_nj <- 2
+                  Vis$tiplab_padding_nj <- 0.1
+                  Vis$branch_size_nj <- 2.5
+                } else {
+                  Vis$labelsize_nj <- 2.5
+                  Vis$tippointsize_nj <- 2.5
+                  Vis$nodepointsize_nj <- 1.5
+                  Vis$tiplab_padding_nj <- 0.05
+                  Vis$branch_size_nj <- 2
+                }
+              }
+            } else {
+              Vis$labelsize_nj <- 4
+              Vis$tippointsize_nj <- 4
+              Vis$nodepointsize_nj <- 2.5
+              Vis$tiplab_padding_nj <- 0.2
+              Vis$branch_size_nj <- 3.5
+            }
+            
+            Vis$nj_tree <- ggtree(Vis$nj)
+            
+            # Get upper and lower end of x range
+            Vis$nj_max_x <- max(Vis$nj_tree$data$x)
+            Vis$nj_min_x <- min(Vis$nj_tree$data$x)
+            
+            # Get parent node numbers
+            Vis$nj_parentnodes <- Vis$nj_tree$data$parent
+            
+            # Update visualization control inputs
+            if(!is.null(input$nj_tiplab_size)) {
+              updateNumericInput(session, "nj_tiplab_size", value = Vis$labelsize_nj)
+            }
+            if(!is.null(input$nj_tippoint_size)) {
+              updateSliderInput(session, "nj_tippoint_size", value = Vis$tippointsize_nj)
+            }
+            if(!is.null(input$nj_nodepoint_size)) {
+              updateSliderInput(session, "nj_nodepoint_size", value = Vis$nodepointsize_nj)
+            }
+            if(!is.null(input$nj_tiplab_padding)) {
+              updateSliderInput(session, "nj_tiplab_padding", value = Vis$tiplab_padding_nj)
+            }
+            if(!is.null(input$nj_branch_size)) {
+              updateNumericInput(session, "nj_branch_size", value = Vis$branch_size_nj)
+            }
+            if(!is.null(input$nj_treescale_width)) {
+              updateNumericInput(session, "nj_treescale_width", value = round(ceiling(Vis$nj_max_x) * 0.1, 0))
+            }
+            if(!is.null(input$nj_rootedge_length)) {
+              updateSliderInput(session, "nj_rootedge_length", value = round(ceiling(Vis$nj_max_x) * 0.05, 0))
+            }
+            
+            output$tree_nj <- renderPlot({
+              nj_tree()
+            })
+            
+            Vis$nj_true <- TRUE
+          }
+        } else if (input$tree_algo == "UPGMA") {
+          
+          log_print("Rendering UPGMA tree")
+          
+          output$upgma_field <- renderUI({
+            addSpinner(
+              plotOutput("tree_upgma", width = paste0(as.character(as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), "px"), height = paste0(as.character(input$upgma_scale), "px")),
+              spin = "dots",
+              color = "#ffffff"
+            )
+          })
+          
+          Vis$meta_upgma <- select(DB$meta_true, -2)
+          
+          if(length(unique(gsub(" ", "_", colnames(Vis$meta_upgma)))) < length(gsub(" ", "_", colnames(Vis$meta_upgma)))) {
+            show_toast(
+              title = "Conflicting Custom Variable Names",
+              type = "warning",
+              position = "bottom-end",
+              timer = 6000
+            )
+          } else {
+            
+            # Create phylogenetic tree data
+            Vis$upgma <- phangorn::upgma(hamming_nj())
+            
+            # Create phylogenetic tree meta data
+            Vis$meta_upgma <- mutate(Vis$meta_upgma, taxa = Index) %>%
+              relocate(taxa)
+            
+            # Get number of included entries calculate start values for tree 
+            if(!is.null(input$upgma_layout)) {
+              if(input$upgma_layout == "circular" | input$upgma_layout == "inward") {
+                if(sum(DB$data$Include) < 21) {
+                  Vis$labelsize_upgma <- 5.5
+                  Vis$tippointsize_upgma <- 5.5
+                  Vis$nodepointsize_upgma <- 4
+                  Vis$tiplab_padding_upgma <- 0.25
+                  Vis$branch_size_upgma <- 4.5
+                } else if (between(sum(DB$data$Include), 21, 40)) {
+                  Vis$labelsize_upgma <- 5
+                  Vis$tippointsize_upgma <- 5
+                  Vis$nodepointsize_upgma <- 3.5
+                  Vis$tiplab_padding_upgma <- 0.2
+                  Vis$branch_size_upgma <- 4
+                } else if (between(sum(DB$data$Include), 41, 60)) {
+                  Vis$labelsize_upgma <- 4.5
+                  Vis$tippointsize_upgma <- 4.5
+                  Vis$nodepointsize_upgma <- 3
+                  Vis$tiplab_padding_upgma <- 0.15
+                  Vis$branch_size_upgma <- 3.5
+                } else if (between(sum(DB$data$Include), 61, 80)) {
+                  Vis$labelsize_upgma <- 4
+                  Vis$tippointsize_upgma <- 4
+                  Vis$nodepointsize_upgma <- 2.5
+                  Vis$tiplab_padding_upgma <- 0.1
+                  Vis$branch_size_upgma <- 3
+                } else if (between(sum(DB$data$Include), 81, 100)) {
+                  Vis$labelsize_upgma <- 3.5
+                  Vis$tippointsize_upgma <- 3.5
+                  Vis$nodepointsize_upgma <- 2
+                  Vis$tiplab_padding_upgma <- 0.1
+                  Vis$branch_size_upgma <- 2.5
+                } else {
+                  Vis$labelsize_upgma <- 3
+                  Vis$tippointsize_upgma <- 3
+                  Vis$nodepointsize_upgma <- 1.5
+                  Vis$tiplab_padding_upgma <- 0.05
+                  Vis$branch_size_upgma <- 2
+                }
+              } else {
+                if(sum(DB$data$Include) < 21) {
+                  Vis$labelsize_upgma <- 5
+                  Vis$tippointsize_upgma <- 5
+                  Vis$nodepointsize_upgma <- 4
+                  Vis$tiplab_padding_upgma <- 0.25
+                  Vis$branch_size_upgma <- 4.5
+                } else if (between(sum(DB$data$Include), 21, 40)) {
+                  Vis$labelsize_upgma <- 4.5
+                  Vis$tippointsize_upgma <- 4.5
+                  Vis$nodepointsize_upgma <- 3.5
+                  Vis$tiplab_padding_upgma <- 0.2
+                  Vis$branch_size_upgma <- 4
+                } else if (between(sum(DB$data$Include), 41, 60)) {
+                  Vis$labelsize_upgma <- 4
+                  Vis$tippointsize_upgma <- 4
+                  Vis$nodepointsize_upgma <- 3
+                  Vis$tiplab_padding_upgma <- 0.15
+                  Vis$branch_size_upgma <- 3.5
+                } else if (between(sum(DB$data$Include), 61, 80)) {
+                  Vis$labelsize_upgma <- 3.5
+                  Vis$tippointsize_upgma <- 3.5
+                  Vis$nodepointsize_upgma <- 2.5
+                  Vis$tiplab_padding_upgma <- 0.1
+                  Vis$branch_size_upgma <- 3
+                } else if (between(sum(DB$data$Include), 81, 100)) {
+                  Vis$labelsize_upgma <- 3
+                  Vis$tippointsize_upgma <- 3
+                  Vis$nodepointsize_upgma <- 2
+                  Vis$tiplab_padding_upgma <- 0.1
+                  Vis$branch_size_upgma <- 2.5
+                } else {
+                  Vis$labelsize_upgma <- 2.5
+                  Vis$tippointsize_upgma <- 2.5
+                  Vis$nodepointsize_upgma <- 1.5
+                  Vis$tiplab_padding_upgma <- 0.05
+                  Vis$branch_size_upgma <- 2
+                }
+              }
+            } else {
+              Vis$labelsize_upgma <- 4
+              Vis$tippointsize_upgma <- 4
+              Vis$nodepointsize_upgma <- 2.5
+              Vis$tiplab_padding_upgma <- 0.2
+              Vis$branch_size_upgma <- 3.5
+            }
+            
+            Vis$upgma_tree <- ggtree(Vis$upgma)
+            
+            # Get upper and lower end of x range
+            Vis$upgma_max_x <- max(Vis$upgma_tree$data$x)
+            Vis$upgma_min_x <- min(Vis$upgma_tree$data$x)
+            
+            # Get parent node numbers
+            Vis$upgma_parentnodes <- Vis$upgma_tree$data$parent
+            
+            # Update visualization control inputs
+            if(!is.null(input$upgma_tiplab_size)) {
+              updateNumericInput(session, "upgma_tiplab_size", value = Vis$labelsize_upgma)
+            }
+            if(!is.null(input$upgma_tippoint_size)) {
+              updateSliderInput(session, "upgma_tippoint_size", value = Vis$tippointsize_upgma)
+            }
+            if(!is.null(input$upgma_nodepoint_size)) {
+              updateSliderInput(session, "upgma_nodepoint_size", value = Vis$nodepointsize_upgma)
+            }
+            if(!is.null(input$upgma_tiplab_padding)) {
+              updateSliderInput(session, "upgma_tiplab_padding", value = Vis$tiplab_padding_upgma)
+            }
+            if(!is.null(input$upgma_branch_size)) {
+              updateNumericInput(session, "upgma_branch_size", value = Vis$branch_size_upgma)
+            }
+            if(!is.null(input$upgma_treescale_width)) {
+              updateNumericInput(session, "upgma_treescale_width", value = round(ceiling(Vis$upgma_max_x) * 0.1, 0))
+            }
+            if(!is.null(input$upgma_rootedge_length)) {
+              updateSliderInput(session, "upgma_rootedge_length", value = round(ceiling(Vis$upgma_max_x) * 0.05, 0))
+            }
+            
+            output$tree_upgma <- renderPlot({
+              upgma_tree()
+            })
+            
+            Vis$upgma_true <- TRUE
+          }
+        } else {
+          
+          log_print("Rendering MST graph")
+          
+          output$mst_field <- renderUI({
+            if(input$mst_background_transparent == TRUE) {
+              visNetworkOutput("tree_mst", width = paste0(as.character(as.numeric(input$mst_scale) * as.numeric(input$mst_ratio)), "px"), height = paste0(as.character(input$mst_scale), "px"))
+            } else {
+              addSpinner(
+                visNetworkOutput("tree_mst", width = paste0(as.character(as.numeric(input$mst_scale) * as.numeric(input$mst_ratio)), "px"), height = paste0(as.character(input$mst_scale), "px")),
+                spin = "dots",
+                color = "#ffffff"
+              )
+            }
+          })
+          
+          if(nrow(DB$meta_true) > 100) {
+            
+            log_print("Over 100 isolates in MST graph")
+            
+            show_toast(
+              title = "Computation might take a while",
+              type = "warning",
+              position = "bottom-end",
+              timer = 10000
+            )
+          }
+          
+          meta_mst <- DB$meta_true
+          Vis$meta_mst <- meta_mst
+          
+          # prepare igraph object
+          Vis$ggraph_1 <- hamming_mst() |>
+            as.matrix() |>
+            graph.adjacency(weighted = TRUE) |>
+            igraph::mst() 
+          
+          output$tree_mst <- renderVisNetwork({
+            mst_tree()
+          })
+          
+          Vis$mst_true <- TRUE
+        }
+      }
+    }
+  })
+  
+  # _______________________ ####
+  
+  ## Report ----
+  
+  observe({
+    if(!is.null(DB$data)) {
+      if(!is.null(input$tree_algo)) {
+        if(input$tree_algo == "Minimum-Spanning") {
+          shinyjs::disable("rep_plot_report")
+          updateCheckboxInput(session, "rep_plot_report", value = FALSE)
+        } else {
+          shinyjs::enable("rep_plot_report")
+        }
+      }
+    }
+  })
+  
+  ### Report creation UI ----
+  
+  observeEvent(input$create_rep, {
+    
+    if((input$tree_algo == "Minimum-Spanning" & isTRUE(Vis$mst_true)) |
+       (input$tree_algo == "UPGMA" & isTRUE(Vis$upgma_true)) |
+       (input$tree_algo == "Neighbour-Joining" & isTRUE(Vis$nj_true))) {
+      # Get currently selected missing value handling option
+      if(input$na_handling == "ignore_na") {
+        na_handling <- "Ignore missing values for pairwise comparison"
+      } else if(input$na_handling == "omit") {
+        na_handling <- "Omit loci with missing values for all assemblies"
+      } else if(input$na_handling == "category") {
+        na_handling <- "Treat missing values as allele variant"
+      }
+      
+      extra_var <- character()
+      if(input$tree_algo == "Minimum-Spanning") {
+        shinyjs::runjs("mstReport();")
+        if(isTRUE(input$mst_color_var)) {
+          extra_var <- c(extra_var, input$mst_col_var)
+        }
+      } else if(input$tree_algo == "Neighbour-Joining") {
+        if(isTRUE(input$nj_mapping_show)) {
+          extra_var <- c(extra_var, input$nj_color_mapping)
+        }
+        if(isTRUE(input$nj_tipcolor_mapping_show)) {
+          extra_var <- c(extra_var, input$nj_tipcolor_mapping)
+        }
+        if(isTRUE(input$nj_tipshape_mapping_show)) {
+          extra_var <- c(extra_var, input$nj_tipshape_mapping)
+        }
+        if(isTRUE(input$nj_tiles_show_1)) {
+          extra_var <- c(extra_var, input$nj_fruit_variable)
+        }
+        if(isTRUE(input$nj_tiles_show_2)) {
+          extra_var <- c(extra_var, input$nj_fruit_variable_2)
+        }
+        if(isTRUE(input$nj_tiles_show_3)) {
+          extra_var <- c(extra_var, input$nj_fruit_variable_3)
+        }
+        if(isTRUE(input$nj_tiles_show_4)) {
+          extra_var <- c(extra_var, input$nj_fruit_variable_4)
+        }
+        if(isTRUE(input$nj_tiles_show_5)) {
+          extra_var <- c(extra_var, input$nj_fruit_variable_5)
+        }
+        if(isTRUE(input$nj_heatmap_show)) {
+          extra_var <- c(extra_var, input$nj_heatmap_select)
+        }
+      } else if(input$tree_algo == "UPGMA") {
+        if(isTRUE(input$UPGMA_mapping_show)) {
+          extra_var <- c(extra_var, input$UPGMA_color_mapping)
+        }
+        if(isTRUE(input$UPGMA_tipcolor_mapping_show)) {
+          extra_var <- c(extra_var, input$UPGMA_tipcolor_mapping)
+        }
+        if(isTRUE(input$UPGMA_tipshape_mapping_show)) {
+          extra_var <- c(extra_var, input$UPGMA_tipshape_mapping)
+        }
+        if(isTRUE(input$UPGMA_tiles_show_1)) {
+          extra_var <- c(extra_var, input$UPGMA_fruit_variable)
+        }
+        if(isTRUE(input$UPGMA_tiles_show_2)) {
+          extra_var <- c(extra_var, input$UPGMA_fruit_variable_2)
+        }
+        if(isTRUE(input$UPGMA_tiles_show_3)) {
+          extra_var <- c(extra_var, input$UPGMA_fruit_variable_3)
+        }
+        if(isTRUE(input$UPGMA_tiles_show_4)) {
+          extra_var <- c(extra_var, input$UPGMA_fruit_variable_4)
+        }
+        if(isTRUE(input$UPGMA_tiles_show_5)) {
+          extra_var <- c(extra_var, input$UPGMA_fruit_variable_5)
+        }
+        if(isTRUE(input$UPGMA_heatmap_show)) {
+          extra_var <- c(extra_var, input$UPGMA_heatmap_select)
+        }
+      }
+      
+      showModal(
+        modalDialog(
+          fluidRow(
+            column(
+              width = 12,
+              fluidRow(
+                column(
+                  width = 4,
+                  align = "left",
+                  HTML(
+                    paste(
+                      tags$span(style='color:black; font-size: 15px; font-weight: 900', 'General')
+                    )
+                  )
+                ),
+                column(
+                  width = 3,
+                  align = "left",
+                  checkboxInput(
+                    "rep_general",
+                    label = "",
+                    value = TRUE
+                  )
+                )
+              ),
+              fluidRow(
+                column(
+                  width = 12,
+                  align = "left",
+                  fluidRow(
+                    column(
+                      width = 3,
+                      checkboxInput(
+                        "rep_date_general", 
+                        label = h5("Date", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 7,
+                      dateInput(
+                        "mst_date_general_select",
+                        "",
+                        max = Sys.Date()
+                      )
+                    )
+                  ),
+                  fluidRow(
+                    column(
+                      width = 3,
+                      checkboxInput(
+                        "rep_operator_general", 
+                        label = h5("Operator", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 8,
+                      textInput(
+                        "mst_operator_general_select",
+                        ""
+                      ) 
+                    )
+                  ),
+                  fluidRow(
+                    column(
+                      width = 3,
+                      checkboxInput(
+                        "rep_institute_general", 
+                        label = h5("Institute", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 8,
+                      textInput(
+                        "mst_institute_general_select",
+                        ""
+                      ) 
+                    )
+                  ),
+                  fluidRow(
+                    column(
+                      width = 3,
+                      checkboxInput(
+                        "rep_comm_general", 
+                        label = h5("Comment", style = "color:black;")
+                      )
+                    ),
+                    column(
+                      width = 8,
+                      textAreaInput(
+                        inputId = "mst_comm_general_select",
+                        label = "",
+                        width = "100%",
+                        height = "60px",
+                        cols = NULL,
+                        rows = NULL,
+                        placeholder = NULL,
+                        resize = "vertical"
+                      ) 
+                    )
+                  )
+                )
+              ),
+              hr(),
+              fluidRow(
+                column(
+                  width = 4,
+                  align = "left",
+                  HTML(
+                    paste(
+                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Isolate Table')
+                    )
+                  )
+                ),
+                column(
+                  width = 3,
+                  align = "left",
+                  checkboxInput(
+                    "rep_entrytable",
+                    label = "",
+                    value = TRUE
+                  )
+                ),
+                column(
+                  width = 4,
+                  align = "left",
+                  HTML(
+                    paste(
+                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Include Plot')
+                    )
+                  )
+                ),
+                column(
+                  width = 1,
+                  align = "left",
+                  checkboxInput(
+                    "rep_plot_report",
+                    label = "",
+                    value = TRUE
+                  )
+                )
+              ),
+              fluidRow(
+                column(
+                  width = 6,
+                  align = "left",
+                  div(
+                    class = "rep_tab_sel",
+                    pickerInput("select_rep_tab",
+                                label = "",
+                                choices = names(DB$meta)[-2],
+                                selected = c("Assembly Name", "Scheme", "Isolation Date",
+                                             "Host", "Country", "City", extra_var),
+                                options = list(
+                                  size = 10,
+                                  `actions-box` = TRUE,
+                                  style = "background-color: white; border-radius: 5px;"
+                                ),
+                                multiple = TRUE)
+                  )
+                )
+              ),
+              hr(),
+              fluidRow(
+                column(
+                  width = 4,
+                  align = "left",
+                  HTML(
+                    paste(
+                      tags$span(style='color: black; font-size: 15px; font-weight: 900', 'Analysis Parameter')
+                    )
+                  )
+                ),
+                column(
+                  width = 3,
+                  align = "left",
+                  checkboxInput(
+                    "rep_analysis",
+                    label = "",
+                    value = TRUE
+                  )
+                )
+              ),
+              fluidRow(
+                column(
+                  width = 6,
+                  align = "left",
+                  fluidRow(
+                    column(
+                      width = 4,
+                      checkboxInput(
+                        "rep_cgmlst_analysis",
+                        label = h5("Scheme", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 8,
+                      align = "right",
+                      HTML(
+                        paste(
+                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', DB$scheme)
+                        )
+                      )
+                    )
+                  ),
+                  fluidRow(
+                    column(
+                      width = 4,
+                      checkboxInput(
+                        "rep_tree_analysis",
+                        label = h5("Tree", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 8,
+                      align = "right",
+                      HTML(
+                        paste(
+                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', input$tree_algo)
+                        )
+                      )
+                    )
+                  )
+                ),
+                column(
+                  width = 6,
+                  align = "left",
+                  fluidRow(
+                    column(2),
+                    column(
+                      width = 4,
+                      checkboxInput(
+                        "rep_distance",
+                        label = h5("Distance", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 5,
+                      align = "right",
+                      HTML(
+                        paste(
+                          tags$span(style='color: black; position: relative; top: 17px; font-style: italic', 'Hamming')
+                        )
+                      )
+                    )
+                  ),
+                  fluidRow(
+                    column(2),
+                    column(
+                      width = 4,
+                      checkboxInput(
+                        "rep_version",
+                        label = h5("Version", style = "color:black;"),
+                        value = TRUE
+                      )
+                    ),
+                    column(
+                      width = 5,
+                      align = "right",
+                      HTML(
+                        paste(
+                          tags$span(style='color:black; position: relative; top: 17px; font-style: italic', phylotraceVersion)
+                        )
+                      )
+                    )
+                  )
+                )
+              ),
+              fluidRow(
+                column(
+                  width = 3,
+                  align = "left",
+                  checkboxInput(
+                    "rep_missval",
+                    label = h5("NA handling", style = "color:black;"),
+                    value = TRUE
+                  )
+                ),
+                column(
+                  width = 7,
+                  align = "right",
+                  HTML(
+                    paste(
+                      tags$span(style='color: black; position: relative; top: 17px; font-style: italic; right: 35px;', na_handling)
+                    )
+                  )
+                )
+              )
+            )
+          ),
+          title = "cgMLST Report Generation",
+          easyClose = TRUE,
+          footer = tagList(
+            modalButton("Cancel"),
+            downloadBttn(
+              "download_report",
+              style = "simple",
+              label = "Save",
+              size = "sm",
+              icon = icon("download")
+            )
+          )
+        )
+      )
+    } else {
+      show_toast(
+        title = "No tree created",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    }
+  })
+  
+  observe({
+    if(!is.null(input$rep_general)) {
+      if(isFALSE(input$rep_general)) {
+        shinyjs::disable('rep_date_general') 
+        shinyjs::disable('rep_operator_general') 
+        shinyjs::disable('rep_institute_general') 
+        shinyjs::disable('rep_comm_general') 
+        shinyjs::disable('mst_date_general_select') 
+        shinyjs::disable('mst_operator_general_select') 
+        shinyjs::disable('mst_institute_general_select') 
+        shinyjs::disable('mst_comm_general_select') 
+      } else {
+        shinyjs::enable('rep_date_general') 
+        shinyjs::enable('rep_operator_general') 
+        shinyjs::enable('rep_institute_general') 
+        shinyjs::enable('rep_comm_general')
+        shinyjs::enable('mst_date_general_select') 
+        shinyjs::enable('mst_operator_general_select') 
+        shinyjs::enable('mst_institute_general_select') 
+        shinyjs::enable('mst_comm_general_select') 
+      }
+    }
+    
+    if(!is.null(input$rep_analysis)) {
+      if(isFALSE(input$rep_analysis)) {
+        shinyjs::disable('rep_cgmlst_analysis') 
+        shinyjs::disable('rep_tree_analysis') 
+        shinyjs::disable('rep_distance') 
+        shinyjs::disable('rep_missval') 
+        shinyjs::disable('rep_version') 
+      } else {
+        shinyjs::enable('rep_cgmlst_analysis') 
+        shinyjs::enable('rep_tree_analysis') 
+        shinyjs::enable('rep_distance') 
+        shinyjs::enable('rep_missval') 
+        shinyjs::enable('rep_version') 
+      }
+    }
+    
+    if(length(input$select_rep_tab) > 0) {
+      updateCheckboxInput(session, "rep_entrytable", value = TRUE)
+    } else {
+      updateCheckboxInput(session, "rep_entrytable", value = FALSE)
+    }
+  })
+  
+  ### Save Report ----
+  
+  #### Get Report elements ----
+  
+  observe({
+    if(!is.null(DB$data)){
+      if(!is.null(input$tree_algo)) {
+        req(c(input$rep_entrytable, input$rep_general,
+              input$rep_date_general, input$rep_operator_general,
+              input$rep_institute_general, input$rep_comm_general,
+              input$rep_analysis, input$rep_cgmlst_analysis,
+              input$rep_tree_analysis, input$rep_distance,
+              input$rep_missval, input$rep_version,
+              input$rep_plot_report, input$select_rep_tab))
+        Report$report_df <- data.frame(Element = c("entry_table", "general_show",
+                                                   "general_date", "operator",
+                                                   "institute", "comment",
+                                                   "analysis_show", "scheme",
+                                                   "tree", "distance", "na_handling", "version",
+                                                   "plot"),
+                                       Include = c(input$rep_entrytable, input$rep_general,
+                                                   input$rep_date_general, input$rep_operator_general,
+                                                   input$rep_institute_general, input$rep_comm_general,
+                                                   input$rep_analysis, input$rep_cgmlst_analysis,
+                                                   input$rep_tree_analysis, input$rep_distance,
+                                                   input$rep_missval, input$rep_version,
+                                                   input$rep_plot_report))
+      }
+    }
+  })
+  
+  #### Get Report values ----
+  
+  observeEvent(input$create_tree, {
+    if(input$tree_algo == "Minimum-Spanning") {
+      Report$report_list_mst <- list(entry_table = DB$meta_true,
+                                     scheme = DB$schemeinfo, 
+                                     tree = input$tree_algo,
+                                     na_handling = if(anyNA(DB$allelic_profile_true)){input$na_handling} else {NULL},
+                                     distance = "Hamming Distances",
+                                     version = c(phylotraceVersion, "2.5.1"),
+                                     plot = "MST")
+    } else if(input$tree_algo == "Neighbour-Joining") {
+      Report$report_list_nj <- list(entry_table = DB$meta_true,
+                                    scheme = DB$schemeinfo, 
+                                    tree = input$tree_algo,
+                                    na_handling = input$na_handling,
+                                    distance = "Hamming Distances",
+                                    version = c(phylotraceVersion, "2.5.1"),
+                                    plot = "NJ")
+    } else {
+      Report$report_list_upgma <- list(entry_table = DB$meta_true,
+                                       scheme = DB$schemeinfo, 
+                                       tree = input$tree_algo,
+                                       na_handling = input$na_handling,
+                                       distance = "Hamming Distances",
+                                       version = c(phylotraceVersion, "2.5.1"),
+                                       plot = "UPGMA")
+    }
+  })
+  
+  # Save plot for Report
+  plot.report <- reactive({
+    if(input$tree_algo == "Neighbour-Joining") {
+      jpeg(paste0(getwd(), "/Report/NJ.jpeg"), width = (as.numeric(input$nj_scale) * as.numeric(input$nj_ratio)), height = as.numeric(input$nj_scale), quality = 100)
+      print(nj_tree())
+      dev.off()
+    } else if(input$tree_algo == "UPGMA") {
+      jpeg(paste0(getwd(), "/Report/UPGMA.jpeg"), width = (as.numeric(input$upgma_scale) * as.numeric(input$upgma_ratio)), height = as.numeric(input$upgma_scale), quality = 100)
+      print(upgma_tree())
+      dev.off()
+    } else if (input$tree_algo == "Minimum-Spanning") {
+      shinyjs::runjs("mstReport();")
+      decoded_data <- base64enc::base64decode(input$canvas_data)
+      writeBin(decoded_data, paste0(getwd(), "/Report/MST.jpg"))
+    }
+  })
+  
+  #### Event Save Report ----
+  output$download_report <- downloadHandler(
+    filename = function() {
+      if(input$tree_algo == "Minimum-Spanning") {
+        paste0("MST_Report_", Sys.Date(), ".html")
+      } else if(input$tree_algo == "Neighbour-Joining") {
+        paste0("NJ_Report_", Sys.Date(), ".html")
+      } else {paste0("UPGMA_Report_", Sys.Date(), ".html")}
+    },
+    content = function(file) {
+      if(input$tree_algo == "Minimum-Spanning") {
+        plot.report()
+        
+        report <- c(Report$report_list_mst, 
+                    "general_date" = as.character(input$mst_date_general_select),
+                    "operator" = input$mst_operator_general_select,
+                    "institute" = input$mst_institute_general_select,
+                    "comment" = input$mst_comm_general_select,
+                    "report_df" = Report$report_df)
+        
+        report[["table_columns"]] <- input$select_rep_tab
+        
+        # Save data to an RDS file if any elements were selected
+        if (!is.null(report)) {
+          
+          log_print("Creating MST report")
+          
+          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
+          
+          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
+          
+          file.copy(paste0(getwd(), "/Report/Report.html"), file)
+        } else {
+          log_print("Creating MST report failed (report is null)")
+        }
+      } else if(input$tree_algo == "Neighbour-Joining") {
+        plot.report()
+        report <- c(Report$report_list_nj, 
+                    "general_date" = as.character(input$mst_date_general_select),
+                    "operator" = input$mst_operator_general_select,
+                    "institute" = input$mst_institute_general_select,
+                    "comment" = input$mst_comm_general_select,
+                    "report_df" = Report$report_df)
+        
+        report[["table_columns"]] <- input$select_rep_tab
+        
+        # Save data to an RDS file if any elements were selected
+        if (!is.null(report)) {
+          log_print("Creating NJ report")
+          
+          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
+          
+          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
+          
+          file.copy(paste0(getwd(), "/Report/Report.html"), file)
+        } else {
+          log_print("Creating NJ report failed (report is null)")
+        }
+        
+      } else {
+        plot.report()
+        report <- c(Report$report_list_upgma, 
+                    "general_date" = as.character(input$mst_date_general_select),
+                    "operator" = input$mst_operator_general_select,
+                    "institute" = input$mst_institute_general_select,
+                    "comment" = input$mst_comm_general_select,
+                    "report_df" = Report$report_df)
+        
+        report[["table_columns"]] <- input$select_rep_tab
+        
+        # Save data to an RDS file if any elements were selected
+        if (!is.null(report)) {
+          log_print("Creating UPGMA report")
+          
+          saveRDS(report, file = paste0(getwd(), "/Report/selected_elements.rds"))
+          
+          rmarkdown::render(paste0(getwd(), "/Report/Report.Rmd"))
+          
+          file.copy(paste0(getwd(), "/Report/Report.html"), file)
+        } else {
+          log_print("Creating UPGMA report failed (report is null)")
+        }
+        
+      }
+      removeModal()
+    }
+  )
+  
+  
+  # _______________________ ####
+  
+  ## Gene Screening  ----
+  
+  ### Render UI Elements ----
+  
+  # Rendering results table
+  output$gs_results_table <- renderUI({
+    req(DB$data)
+    if(!is.null(Screening$selected_isolate)) {
+      if(length(Screening$selected_isolate) > 0) {
+        fluidRow(
+          div(class = "loci_table",
+              DT::dataTableOutput("gs_profile_table")),
+          br(),
+          HTML(
+            paste0("<span style='color: white; font-size: 12px'>", 
+                   '<strong>RSL</strong> = <em>Reference Sequence Length</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>%CRS</strong> = <em>% Coverage of Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>%IRS</strong> = <em>% Identity to Reference Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>ACS</strong> = <em>Accession of Closest Sequence</em>&nbsp&nbsp|&nbsp&nbsp',
+                   '<strong>NCS</strong> = <em>Name of Closest Sequence</em>')
+            
+          )
+        )
+      } else {
+        fluidRow(
+          br(), br(),
+          p(
+            HTML(
+              paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
+                     'Select entry from the table to display resistance profile')
+              
+            )
+          )
+        )
+      }
+    } else {
+      fluidRow(
+        br(), br(),
+        p(
+          HTML(
+            paste0("<span style='color: white; position: relative; top: 30px; left: 300px; font-size: 12px; font-style: italic'>", 
+                   'Select entry from the table to display resistance profile')
+            
+          )
+        )
+      )
+    }
+  })
+  
+  # Gene screening download button
+  output$gs_download <- renderUI({
+    req(DB$data)
+    if(!is.null(Screening$selected_isolate)) {
+      if(length(Screening$selected_isolate) > 0) {
+        fluidRow(
+          downloadBttn(
+            "download_resistance_profile",
+            style = "simple",
+            label = "Profile Table",
+            size = "sm",
+            icon = icon("download"),
+            color = "primary"
+          ),
+          bsTooltip("download_resistance_profile_bttn", 
+                    HTML(paste0("Save resistance profile table for</br>",
+                                Screening$selected_isolate)), 
+                    placement = "bottom", trigger = "hover")
+        )
+      } else {NULL}
+    } else {NULL}
+  })
+  
+  # Conditionally render table selectiom interface
+  output$gs_table_selection <- renderUI({
+    req(DB$data, input$gs_view)
+    if(input$gs_view == "Table") {
+      fluidRow(
+        column(1),
+        column(
+          width = 10,
+          div(class = "loci_table",
+              dataTableOutput("gs_isolate_table"))
+        )
+      )
+    } else {NULL}
+  })
+  
+  # Resistance profile table output display
+  output$gs_profile_display <- renderUI({
+    req(DB$data)
+    if(!is.null(DB$meta_gs) & !is.null(input$gs_view)) {
+      if(input$gs_view == "Table") {
+        column(
+          width = 10,
+          hr(), 
+          fluidRow(
+            column(
+              width = 4,
+              p(
+                HTML(
+                  paste0("<span style='color: white; font-size: 18px'>", 
+                         "Gene Screening Results</br>",
+                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
+                         "Comprising genes for resistance, virulence, stress, etc.")
+                )
+              )
+            ),
+            column(
+              width = 4,
+              uiOutput("gs_download")
+            )
+          ),
+          br(),
+          uiOutput("gs_results_table")
+        )
+      } else {
+        column(
+          width = 10,
+          fluidRow(
+            column(
+              width = 4,
+              p(
+                HTML(
+                  paste0("<span style='color: white; font-size: 18px'>", 
+                         "Gene Screening Results</br>",
+                         "<span style='color: white; font-size: 12px; font-style:italic'>", 
+                         "Comprising genes for resistance, virulence, stress, etc.")
+                )
+              )
+            ),
+            column(
+              width = 4,
+              div(
+                class = "gs-picker",
+                pickerInput(
+                  "gs_profile_select",
+                  "",
+                  choices = list(
+                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+                    },
+                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
+                    },
+                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
+                    }
+                  ),
+                  choicesOpt = list(
+                    disabled = c(
+                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
+                    )
+                  ),
+                  options = list(
+                    `live-search` = TRUE,
+                    size = 10,
+                    style = "background-color: white; border-radius: 5px;"
+                  )
+                )
+              )
+            ),
+            column(
+              width = 3,
+              uiOutput("gs_download")
+            )
+          ),
+          br(),
+          uiOutput("gs_results_table")
+        )
+      }
+    } else {NULL}
+  })
+  
+  # Screening sidebar
+  output$screening_sidebar <- renderUI({
+    req(DB$data)
+    if(!is.null(DB$meta_gs)) {
+      column(
+        width = 12,
+        align = "center",
+        br(), br(),
+        p(
+          HTML(
+            paste(
+              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Toggle View')
+            )
+          )
+        ),
+        radioGroupButtons(
+          inputId = "gs_view",
+          choices = c("Picker", "Table"),
+          selected = "Picker",
+          checkIcon = list(
+            yes = icon("square-check"),
+            no = icon("square")
+          )
+        ),
+        br()
+      )
+    } else {NULL}
+  })
+  
+  # Resistance profile table
+  observe({
+    req(DB$meta_gs, Screening$selected_isolate, DB$database, DB$scheme, DB$data)
+    
+    if(length(Screening$selected_isolate) > 0 & any(Screening$selected_isolate %in% DB$data$`Assembly ID`)) {
+      iso_select <- Screening$selected_isolate
+      iso_path <- file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
+                            iso_select, "resProfile.tsv")
+      
+      res_profile <- read.delim(iso_path)
+      
+      colnames(res_profile) <- c(
+        "Protein Identifier",	"Contig ID", "Start", "Stop", "Strand", "Gene Symbol", 
+        "Sequence Name", "Scope", "Element Type",  "Element Subtype", "Class", 
+        "Subclass", "Method", "Target Length", "RSL",	"%CRS", "%IRS", 
+        "Alignment Length", "ACS", "Name of Closest Sequence", "HMM ID", "HMM Description")
+      
+      Screening$res_profile <- res_profile %>%
+        relocate(c("Gene Symbol", "Sequence Name", "Element Subtype", "Class", 
+                   "Subclass", "Scope", "Contig ID", "Target Length", "Alignment Length",
+                   "Start", "Stop", "Strand"))
+      
+      # Generate gene profile table
+      output$gs_profile_table <- DT::renderDataTable(
+        Screening$res_profile,
+        selection = "single",
+        rownames= FALSE,
+        options = list(pageLength = 10, scrollX = TRUE,
+                       autoWidth = TRUE,
+                       columnDefs = list(list(width = '400px', targets = c("Sequence Name",
+                                                                           "Name of Closest Sequence"))),
+                       columnDefs = list(list(width = 'auto', targets = "_all")),
+                       columnDefs = list(list(searchable = TRUE,
+                                              targets = "_all")),
+                       initComplete = DT::JS(
+                         "function(settings, json) {",
+                         "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                         "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                         # "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                         # "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                         "}"
+                       ),
+                       drawCallback = DT::JS(
+                         "function(settings) {",
+                         # "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                         # "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                         "}"
+                       ))
+      )
+    } else {
+      output$gs_profile_table <- NULL
+    }
+  })
+
+  #Resistance profile selection table
+  observe({
+    req(DB$meta, DB$data)
+    output$gs_isolate_table <- renderDataTable(
+      select(DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ], -c(3, 4, 10, 11, 12)),
+      selection = "single",
+      rownames= FALSE,
+      options = list(pageLength = 10,
+                     columnDefs = list(list(searchable = TRUE,
+                                            targets = "_all")),
+                     initComplete = DT::JS(
+                       "function(settings, json) {",
+                       "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                       "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                       "}"
+                     ),
+                     drawCallback = DT::JS(
+                       "function(settings) {",
+                       "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                       "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                       "}"
+                     ))
+    )
+  })
+  
+  observe({
+    req(input$screening_res_sel, DB$database, DB$scheme, DB$data)
+    if(!is.null(Screening$status_df) &
+       !is.null(input$screening_res_sel) & 
+       !is.null(Screening$status_df$status) & 
+       !is.null(Screening$status_df$isolate)) {
+      if(length(input$screening_res_sel) > 0) {
+        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
+          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
+            results <- read.delim(file.path(DB$database, gsub(" ", "_", DB$scheme), "Isolates", 
+                                            input$screening_res_sel, "resProfile.tsv"))
+            
+            output$screening_table <- renderDataTable(
+              select(results, c(6, 7, 8, 9, 11)),
+              selection = "single",
+              options = list(pageLength = 10,
+                             columnDefs = list(list(searchable = TRUE,
+                                                    targets = "_all")),
+                             initComplete = DT::JS(
+                               "function(settings, json) {",
+                               "$('th:first-child').css({'border-top-left-radius': '5px'});",
+                               "$('th:last-child').css({'border-top-right-radius': '5px'});",
+                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                               "}"
+                             ),
+                             drawCallback = DT::JS(
+                               "function(settings) {",
+                               "$('tbody tr:last-child td:first-child').css({'border-bottom-left-radius': '5px'});",
+                               "$('tbody tr:last-child td:last-child').css({'border-bottom-right-radius': '5px'});",
+                               "}"
+                             )))
+          } else {output$screening_table <- NULL}
+        }
+      } else {
+        output$screening_table <- NULL
+      }
+    } else {
+      output$screening_table <- NULL
+    }
+      
+  })
+  
+  # Availablity feedback
+  output$gene_screening_info <- renderUI({
+    req(DB$data)
+    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
+          )
+        )
+      )
+    } else {
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
+          )
+        )
+      )
+    }
+  })
+  
+  output$gene_resistance_info <- renderUI({
+    req(DB$data)
+    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-check" style="font-size:20px;color:#90EE90; position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, "available for gene screening with NCBI/AMRFinder."))
+          )
+        )
+      )
+    } else {
+      p(
+        HTML(
+          paste(
+            '<i class="fa-solid fa-xmark" style="font-size:20px;color:#ff0000;position:relative; top:27px;margin-right: 10px;"></i>',
+            tags$span(style="color: white; font-size: 15px; position:relative; top:25px", 
+                      paste(DB$scheme, " not available for gene screening with NCBI/AMRFinder."))
+          )
+        )
+      )
+    }
+  })
+  
+  # Screening Interface
+  
+  output$screening_interface <- renderUI({
+    req(DB$data)
+    if(gsub(" ", "_", DB$scheme) %in% amrfinder_species) {
+      column(
+        width = 12,
+        fluidRow(
+          column(1),
+          column(
+            width = 3,
+            align = "center",
+            br(), br(),
+            p(
+              HTML(
+                paste(
+                  tags$span(style='color: white; font-size: 15px; margin-bottom: 0px', 'Select Isolates for Screening')
+                )
+              )
+            ),
+            if(Screening$picker_status) {
+              div(
+                class = "screening_div",
+                pickerInput(
+                  "screening_select",
+                  "",
+                  choices = list(
+                    Unscreened = if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
+                    },
+                    Screened =  if (length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]) == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+                    },
+                    `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
+                      as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
+                    } else {
+                      DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
+                    }
+                  ),
+                  choicesOpt = list(
+                    disabled = c(
+                      rep(FALSE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])),
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])),
+                      rep(TRUE, length(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]))
+                    )
+                  ),
+                  options = list(
+                    `live-search` = TRUE,
+                    `actions-box` = TRUE,
+                    size = 10,
+                    style = "background-color: white; border-radius: 5px;"
+                  ),
+                  multiple = TRUE
+                )
+              )
+            } else {
+              div(
+                class = "screening_div",
+                pickerInput(
+                  "screening_select",
+                  "",
+                  choices = Screening$picker_choices,
+                  selected = Screening$picker_selected,
+                  options = list(
+                    `live-search` = TRUE,
+                    `actions-box` = TRUE,
+                    size = 10,
+                    style = "background-color: white; border-radius: 5px;"
+                  ),
+                  multiple = TRUE
+                ) 
+              )
+            },
+            br(), br(),
+            uiOutput("genome_path_gs")
+          ),
+          column(
+            width = 3,
+            uiOutput("screening_start")
+          ),
+          column(
+            width = 3,
+            align = "center",
+            br(), br(),
+            uiOutput("screening_result_sel")
+          ),
+          column(1)
+        ),
+        fluidRow(
+          column(1),
+          column(
+            width = 10,
+            br(), br(), 
+            uiOutput("screening_result"),
+            br(), br(), br(), br()
+          )
+        )
+      )
+    }
+  })
+  
+  ### Screening Events ----
+  
+  observe({
+    req(DB$data, input$gs_view)
+    if(input$gs_view == "Table") {
+      meta_gs <- DB$meta_gs[which(DB$meta_gs$Screened == "Yes"), ]
+      Screening$selected_isolate <- meta_gs$`Assembly ID`[input$gs_isolate_table_rows_selected]
+    } else if(input$gs_view == "Picker") {
+      Screening$selected_isolate <- input$gs_profile_select
+    }
+  })
+  
+  output$download_resistance_profile <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save resistance profile table ", Screening$selected_isolate, "_Profile.csv"))
+      
+      paste0(format(Sys.Date()), "_", Screening$selected_isolate, "_Profile.csv")
+    },
+    content = function(file) {
+      write.table(
+        Screening$res_profile,
+        file, 
+        sep = ";",
+        row.names = FALSE, 
+        quote = FALSE
+      ) 
+    }
+  )
+  
+  # Reset screening 
+  observeEvent(input$screening_reset_bttn, {
+    log_print("Reset gene screening")
+    
+    # reset status file
+    sapply(Screening$status_df$isolate, remove.screening.status)
+    
+    # set feedback variables
+    Screening$status <- "idle"
+    Screening$status_df <- NULL
+    Screening$choices <- NULL
+    Screening$picker_status <- TRUE
+    Screening$first_result <- NULL
+    
+    # change reactive UI
+    output$screening_table <- NULL
+    output$screening_result <- NULL
+    output$screening_fail <- NULL
+    
+    updatePickerInput(session, "screening_select", selected = character(0))
+    
+    # disable isolate picker
+    shinyjs::runjs("$('#screening_select').prop('disabled', false);")
+    shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
+  })
+  
+  # Cancel screening
+  observeEvent(input$screening_cancel, {
+    showModal(
+      modalDialog(
+        paste0(
+          "Gene screening is still pending. Stopping this process will cancel the screening."
+        ),
+        title = "Reset Multi Typing",
+        fade = TRUE,
+        easyClose = TRUE,
+        footer = tagList(
+          modalButton("Cancel"),
+          actionButton("conf_screening_cancel", "Stop", class = "btn btn-danger")
+        )
+      )
+    )
+  })
+  
+  observeEvent(input$conf_screening_cancel, {
+    log_print("Cancelled gene screening")
+    removeModal()
+    
+    show_toast(
+      title = "Gene Screening Terminated",
+      type = "warning",
+      position = "bottom-end",
+      timer = 6000
+    )
+    
+    # terminate screening
+    system(paste("kill $(pgrep -f 'execute/screening.sh')"), wait = FALSE)
+    system(paste("killall -TERM tblastn"), wait = FALSE)
+    
+    # reset status file
+    sapply(Screening$status_df$isolate, remove.screening.status)
+    
+    # set feedback variables
+    Screening$status <- "idle"
+    Screening$status_df <- NULL
+    Screening$choices <- NULL
+    Screening$picker_status <- TRUE
+    Screening$first_result <- NULL
+    
+    # change reactive UI
+    output$screening_table <- NULL
+    output$screening_result <- NULL
+    
+    updatePickerInput(session, "screening_select", selected = character(0))
+    
+    # disable isolate picker
+    shinyjs::runjs("$('#screening_select').prop('disabled', false);")
+    shinyjs::runjs("$('#screening_select').selectpicker('refresh');")
+  })
+  
+  # Get selected assembly
+  observe({
+    req(DB$data, Screening$status)
+    if (length(input$screening_select) < 1) {
+      output$genome_path_gs <- renderUI(HTML(
+        paste("<span style='color: white; font-style:italic'>", length(input$screening_select), " isolate(s) queried for screening")
+      ))
+      
+      output$screening_start <- NULL
+      
+    } else if (length(input$screening_select) > 0) {
+      
+      output$screening_start <- renderUI({
+        
+        fluidRow(
+          column(
+            width = 12,
+            br(), br(), 
+            if(length(input$screening_select) < 1) {
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+                    paste("<span style='color: white; font-style:italic'>", 
+                          "&nbsp Select Isolate(s) for Screening")))
+                )
+              )
+            } else if(Screening$status == "finished") {
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:white"></i>',
+                    paste("<span style='color: white; font-style:italic'>", 
+                          "&nbsp Reset to Perform Screening Again")))
+                ),
+                actionButton(
+                  "screening_reset_bttn",
+                  "Reset",
+                  icon = icon("arrows-rotate")
+                ),
+                if(!is.null(Screening$status_df)) {
+                  p(
+                    HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
+                               sum(Screening$status_df$status != "unfinished"), "/",
+                               nrow(Screening$status_df), " Isolate(s) screened"))
+                  )
+                }
+              )
+            } else if(Screening$status == "idle") {
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
+                    paste("<span style='color: white;'>",
+                          "&nbsp Screening Ready")))
+                ),
+                actionButton(
+                  inputId = "screening_start_button",
+                  label = "Start",
+                  icon = icon("circle-play")
+                )
+              )
+            } else if(Screening$status == "started") {
+              column(
+                width = 12,
+                align = "center",
+                p(
+                  HTML(paste(
+                    '<i class="fa-solid fa-clock" style="font-size:15px;color:white"></i>',
+                    paste("<span style='color: white;'>",
+                          "&nbsp Running Screening ...")))
+                ),
+                fluidRow(
+                  column(3),
+                  column(
+                    width = 3,
+                    actionButton(
+                      inputId = "screening_cancel",
+                      label = "Terminate",
+                      icon = icon("ban")
+                    )
+                  ),
+                  column(
+                    width = 3,
+                    HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:22px;color:white;margin-top:27px;position:relative;left:20px"></i>'))
+                  )
+                ),
+                if(!is.null(Screening$status_df)) {
+                  p(
+                    HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
+                               sum(Screening$status_df$status != "unfinished"), "/",
+                               nrow(Screening$status_df), " isolate(s) screened"))
+                  )
+                }
+              )
+            }
+          )
+        )
+      })
+    } else {NULL}
+  })
+  
+  #### Running Screening ----
+  
+  observeEvent(input$screening_start_button, {
+    
+    if(tail(readLogFile(), 1) != "0") {
+      show_toast(
+        title = "Pending Multi Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      
+      log_print("Started gene screening")
+      
+      Screening$status <- "started"
+      Screening$picker_choices <- list(
+        Unscreened = if (sum(DB$data$Screened == "No") == 1) {
+          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "No")])
+        } else {
+          DB$data$`Assembly ID`[which(DB$data$Screened == "No")]
+        },
+        Screened =  if (sum(DB$data$Screened == "Yes") == 1) {
+          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")])
+        } else {
+          DB$data$`Assembly ID`[which(DB$data$Screened == "Yes")]
+        },
+        `No Assembly File` =  if (sum(DB$data$Screened == "NA") == 1) {
+          as.list(DB$data$`Assembly ID`[which(DB$data$Screened == "NA")])
+        } else {
+          DB$data$`Assembly ID`[which(DB$data$Screened == "NA")]
+        }
+      )
+      Screening$picker_selected <- input$screening_select
+      Screening$picker_status <- FALSE
+      
+      show_toast(
+        title = "Gene screening started",
+        type = "success",
+        position = "bottom-end",
+        timer = 6000
+      )
+      
+      Screening$meta_df <- data.frame(wd = getwd(),
+                                 selected = paste(
+                                   file.path(DB$database, gsub(" ", "_", DB$scheme),
+                                             "Isolates", input$screening_select,
+                                             paste0(input$screening_select, ".zip")), 
+                                   collapse = " "),
+                                 species = gsub(" ", "_", DB$scheme))
+      
+      Screening$status_df <- data.frame(isolate = basename(gsub(".zip", "", str_split_1(Screening$meta_df$selected, " "))), 
+                                        status = "unfinished")
+      
+       # Reset screening status
+      sapply(Screening$status_df$isolate, remove.screening.status)
+      
+      saveRDS(Screening$meta_df, paste0(getwd(), "/execute/screening_meta.rds"))
+      
+      # Disable pickerInput
+      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').prop('disabled', true);"))
+      shinyjs::delay(200, shinyjs::runjs("$('#screening_select').selectpicker('refresh');"))
+    
+      # System execution screening.sh
+      system(paste("bash", paste0(getwd(), "/execute/screening.sh")), wait = FALSE)
+    }
+  })
+  
+  observe({
+    req(DB$data, Screening$status, input$screening_res_sel, Screening$status_df)
+    if(!is.null(Screening$status_df) &
+       !is.null(Screening$status_df$status) & 
+       !is.null(Screening$status_df$isolate) &
+       !is.null(input$screening_res_sel)) {
+      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
+        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
+          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "success") {
+            output$screening_result <- renderUI(
+              column(
+                width = 12,
+                hr(), br(),
+                dataTableOutput("screening_table") 
+              )
+            )
+          } else {
+            output$screening_result <- renderUI(
+              column(
+                width = 12,
+                hr(), br(),
+                verbatimTextOutput("screening_fail")
+              )
+            )
+          }
+        }
+      } else {
+        output$screening_result <- NULL
+      }
+    } else {
+      output$screening_result <- NULL
+    }
+  })
+  
+  observe({
+    req(DB$data, Screening$status, input$screening_res_sel)
+    if(!is.null(Screening$status_df) &
+       !is.null(Screening$status_df$status) & 
+       !is.null(Screening$status_df$isolate) &
+       !is.null(input$screening_res_sel)) {
+      if(Screening$status != "idle" & length(input$screening_res_sel) > 0) {
+        if(any(Screening$status_df$isolate == input$screening_res_sel)) {
+          if(Screening$status_df$status[which(Screening$status_df$isolate == input$screening_res_sel)] == "fail") {
+            output$screening_fail <- renderPrint({
+              cat(paste(readLines(file.path(DB$database, gsub(" ", "_", DB$scheme),
+                                            "Isolates", input$screening_res_sel, "status.txt")),"\n"))
+            })
+          }
+        }
+      } else {
+        output$screening_fail <- NULL
+      }
+    } else {
+      output$screening_fail <- NULL
+    }
+  })
+  
+  observe({
+    req(DB$data)
+    if(!is.null(Screening$status)) {
+      if(Screening$status != "idle") {
+        
+        # start status screening for user feedback
+        check_screening()
+        
+        if(isTRUE(Screening$first_result)) {
+          output$screening_result_sel <- renderUI(
+            column(
+              width = 12,
+              align = "center",
+              selectInput(
+                "screening_res_sel",
+                label = h5("Select Result", style = "color:white; margin-bottom: 28px; margin-top: -10px;"),
+                choices = ""
+              ),
+              if(!is.null(Screening$status_df)) {
+                p(HTML(paste("<span style='color: white; font-style:italic; position: relative; top:41px'>", 
+                             if(sum(Screening$status_df$status == "success") == 1) {
+                               "1 success &nbsp / &nbsp"
+                             } else {
+                               paste0(sum(Screening$status_df$status == "success"), " successes &nbsp / &nbsp")
+                             },
+                             if(sum(Screening$status_df$status == "fail") == 1) {
+                               "1 failure"
+                             } else {
+                               paste0(sum(Screening$status_df$status == "fail"), " failures")
+                             })))
+              }
+            )
+          )
+          
+          Screening$first_result <- FALSE
+        }
+      } else if(Screening$status == "idle") {
+        output$screening_result_sel <- NULL
+      }
+    }
+  }) 
+    
+  check_screening <- reactive({
+    invalidateLater(500, session)
+    
+    req(Screening$status_df)
+    
+    if(Screening$status == "started") {
+      
+      Screening$status_df$status <- sapply(Screening$status_df$isolate, check_status)
+      
+      if(any("unfinished" != Screening$status_df$status) &
+         !identical(Screening$choices, Screening$status_df$isolate[which(Screening$status_df$status != "unfinished")])) {
+        
+        status_df <- Screening$status_df[which(Screening$status_df$status != "unfinished"),]
+        
+        Screening$choices <- Screening$status_df$isolate[which(Screening$status_df$status == "success" |
+                                                                 Screening$status_df$status == "fail")]
+        
+        if(sum(Screening$status_df$status != "unfinished") > 0) {
+          if(is.null(Screening$first_result)) {
+            Screening$first_result <- TRUE
+          }
+        }
+        
+        if(tail(status_df$status, 1) == "success") {
+          
+          # Changing "Screened" metadata variable in database
+          Database <- readRDS(file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+          
+          Database[["Typing"]]$Screened[which(Database[["Typing"]]["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
+
+          saveRDS(Database, file.path(DB$database, gsub(" ", "_", DB$scheme), "Typing.rds"))
+
+          DB$data$Screened[which(DB$data["Assembly ID"] == tail(Screening$choices, 1))] <- "Yes"
+          
+          DB$meta_gs <- select(DB$data, c(1, 3:13))
+          DB$meta <- select(DB$data, 1:(13 + nrow(DB$cust_var)))
+          DB$meta_true <- DB$meta[which(DB$data$Include == TRUE),]
+          
+          show_toast(
+            title = paste("Successful screening of", tail(Screening$choices, 1)),
+            type = "success",
+            position = "bottom-end",
+            timer = 6000)
+          
+          updateSelectInput(session = session,
+                            inputId = "screening_res_sel",
+                            choices = Screening$choices,
+                            selected = tail(Screening$choices, 1))
+          
+        } else if(tail(status_df$status, 1) == "fail") {
+          
+          show_toast(
+            title = paste("Failed screening of", tail(status_df$isolate, 1)),
+            type = "error",
+            position = "bottom-end",
+            timer = 6000)
+          
+          updateSelectInput(session = session,
+                            inputId = "screening_res_sel",
+                            choices = Screening$choices,
+                            selected = tail(Screening$choices, 1))
+        }
+        
+        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+          Screening$status <- "finished"
+        }
+      } else {
+        if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+          Screening$status <- "finished"
+        }
+      }
+      
+      if(sum("unfinished" != Screening$status_df$status) == length(Screening$status_df$status)) {
+        Screening$status <- "finished"
+      }
+    }
+  }) 
+  
+  
+  # _______________________ ####
+  
+  ## Typing  ----
+  
+  # Render Single/Multi Switch
+  
+  readLogFile <- reactive({
+    invalidateLater(5000, session)
+    readLines(paste0(getwd(), "/logs/script_log.txt"))
+  })
+  
+  # Render sidebar dependent on data presence
+  # No sidebar
+  output$typing_sidebar <- renderUI({
+    if(!is.null(DB$exist)) {
+      if(DB$exist) {
+        NULL
+      } else {
+        column(
+          width = 12,
+          align = "center",
+          br(), br(),
+          p(
+            HTML(
+              paste(
+                tags$span(style='color: white; font-size: 18px; margin-bottom: 0px', 'Typing Mode')
+              )
+            )
+          ),
+          radioGroupButtons(
+            inputId = "typing_mode",
+            choices = c("Single", "Multi"),
+            selected = "Single",
+            checkIcon = list(
+              yes = icon("square-check"),
+              no = icon("square")
+            )
+          ),
+          br()
+        )
+      }
+    }
+    
+  })
+  
+  # No db typing message
+  output$typing_no_db <- renderUI({
+    if(!is.null(DB$exist)) {
+      if(DB$exist) {
+        column(
+          width = 4,
+          align = "left",
+          br(),
+          br(),
+          br(),
+          br(),
+          p(
+            HTML(
+              paste0(
+                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 50px', 'To initiate allelic typing, a cgMLST scheme must be downloaded first.'
+                )
+              )
+            )
+          )
+        )
+      } else {NULL}
+    } else {NULL}
+  })
+  
+  ### Single Typing ----
+  
+  #### Render UI Elements ----
+  
+  # Render single typing naming issues
+  output$single_select_issues <- renderUI({
+    req(input$assembly_id)
+    
+    if(nchar(trimws(input$assembly_id)) < 1) {
+      ass_id <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
+    } else {
+      ass_id <- trimws(input$assembly_id)
+    }
+    
+    if(ass_id %in% unlist(DB$data["Assembly ID"])) {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Assembly ID already present in database.")))
+    } else if (ass_id == "") {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Empty Assembly ID.")))
+    } else if (grepl("[()/\\:*?\"<>|]", ass_id)) {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Invalid Assembly ID. Avoid special characters.")))
+    } else if(grepl(" ", ass_id)) {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+        paste("<span style='color: white; font-style:italic'>", 
+              "&nbsp Invalid Assembly ID. Avoid empty spaces.")))
+    } else {HTML(paste(
+      '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
+      paste("<span style='color: white; font-style:italic'>",
+            "&nbsp Assembly ID compatible with local database.")))}
+  })
+  
+  # Render Typing Results if finished
+  observe({
+    if(Typing$progress_format_end == 999999) {
+      if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
+        if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
+          output$typing_result_table <- renderRHandsontable({
+            Typing$typing_result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
+            Typing$typing_result_table <- mutate_all(Typing$typing_result_table, as.character)
+            if(nrow(Typing$typing_result_table) > 0) {
+              if(nrow(Typing$typing_result_table) > 15) {
+                rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
+                              stretchH = "all", height = 500, readOnly = TRUE,
+                              contextMenu = FALSE) %>%
+                  hot_cols(columnSorting = TRUE) %>%
+                  hot_rows(rowHeights = 25) %>%
+                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter",
+                          cellWidths = list(100, 160, NULL)) %>%
+                  hot_col("Value", renderer=htmlwidgets::JS(
+                    "function(instance, td, row, col, prop, value, cellProperties) {
+                      if (value.length > 8) {
+                        value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                      }
+                      td.innerHTML = value;
+                      td.style.textAlign = 'center';
+                      return td;
+                     }"
+                  ))
+              } else {
+                rhandsontable(Typing$typing_result_table, rowHeaders = NULL, 
+                              stretchH = "all", readOnly = TRUE,
+                              contextMenu = FALSE,) %>%
+                  hot_cols(columnSorting = TRUE) %>%
+                  hot_rows(rowHeights = 25) %>%
+                  hot_col(1:ncol(Typing$typing_result_table), valign = "htMiddle", halign = "htCenter",
+                          cellWidths = list(100, 160, NULL)) %>%
+                  hot_col("Value", renderer=htmlwidgets::JS(
+                    "function(instance, td, row, col, prop, value, cellProperties) {
+                      if (value.length > 8) {
+                        value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                      }
+                      td.innerHTML = value;
+                      td.style.textAlign = 'center';
+                      return td;
+                     }"
+                  ))
+              }
+            }
+          })
+          
+          output$single_typing_results <- renderUI({
+            result_table <- readRDS(paste0(getwd(), "/execute/event_df.rds"))
+            number_events <- nrow(result_table)
+            
+            n_new <- length(grep("New Variant", result_table$Event))
+            
+            n_missing <- number_events - n_new
+            
+            # Show results table only if successful typing 
+            if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
+              if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
+                if(number_events > 0) {
+                  column(
+                    width = 12,
+                    HTML(paste("<span style='color: white;'>", 
+                               length(Typing$scheme_loci_f) - number_events,
+                               "loci were assigned a variant from local scheme.")),
+                    br(), 
+                    HTML(paste("<span style='color: white;'>", 
+                               n_missing,
+                               if(n_missing == 1) " locus not assigned (<i>NA</i>)." else " loci not assigned (<i>NA</i>).")),
+                    br(),
+                    HTML(paste("<span style='color: white;'>", 
+                               n_new,
+                               if(n_new == 1) " locus with new variant."  else " loci with new variants.")),
+                    br(), br(),
+                    rHandsontableOutput("typing_result_table")
+                  )
+                } else {
+                  column(
+                    width = 12,
+                    HTML(paste("<span style='color: white;'>", 
+                               length(Typing$scheme_loci_f),
+                               "successfully assigned from local scheme."))
+                  )
+                }
+              }
+            }
+          })
+          
+        } else {
+          
+          output$single_typing_results <- NULL
+          
+        }
+      } else {
+        output$single_typing_results <- NULL
+      }
+    }
+    
+  })
+  
+  # Render Initiate Typing UI
+  output$initiate_typing_ui <- renderUI({
+    column(
+      width = 4,
+      align = "center",
+      br(),
+      br(),
+      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+      br(),
+      br(),
+      p(
+        HTML(
+          paste(
+            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File (FASTA)')
+          )
+        )
+      ),
+      fluidRow(
+        column(1),
+        column(
+          width = 11,
+          align = "center",
+          shinyFilesButton(
+            "genome_file",
+            "Browse" ,
+            icon = icon("file"),
+            title = "Select the assembly in .fasta/.fna/.fa format:",
+            multiple = FALSE,
+            buttonType = "default",
+            class = NULL,
+            root = path_home()
+          ),
+          br(),
+          br(),
+          uiOutput("genome_path"),
+          br()
+        )
+      )
+    )
+  })
+  
+  # Render Declare Metadata UI
+  
+  observe({
+    if (nrow(Typing$single_path) < 1) {
+      output$genome_path <- renderUI(HTML(
+        paste("<span style='color: white; margin-left:-30px'>", "No file selected.")
+      ))
+      
+      # dont show subsequent metadata declaration and typing start UI
+      output$metadata_single_box <- NULL
+      output$start_typing_ui <- NULL
+      
+    } else if (nrow(Typing$single_path) > 0) {
+      
+      if (str_detect(str_sub(Typing$single_path$name, start = -6), ".fasta") | 
+          str_detect(str_sub(Typing$single_path$name, start = -6), ".fna") | 
+          str_detect(str_sub(Typing$single_path$name, start = -6), ".fa")) {
+        
+        # Render selected assembly path
+        output$genome_path <- renderUI({
+          HTML(
+            paste(
+              "<span style='color: white; margin-left:-30px; font-weight: bolder'>",
+              as.character(Typing$single_path$name)
+            )
+          )
+        })
+        
+        # Render metadata declaration box
+        output$metadata_single_box <- renderUI({
+          
+          # Render placeholder 
+          updateTextInput(session, "assembly_id", value = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
+          updateTextInput(session, "assembly_name", value = as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name))))
+          
+          column(
+            width = 3,
+            align = "center",
+            br(), br(),
+            h3(p("Declare Metadata"), style = "color:white; margin-left:-40px"),
+            br(), br(),
+            div(
+              class = "multi_meta_box",
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "90%",
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("assembly_id",
+                                value = "",
+                                label = "",
+                                width = "80%")
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 12,
+                    uiOutput("single_select_issues")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("assembly_name",
+                                label = "",
+                                width = "80%")
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      dateInput("append_isodate",
+                                label = "",
+                                width = "80%",
+                                max = Sys.Date())
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("append_host",
+                                label = "",
+                                width = "80%")
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table_country",
+                      pickerInput(
+                        "append_country",
+                        label = "",
+                        choices = list("Common" = sel_countries,
+                                       "All Countries" = country_names),
+                        options = list(
+                          `live-search` = TRUE,
+                          `actions-box` = TRUE,
+                          size = 10,
+                          style = "background-color: white; border-radius: 5px;"
+                        ),
+                        width = "90%"
+                      )
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput(
+                        "append_city",
+                        label = "",
+                        width = "80%"
+                      )
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 12,
+                    align = "center",
+                    br(), br(),
+                    actionButton(
+                      inputId = "conf_meta_single",
+                      label = "Confirm"
+                    ),
+                    br()
+                  )
+                ),
+                br()
+              )
+            )
+          )
+        })
+      } else {
+        show_toast(
+          title = "Wrong file type (only fasta/fna/fa)",
+          type = "error",
+          position = "bottom-end",
+          timer = 6000
+        )
+      }
+    }
+  })
+  
+  # Get genome datapath
+  
+  observe({
+    # Get selected Genome in Single Mode
+    shinyFileChoose(input,
+                    "genome_file",
+                    roots = c(Home = path_home(), Root = "/"),
+                    defaultRoot = "Home",
+                    session = session,
+                    filetypes = c('', 'fasta', 'fna', 'fa'))
+    Typing$single_path <- parseFilePaths(roots = c(Home = path_home(), Root = "/"), input$genome_file)
+    
+  })
+  
+  #### Run blat ----
+  
+  observeEvent(input$typing_start, {
+    
+    log_print("Input typing_start")
+    
+    if(tail(readLogFile(), 1) != "0") {
+      show_toast(
+        title = "Pending Multi Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if (Screening$status == "started") {
+      show_toast(
+        title = "Pending Gene Screening",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      
+      if(!is.null(DB$data)) {
+        if(sum(apply(DB$data, 1, anyNA)) >= 1) {
+          DB$no_na_switch <- TRUE
+        } else {
+          DB$no_na_switch <- FALSE
+        }
+      }
+      
+      # Activate entry detection
+      DB$check_new_entries <- TRUE
+      
+      Typing$single_end <- FALSE
+      
+      Typing$progress_format_start <- 0
+      Typing$progress_format_end <- 0
+      
+      # Remove Initiate Typing UI 
+      output$initiate_typing_ui <- NULL
+      output$metadata_single_box <- NULL
+      output$start_typing_ui <- NULL
+      
+      # status feedback
+      Typing$status <- "Processing"
+      
+      # Locate folder containing cgMLST scheme
+      search_string <- paste0(gsub(" ", "_", DB$scheme), "_alleles")
+      
+      scheme_folders <- dir_ls(paste0(DB$database, "/", gsub(" ", "_", DB$scheme)))
+      
+      if (any(grepl(search_string, scheme_folders))) {
+        
+        # reset results file 
+        if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
+          unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
+        }
+        
+        # blat initiate index
+        scheme_select <- as.character(scheme_folders[which(grepl(search_string, scheme_folders))])
+        
+        show_toast(
+          title = "Typing Initiated",
+          type = "success",
+          position = "bottom-end",
+          timer = 6000
+        )
+        
+        log_print("Initiated single typing")
+        
+        ### Run blat Typing
+        
+        single_typing_df <- data.frame(
+          db_path = DB$database,
+          wd = getwd(),
+          save = input$save_assembly_st,
+          scheme = paste0(gsub(" ", "_", DB$scheme)),
+          genome = Typing$single_path$datapath,
+          alleles = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", search_string)
+        )
+        
+        saveRDS(single_typing_df, "execute/single_typing_df.rds")
+        
+        # Execute single typing script
+        system(paste("bash", paste0(getwd(), "/execute/single_typing.sh")), 
+               wait = FALSE)
+        
+        scheme_loci <- list.files(path = scheme_select, full.names = TRUE)
+        
+        # Filter the files that have FASTA extensions
+        Typing$scheme_loci_f <-
+          scheme_loci[grep("\\.(fasta|fa|fna)$", scheme_loci, ignore.case = TRUE)]
+        
+        output$single_typing_progress <- renderUI({
+          fluidRow(
+            br(), br(), 
+            column(width = 1),
+            column(
+              width = 3,
+              h3(p("Pending Single Typing ..."), style = "color:white")
+            ),
+            br(), br(), br(), 
+            fluidRow(
+              column(width = 1),
+              column(
+                width = 4,
+                br(), br(), br(),
+                fluidRow(
+                  column(
+                    width = 12,
+                    uiOutput("reset_single_typing"),
+                    HTML(
+                      paste(
+                        "<span style='color: white; font-weight: bolder'>",
+                        as.character(Typing$single_path$name)
+                      )
+                    ),
+                    br(), br(),
+                    progressBar(
+                      "progress_bar",
+                      value = 0,
+                      display_pct = TRUE,
+                      title = ""
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 12,
+                    uiOutput("typing_formatting"),
+                    uiOutput("typing_fin")
+                  )
+                )
+              ),
+              column(1),
+              column(
+                width = 5,
+                br(), br(), br(),
+                uiOutput("single_typing_results")
+              )
+            )
+          )
+        })
+      } else {
+        log_print("Folder containing cgMLST alleles not in working directory")
+        
+        show_alert(
+          title = "Error",
+          text = paste0(
+            "Folder containing cgMLST alleles not in working directory.",
+            "\n",
+            "Download cgMLST Scheme for selected Organism first."
+          ),
+          type = "error"
+        )
+      }
+    }
+  })
+  
+  # Function to update Progress Bar
+  update <- reactive({
+    invalidateLater(3000, session)
+    
+    # write progress in process tracker
+    cat(
+      c(length(list.files(paste0(getwd(), "/execute/blat_single/results"))),
+        readLines(paste0(getwd(), "/logs/progress.txt"))[-1]), 
+      file = paste0(getwd(), "/logs/progress.txt"),
+      sep = "\n"
+    )
+    
+    progress <- readLines(paste0(getwd(), "/logs/progress.txt"))
+    
+    # if typing with blat is finished -> "attaching" phase started
+    if(!is.na(progress[1])) {
+      if(!is.na(progress[2])) {
+        if(progress[2] == "888888") {
+          Typing$progress_format_start <- progress[2]
+          Typing$pending_format <- progress[2]
+          Typing$status <- "Attaching"
+        }
+      }
+      # "attaching" phase completed
+      if(!is.na(progress[3])) {
+        if(progress[3] == "999999") {
+          Typing$progress_format_end <- progress[3]
+          Typing$entry_added <- progress[3]
+          Typing$status <- "Finalized"
+        }
+      }
+      Typing$progress <- as.numeric(progress[1])
+      floor((Typing$progress / length(Typing$scheme_loci_f)) * 100)
+    } else {
+      floor((Typing$progress / length(Typing$scheme_loci_f)) * 100)
+    }
+  })
+  
+  # Observe Typing Progress
+  observe({
+    
+    if(readLogFile()[1] == "0") {
+      # Update Progress Bar
+      updateProgressBar(
+        session = session,
+        id = "progress_bar",
+        value = update(),
+        total = 100,
+        title = paste0(as.character(Typing$progress), "/", length(Typing$scheme_loci_f), " loci screened")
+      )
+    }
+    
+    if (Typing$progress_format_start == 888888) {
+      output$typing_formatting <- renderUI({
+        column(
+          width = 12,
+          align = "center",
+          br(),
+          fluidRow(
+            column(
+              width = 6,
+              HTML(paste("<span style='color: white;'>", "Transforming data ..."))
+            ),
+            column(
+              width = 3,
+              align = "left",
+              HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:20px;color:white"></i>'))
+            )
+          )
+        )
+      })
+    } else {
+      output$typing_formatting <- NULL
+    }
+    
+    # Render when finalized  
+    if (Typing$progress_format_end == 999999) {
+      
+      output$typing_formatting <- NULL
+      
+      output$typing_fin <- renderUI({
+        fluidRow(
+          column(
+            width = 12,
+            align = "center",
+            br(), br(),
+            if(file.exists(paste0(getwd(),"/logs/single_typing_log.txt"))) {
+              if(str_detect(tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1), "Successful")) {
+                req(Typing$scheme_loci_f, Typing$typing_result_table)
+                if(sum(Typing$typing_result_table$Event != "New Variant") >  (0.5 * length(Typing$scheme_loci_f))){
+                  HTML(
+                    paste("<span style='color: white;'>", 
+                          sub(".*Successful", "Finished", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
+                          paste("<span style='color: orange;'>", "Warning: Isolate contains large number of failed allele assignments."),
+                          paste("<span style='color: white;'>", "Reset to start another typing process."),
+                          sep = '<br/>\n'))                    
+                } else {
+                  HTML(paste("<span style='color: white;'>", 
+                             sub(".*Successful", "Successful", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
+                             "Reset to start another typing process.", sep = '<br/>'))
+                }
+              } else {
+                HTML(paste("<span style='color: white;'>", 
+                           sub(".*typing", "Typing", tail(readLines(paste0(getwd(),"/logs/single_typing_log.txt")), 1)),
+                           "Reset to start another typing process.", sep = '<br/>'))
+              }
+            },
+            br(), br(),
+            actionButton(
+              "reset_single_typing",
+              "Reset",
+              icon = icon("arrows-rotate")
+            )
+          )
+        )
+      })
+    } else {
+      output$typing_fin <- NULL
+      output$single_typing_results <- NULL
+    }
+    
+  })
+  
+  #### Declare Metadata  ----
+  
+  observeEvent(input$conf_meta_single, {
+    
+    if(nchar(trimws(input$assembly_id)) < 1) {
+      ass_id <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
+    } else {
+      ass_id <- trimws(input$assembly_id)
+    }
+    
+    if(nchar(trimws(input$assembly_name)) < 1) {
+      ass_name <- as.character(gsub("\\.fasta|\\.fna|\\.fa", "", basename(Typing$single_path$name)))
+    } else {
+      ass_name <- trimws(input$assembly_name)
+    }
+    
+    if(ass_id %in% unlist(DB$data["Assembly ID"])) {
+      show_toast(
+        title = "Assembly ID already present",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (isFALSE(Typing$reload)) {
+      show_toast(
+        title = "Reload Database first",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if (ass_id == "") {
+    show_toast(
+      title = "Empty Assembly ID",
+      type = "error",
+      position = "bottom-end",
+      timer = 3000
+      )
+    } else if (grepl("[()/\\:*?\"<>|]", ass_id)) {
+      show_toast(
+        title = "Invalid Assembly ID. No special characters allowed: ()/\\:*?\"<>|",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if(grepl(" ", ass_id)) {
+      show_toast(
+        title = "Empty spaces in Assembly ID not allowed",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if(Screening$status == "started") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      
+      log_print("Single typing metadata confirmed")
+      
+      meta_info <- data.frame(assembly_id = ass_id,
+                              assembly_name = ass_name,
+                              cgmlst_typing = DB$scheme,
+                              append_isodate = input$append_isodate,
+                              append_host = trimws(input$append_host),
+                              append_country = trimws(input$append_country),
+                              append_city = trimws(input$append_city),
+                              append_analysisdate = Sys.Date(),
+                              db_directory = getwd()) 
+      
+      saveRDS(meta_info, paste0(
+        getwd(),
+        "/execute/meta_info_single.rds"
+      ))
+      
+      show_toast(
+        title = "Metadata declared",
+        type = "success",
+        position = "bottom-end",
+        timer = 3000
+      )
+      
+      # Render Start Typing UI
+      output$start_typing_ui <- renderUI({
+        div(
+          class = "multi_start_col",
+          column(
+            width = 3,
+            align = "center",
+            br(),
+            br(),
+            h3(p("Start Typing"), style = "color:white"),
+            br(),
+            br(),
+            HTML(
+              paste(
+                "<span style='color: white;'>",
+                "Typing by <strong>",
+                DB$scheme,
+                "</strong> scheme."
+              )
+            ),
+            br(), br(), br(), br(),
+            div(
+              class = "save-assembly",
+              materialSwitch(
+                "save_assembly_st",
+                h5(p("Save Assemblies in Local Database"), style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
+                value = TRUE,
+                right = TRUE)
+            ),
+            HTML(
+              paste(
+                "<span style='color: orange;'>",
+                "Isolates with unsaved assembly files can NOT be applied to screening for resistance genes."
+              )
+            ),
+            br(), br(), br(), br(),
+            actionButton(
+              inputId = "typing_start",
+              label = "Start",
+              icon = icon("circle-play")
+            )
+          )
+        )
+      })
+    }
+  })
+  
+  ####  Events Single Typing ----
+  
+  observeEvent(input$reset_single_typing, {
+    log_print("Reset single typing")
+    
+    Typing$status <- "Inactive"
+    
+    Typing$progress <- 0
+    
+    Typing$progress_format <- 900000
+    
+    output$single_typing_progress <- NULL
+    
+    output$typing_fin <- NULL
+    
+    output$single_typing_results <- NULL
+    
+    output$typing_formatting <- NULL
+    
+    Typing$single_path <- data.frame()
+    
+    # reset results file 
+    if(dir_exists(paste0(getwd(), "/execute/blat_single/results"))) {
+      unlink(list.files(paste0(getwd(), "/execute/blat_single/results"), full.names = TRUE), recursive = TRUE)
+      # Resetting single typing progress logfile bar 
+      con <- file(paste0(getwd(), "/logs/progress.txt"), open = "w")
+      
+      cat("0\n", file = con)   
+      
+      close(con)
+    }
+    
+    output$initiate_typing_ui <- renderUI({
+      column(
+        width = 4,
+        align = "center",
+        br(),
+        br(),
+        h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+        br(),
+        br(),
+        p(
+          HTML(
+            paste(
+              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly File (FASTA)')
+            )
+          )
+        ),
+        fluidRow(
+          column(1),
+          column(
+            width = 11,
+            align = "center",
+            shinyFilesButton(
+              "genome_file",
+              "Browse" ,
+              icon = icon("file"),
+              title = "Select the assembly in .fasta/.fna/.fa format:",
+              multiple = FALSE,
+              buttonType = "default",
+              class = NULL,
+              root = path_home()
+            ),
+            br(),
+            br(),
+            uiOutput("genome_path"),
+            br()
+          )
+        )
+      )
+    })
+  })
+  
+  # Notification for finalized Single typing
+  Typing$single_end <- TRUE
+  Typing$progress_format_end <- 0
+  
+  observe({
+    if(Typing$single_end == FALSE) {
+      if (Typing$progress_format_end == 999999) {
+        show_toast(
+          title = "Single Typing finalized",
+          type = "success",
+          position = "bottom-end",
+          timer = 8000
+        )
+        Typing$single_end <- TRUE
+      }
+    }
+  })
+  
+  ### Multi Typing ----
+  
+  #### Render Multi Typing UI Elements ----
+  output$initiate_multi_typing_ui <- renderUI({
+    column(
+      width = 4,
+      align = "center",
+      br(),
+      br(),
+      h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+      br(), br(),
+      p(
+        HTML(
+          paste(
+            tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+          )
+        )
+      ),
+      fluidRow(
+        column(1),
+        column(
+          width = 11,
+          align = "center",
+          shinyDirButton(
+            "genome_file_multi",
+            "Browse",
+            icon = icon("folder-open"),
+            title = "Select the folder containing the genome assemblies (FASTA)",
+            buttonType = "default",
+            root = path_home()
+          ),
+          br(),
+          br(),
+          uiOutput("multi_select_info"),
+          br()
+        )
+      ),
+      uiOutput("multi_select_tab_ctrls"),
+      br(),
+      fluidRow(
+        column(1),
+        column(
+          width = 11,
+          align = "left",
+          rHandsontableOutput("multi_select_table")
+        )
+      )
+    )
+  })
+  
+  # Render selection info
+  output$multi_select_info <- renderUI({
+    
+    if(!is.null(Typing$multi_path)) {
+      if(length(Typing$multi_path) < 1) {
+        HTML(paste("<span style='color: white; margin-left:-30px'>", 
+                   "No files selected."))
+      } else {
+        HTML(paste("<span style='color: white; margin-left:-30px'>",
+                   sum(hot_to_r(input$multi_select_table)$Include == TRUE),
+                   " files selected."))
+      }
+    }
+  })
+  
+  # Render multi selection table issues
+  output$multi_select_issues <- renderUI({
+    req(Typing$multi_sel_table, input$multi_select_table)
+    if(any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
+       any(duplicated(hot_to_r(input$multi_select_table)$Files))){
+      HTML(
+        paste(
+          paste("<span style='color: orange;'>",
+                "Some name(s) are already present in local database.<br/>"),
+          paste("<span style='color: #ff7334;'>",
+                "Duplicated name(s). <br/>")
+        )
+      )
+    } else if (any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
+               !any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
+      HTML(
+        paste("<span style='color: #e0b300;'>",
+              "Some name(s) are already present in local database.<br/>")
+      )
+    } else if (!any(hot_to_r(input$multi_select_table)$Files %in% dupl_mult_id()) & 
+               any(duplicated(hot_to_r(input$multi_select_table)$Files))) {
+      HTML(
+        paste("<span style='color: #ff7334;'>",
+              "Duplicated name(s). <br/>")
+      )
+    }
+  })
+  
+  output$multi_select_issue_info <- renderUI({
+    req(Typing$multi_sel_table, input$multi_select_table)
+    
+    multi_select_table <- hot_to_r(input$multi_select_table)
+    
+    if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
+       any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)])) |
+       any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
+      
+      if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)])))  {
+        
+        if(any(multi_select_table$Files[which(multi_select_table$Include == TRUE)] %in% dupl_mult_id()) | 
+           any(duplicated(multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
+          HTML(paste(
+            paste(
+              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+              paste("<span style='color: white; font-style:italic'>",
+                  "&nbspRename highlighted isolates or deselect them.</br>")),
+            paste(
+              '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+              paste("<span style='color: white; font-style:italic'>",
+                  "&nbspFilename(s) contain(s) empty spaces."))
+          ))
+        } else {
+          HTML(paste(
+            '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+            paste("<span style='color: white; font-style:italic'>",
+                     "&nbspFilename(s) contain(s) empty spaces.")))
+        }
+      } else {
+        HTML(paste(
+          '<i class="fa-solid fa-circle-exclamation" style="font-size:15px;color:orange"></i>',
+          paste("<span style='color: white; font-style:italic'>", 
+                   "&nbspRename highlighted isolates or deselect them.")))
+      }
+    } else {
+      HTML(paste(
+        '<i class="fa-solid fa-circle-check" style="font-size:15px;color:lightgreen"></i>',
+        paste("<span style='color: white; font-style:italic'>",
+              "&nbspFiles ready for allelic typing.")))
+    }
+  })
+  
+  # Render Metadata Select Box after Folder selection
+  observe({
+    if(!is.null(Typing$multi_sel_table)) {
+      if (nrow(Typing$multi_sel_table) > 0) {
+        
+        output$multi_select_tab_ctrls <- renderUI(
+          fluidRow(
+            column(1),
+            column(
+              width = 2,
+              align = "left",
+              actionButton(
+                "sel_all_mt",
+                "All",
+                icon = icon("check")
+              )
+            ),
+            column(
+              width = 2,
+              align = "left",
+              actionButton(
+                "desel_all_mt",
+                "None",
+                icon = icon("xmark")
+              )
+            ),
+            column(2),
+            column(
+              width = 5,
+              align = "right",
+              br(),
+              uiOutput("multi_select_issues")
+            )
+          )
+        )
+        
+        output$metadata_multi_box <- renderUI({
+          column(
+            width = 3,
+            align = "center",
+            br(),
+            br(),
+            h3(p("Declare Metadata"), style = "color:white;margin-left:-40px"),
+            br(), br(),
+            div(
+              class = "multi_meta_box",
+              box(
+                solidHeader = TRUE,
+                status = "primary",
+                width = "90%",
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly ID", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Assembly Name", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5("Assembly filename", style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Isolation Date", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      dateInput("append_isodate_multi",
+                                label = "",
+                                width = "80%",
+                                max = Sys.Date())
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Host", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("append_host_multi",
+                                label = "",
+                                width = "80%")
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Country", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table_country",
+                      pickerInput(
+                        "append_country_multi",
+                        label = "",
+                        choices = list("Common" = sel_countries,
+                                       "All Countries" = country_names),
+                        options = list(
+                          `live-search` = TRUE,
+                          `actions-box` = TRUE,
+                          size = 10,
+                          style = "background-color: white; border-radius: 5px;"
+                        ),
+                        width = "90%"
+                      )
+                    )  
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("City", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    div(
+                      class = "append_table",
+                      textInput("append_city_multi",
+                                label = "",
+                                width = "80%")
+                    )
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 5,
+                    align = "left",
+                    h5("Typing Date", style = "color:white; margin-top: 30px; margin-left: 15px")
+                  ),
+                  column(
+                    width = 7,
+                    align = "left",
+                    h5(paste0(" ", Sys.Date()), style = "color:white; margin-top: 30px; margin-left: 5px; font-style: italic")
+                  )
+                ),
+                fluidRow(
+                  column(
+                    width = 12,
+                    align = "center",
+                    br(), br(),
+                    actionButton(
+                      inputId = "conf_meta_multi",
+                      label = "Confirm"
+                    ),
+                    br(), br(),
+                    uiOutput("multi_select_issue_info")
+                  )
+                )
+              )    
+            )
+          )
+        }) 
+      } else {
+        output$metadata_multi_box <- NULL
+      }
+    }
+  })
+  
+  # Check if ongoing Multi Typing - Render accordingly
+  observe({
+    # Get selected Genome in Multi Mode
+    shinyDirChoose(input,
+                   "genome_file_multi",
+                   roots = c(Home = path_home(), Root = "/"),
+                   defaultRoot = "Home",
+                   session = session,
+                   filetypes = c('', 'fasta', 'fna', 'fa'))
+    
+    Typing$multi_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)
+    
+    files_selected <- list.files(as.character(Typing$multi_path))
+    Typing$files_filtered <- files_selected[which(!endsWith(files_selected, ".gz") &
+                                                    grepl("\\.fasta|\\.fna|\\.fa", files_selected))]
+    
+    Typing$multi_sel_table <- data.frame(
+      Include = rep(TRUE, length(Typing$files_filtered)),
+      Files = gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", 
+                   Typing$files_filtered),
+      Type = sub(".*(\\.fasta|\\.fasta\\.gz|\\.fna|\\.fna\\.gz|\\.fa|\\.fa\\.gz)$",
+                 "\\1", Typing$files_filtered, perl = F))
+    
+    if(nrow(Typing$multi_sel_table) > 0) {
+      output$multi_select_tab_ctrls <- renderUI(
+        fluidRow(
+          column(1),
+          column(
+            width = 2,
+            align = "left",
+            actionButton(
+              "sel_all_mt",
+              "All",
+              icon = icon("check")
+            )
+          ),
+          column(
+            width = 2,
+            align = "left",
+            actionButton(
+              "desel_all_mt",
+              "None",
+              icon = icon("xmark")
+            )
+          ),
+          column(2),
+          column(
+            width = 5,
+            align = "right",
+            br(),
+            uiOutput("multi_select_issues")
+          )
+        )
+      )
+    } else {
+      output$multi_select_tab_ctrls <- NULL
+    }
+    
+    if(between(nrow(Typing$multi_sel_table), 1, 15)) {
+      output$multi_select_table <- renderRHandsontable({
+        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
+                             stretchH = "all", contextMenu = FALSE
+        ) %>%
+          hot_cols(columnSorting = FALSE) %>%
+          hot_rows(rowHeights = 25) %>%
+          hot_col(2, readOnly = FALSE,
+                  valign = "htBottom") %>%
+          hot_col(3, readOnly = TRUE) %>%
+          hot_col(1,
+                  halign = "htCenter",
+                  valign = "htTop", 
+                  colWidths = 60)
+        
+        htmlwidgets::onRender(rht, sprintf(
+          "function(el, x) {
+        var hot = this.hot;
+        
+        var columnData = hot.getDataAtCol(1); // Change column index if needed
+        var duplicates = {};
+          
+        var highlightInvalidAndDuplicates = function(invalidValues) {
+          
+          var columnData = hot.getDataAtCol(1); // Change column index if needed
+          var duplicates = {};
+
+          // Find all duplicate values
+          for (var i = 0; i < columnData.length; i++) {
+            var value = columnData[i];
+            if (value !== null && value !== undefined) {
+              if (duplicates[value]) {
+                duplicates[value].push(i);
+              } else {
+                duplicates[value] = [i];
+              }
+            }
+          }
+
+          // Reset all cell backgrounds in the column
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            if (cell) {
+              cell.style.background = 'white';
+            }
+          }
+
+          // Highlight duplicates and invalid values
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            var value = columnData[i];
+            if (cell) {
+              if (invalidValues.includes(value)) {
+                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
+              } else if (duplicates[value] && duplicates[value].length > 1) {
+                cell.style.background = '#FF7334'; // Highlight color for duplicates
+              }
+            }
+          }
+        };
+
+        var changefn = function(changes, source) {
+          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
+            highlightInvalidAndDuplicates(%s);
+          }
+        };
+
+        hot.addHook('afterChange', changefn);
+        hot.addHook('afterLoadData', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+        hot.addHook('afterRender', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+
+        highlightInvalidAndDuplicates(%s); // Initial highlight on load
+        
+        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
+          var colData = hot.getDataAtCol(0);
+          for (var i = 0; i < colData.length; i++) {
+            hot.setDataAtCell(i, 0, message.value);
+          }
+          hot.render(); // Re-render the table
+        });
+      }", 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id())))
+      })
+      
+    } else if(nrow(Typing$multi_sel_table) > 15) {
+      output$multi_select_table <- renderRHandsontable({
+        rht <- rhandsontable(Typing$multi_sel_table, rowHeaders = NULL, 
+                             stretchH = "all", height = 500,
+                             contextMenu = FALSE
+        ) %>%
+          hot_cols(columnSorting = FALSE) %>%
+          hot_rows(rowHeights = 25) %>%
+          hot_col(2,
+                  readOnly = FALSE,
+                  valign = "htBottom") %>%
+          hot_col(3, readOnly = TRUE) %>%
+          hot_col(1,
+                  halign = "htCenter",
+                  valign = "htTop", 
+                  colWidths = 60)
+        
+        htmlwidgets::onRender(rht, sprintf(
+          "function(el, x) {
+        var hot = this.hot;
+        
+        var columnData = hot.getDataAtCol(1); // Change column index if needed
+        var duplicates = {};
+          
+        var highlightInvalidAndDuplicates = function(invalidValues) {
+          
+          var columnData = hot.getDataAtCol(1); // Change column index if needed
+          var duplicates = {};
+
+          // Find all duplicate values
+          for (var i = 0; i < columnData.length; i++) {
+            var value = columnData[i];
+            if (value !== null && value !== undefined) {
+              if (duplicates[value]) {
+                duplicates[value].push(i);
+              } else {
+                duplicates[value] = [i];
+              }
+            }
+          }
+
+          // Reset all cell backgrounds in the column
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            if (cell) {
+              cell.style.background = 'white';
+            }
+          }
+
+          // Highlight duplicates and invalid values
+          for (var i = 0; i < columnData.length; i++) {
+            var cell = hot.getCell(i, 1); // Change column index if needed
+            var value = columnData[i];
+            if (cell) {
+              if (invalidValues.includes(value)) {
+                cell.style.background = 'rgb(224, 179, 0)'; // Highlight color for invalid values
+              } else if (duplicates[value] && duplicates[value].length > 1) {
+                cell.style.background = '#FF7334'; // Highlight color for duplicates
+              }
+            }
+          }
+        };
+
+        var changefn = function(changes, source) {
+          if (source === 'edit' || source === 'undo' || source === 'autofill' || source === 'paste') {
+            highlightInvalidAndDuplicates(%s);
+          }
+        };
+
+        hot.addHook('afterChange', changefn);
+        hot.addHook('afterLoadData', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+        hot.addHook('afterRender', function() {
+          highlightInvalidAndDuplicates(%s);
+        });
+
+        highlightInvalidAndDuplicates(%s); // Initial highlight on load
+        
+        Shiny.addCustomMessageHandler('setColumnValue', function(message) {
+          var colData = hot.getDataAtCol(0);
+          for (var i = 0; i < colData.length; i++) {
+            hot.setDataAtCell(i, 0, message.value);
+          }
+          hot.render(); // Re-render the table
+        });
+      }", 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id()), 
+          jsonlite::toJSON(dupl_mult_id())))
+        
+      })
+      
+    } else {
+      output$multi_select_table <- NULL
+    } 
+  })
+  
+  observeEvent(input$conf_meta_multi, {
+    
+    multi_select_table <- hot_to_r(input$multi_select_table)[hot_to_r(input$multi_select_table)$Include == TRUE,]
+    
+    if(any(unlist(gsub(".fasta|.fna|.fa|.fasta.gz|.fna.gz|.fa.gz", "", multi_select_table$Files)) %in% unlist(DB$data["Assembly ID"]))) {
+      show_toast(
+        title = "Assembly ID(s) already present",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (any(duplicated(multi_select_table$Files))) {
+      show_toast(
+        title = "Duplicated filename(s)",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (any(multi_select_table$Files == "")) {
+      show_toast(
+        title = "Empty filename(s)",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (any(grepl("[()/\\:*?\"<>|]", multi_select_table$Files))) {
+      show_toast(
+        title = "Invalid filename(s). No special characters allowed: ()/\\:*?\"<>|",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (!any(multi_select_table$Include == TRUE)) {
+      show_toast(
+        title = "No files selected",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if(any(grepl(" ", multi_select_table$Files[which(multi_select_table$Include == TRUE)]))) {
+      show_toast(
+        title = "Empty spaces in filename(s) not allowed",
+        type = "error",
+        position = "bottom-end",
+        timer = 3000
+      )
+    } else if (isFALSE(Typing$reload)) {
+      show_toast(
+        title = "Reload Database first",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if(Screening$status == "started") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      
+      log_print("Multi typing metadata confirmed")
+      
+      meta_info <- data.frame(cgmlst_typing = DB$scheme,
+                              append_isodate = trimws(input$append_isodate_multi),
+                              append_host = trimws(input$append_host_multi),
+                              append_country = trimws(input$append_country_multi),
+                              append_city = trimws(input$append_city_multi),
+                              append_analysisdate = Sys.Date(),
+                              db_directory = getwd())
+      
+      saveRDS(meta_info, paste0(getwd(), "/execute/meta_info.rds"))
+      
+      show_toast(
+        title = "Metadata declared",
+        type = "success",
+        position = "bottom-end",
+        timer = 3000
+      )
+      
+      output$start_multi_typing_ui <- renderUI({
+        div(
+          class = "multi_start_col",
+          column(
+            width = 3,
+            align = "center",
+            br(),
+            br(),
+            h3(p("Start Typing"), style = "color:white"),
+            br(),
+            br(),
+            HTML(
+              paste(
+                "<span style='color: white;'>",
+                "Typing by <strong>",
+                DB$scheme,
+                "</strong> scheme."
+              )
+            ),
+            br(), br(), br(), br(),
+            div(
+              class = "save-assembly",
+              materialSwitch(
+                "save_assembly_mt",
+                h5(p("Save Assemblies in Local Database"), style = "color:white; padding-left: 0px; position: relative; top: -3px; right: -20px;"),
+                value = TRUE,
+                right = TRUE)
+            ),
+            HTML(
+              paste(
+                "<span style='color: orange;font-style:italic'>",
+                "Isolates with unsaved assembly files can NOT be applied to screening for resistance genes."
+              )
+            ),
+            br(), br(), br(), br(),
+            actionButton(
+              "start_typ_multi",
+              "Start",
+              icon = icon("circle-play")
+            )
+          )
+        )
+      })
+    }
+  })
+  
+  #### Events Multi Typing ----
+  
+  observeEvent(input$sel_all_mt, {
+    session$sendCustomMessage(type = "setColumnValue", message = list(value = TRUE))
+  })
+  
+  observeEvent(input$desel_all_mt, {
+    session$sendCustomMessage(type = "setColumnValue", message = list(value = FALSE))
+  })
+  
+  # Print Log
+  output$print_log <- downloadHandler(
+    filename = function() {
+      log_print(paste0("Save multi typing log ", paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")))
+      paste("Multi_Typing_", Sys.Date(), ".txt", sep = "")
+    },
+    content = function(file) {
+      writeLines(readLines(paste0(getwd(), "/logs/script_log.txt")), file)
+    }
+  )
+  
+  # Reset Multi Typing
+  observeEvent(input$reset_multi, {
+    if(!grepl("Multi Typing", tail(readLines(paste0(getwd(),"/logs/script_log.txt")), n = 1))) {
+      showModal(
+        modalDialog(
+          paste0(
+            "A Multi Typing process is still pending. Stopping this process will cancel the processing."
+          ),
+          title = "Reset Multi Typing",
+          fade = TRUE,
+          easyClose = TRUE,
+          footer = tagList(
+            modalButton("Cancel"),
+            actionButton("conf_multi_kill", "Stop", class = "btn btn-danger")
+          )
+        )
+      )
+    } else {
+      
+      log_print("Reset multi typing")
+      
+      # Reset multi typing result list
+      saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
+      multi_help <- FALSE
+      Typing$result_list <- NULL
+      
+      # Null logfile
+      writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
+      
+      # Reset User Feedback variable
+      Typing$pending_format <- 0
+      Typing$multi_started <- FALSE
+      
+      output$initiate_multi_typing_ui <- renderUI({
+        column(
+          width = 4,
+          align = "center",
+          br(),
+          br(),
+          h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+          br(), br(),
+          p(
+            HTML(
+              paste(
+                tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+              )
+            )
+          ),
+          fluidRow(
+            column(1),
+            column(
+              width = 11,
+              align = "center",
+              shinyDirButton(
+                "genome_file_multi",
+                "Browse",
+                icon = icon("folder-open"),
+                title = "Select the folder containing the genome assemblies (FASTA)",
+                buttonType = "default",
+                root = path_home()
+              ),
+              br(),
+              br(),
+              uiOutput("multi_select_info"),
+              br()
+            )
+          ),
+          uiOutput("multi_select_tab_ctrls"),
+          br(),
+          fluidRow(
+            column(1),
+            column(
+              width = 11,
+              align = "left",
+              rHandsontableOutput("multi_select_table")
+            )
+          )
+        )
+      })
+      
+      output$pending_typing <- NULL
+      output$multi_typing_results <- NULL
+    }
+  })
+  
+  # Confirm Reset after 
+  observeEvent(input$conf_multi_kill, {
+    removeModal()
+    
+    log_print("Kill multi typing")
+    
+    # Kill multi typing and reset logfile  
+    system(paste("bash", paste0(getwd(), "/execute/kill_multi.sh")), 
+           wait = TRUE)
+    
+    show_toast(
+      title = "Execution cancelled",
+      type = "warning",
+      position = "bottom-end",
+      timer = 6000
+    )
+    
+    # Kill multi typing and reset logfile  
+    writeLines("0", paste0(getwd(), "/logs/script_log.txt"))
+    
+    #Reset multi typing result list
+    saveRDS(list(), paste0(getwd(), "/execute/event_list.rds"))
+    multi_help <- FALSE
+    Typing$result_list <- NULL
+    
+    # Reset User Feedback variable
+    Typing$pending_format <- 0
+    output$pending_typing <- NULL
+    output$multi_typing_results <- NULL
+    Typing$failures <- 0
+    Typing$successes <- 0
+    Typing$multi_started <- FALSE
+    
+    output$initiate_multi_typing_ui <- renderUI({
+      column(
+        width = 4,
+        align = "center",
+        br(),
+        br(),
+        h3(p("Initiate Typing"), style = "color:white; margin-left: 15px"),
+        br(), br(),
+        p(
+          HTML(
+            paste(
+              tags$span(style='color: white; font-size: 15px; margin-bottom: 0px; margin-left: 15px', 'Select Assembly Folder')
+            )
+          )
+        ),
+        fluidRow(
+          column(1),
+          column(
+            width = 11,
+            align = "center",
+            shinyDirButton(
+              "genome_file_multi",
+              "Browse",
+              icon = icon("folder-open"),
+              title = "Select the folder containing the genome assemblies (FASTA)",
+              buttonType = "default",
+              root = path_home()
+            ),
+            br(),
+            br(),
+            uiOutput("multi_select_info"),
+            br()
+          )
+        ),
+        uiOutput("multi_select_tab_ctrls"),
+        br(),
+        fluidRow(
+          column(1),
+          column(
+            width = 11,
+            align = "left",
+            rHandsontableOutput("multi_select_table")
+          )
+        )
+      )
+    })
+    
+  })
+  
+  observeEvent(input$start_typ_multi, {
+    log_print("Initiate multi typing")
+    
+    if(readLines(paste0(getwd(), "/logs/progress.txt"))[1] != "0") {
+      show_toast(
+        title = "Pending Single Typing",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else if (Screening$status == "started") {
+      show_toast(
+        title = "Pending Gene Screening",
+        type = "warning",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      removeModal()
+      
+      show_toast(
+        title = "Multi Typing started",
+        type = "success",
+        position = "bottom-end",
+        timer = 10000
+      )
+      
+      Typing$new_table <- NULL
+      
+      # Remove Allelic Typing Controls
+      output$initiate_multi_typing_ui <- NULL
+      output$metadata_multi_box <- NULL
+      output$start_multi_typing_ui <- NULL
+      
+      # Activate entry detection
+      DB$check_new_entries <- TRUE
+      
+      # Initiate Feedback variables
+      Typing$multi_started <- TRUE
+      Typing$pending <- TRUE
+      Typing$failures <- 0
+      Typing$successes <- 0
+      
+      # get selected file table
+      multi_select_table <- hot_to_r(input$multi_select_table)
+      
+      filenames <- paste(multi_select_table$Files[which(multi_select_table$Include == TRUE)], collapse = " ")
+      
+      files <- Typing$multi_sel_table$Files[which(multi_select_table$Include == TRUE)]
+      type <- Typing$multi_sel_table$Type[which(multi_select_table$Include == TRUE)]
+      genome_names <- paste(paste0(gsub(" ", "~", files), type), collapse = " ")
+      
+      # Start Multi Typing Script
+      multi_typing_df <- data.frame(
+        db_path = DB$database,
+        wd = getwd(),
+        save = input$save_assembly_mt,
+        scheme = paste0(gsub(" ", "_", DB$scheme)),
+        genome_folder = as.character(parseDirPath(roots = c(Home = path_home(), Root = "/"), input$genome_file_multi)),
+        filenames = paste0(filenames, collapse= " "),
+        genome_names = genome_names,
+        alleles = paste0(DB$database, "/", gsub(" ", "_", DB$scheme), "/", gsub(" ", "_", DB$scheme), "_alleles")
+      )
+      
+      saveRDS(multi_typing_df, "execute/multi_typing_df.rds")
+      
+      # Execute multi blat script  
+      system(paste("bash", paste0(getwd(), "/execute/multi_typing.sh")), wait = FALSE)
+    }
+  })
+  
+  
+  #### User Feedback ----
+  
+  observe({
+    if(file.exists(paste0(getwd(), "/logs/script_log.txt"))) {
+      if(Typing$multi_started == TRUE) {
+        check_multi_status()
+      } else {
+        Typing$status <- "Inactive"
+      }
+    }
+  })
+  
+  check_multi_status <- reactive({
+    
+    invalidateLater(3000, session)
+    
+    log <- readLines(paste0(getwd(), "/logs/script_log.txt"))
+    
+    # Determine if Single or Multi Typing
+    if(str_detect(log[1], "Multi")) {
+      Typing$pending_mode <- "Multi"
+    } else {
+      Typing$pending_mode <- "Single"
+    }
+    
+    # Check typing status
+    if(str_detect(tail(log, 1), "Attaching")) {
+      Typing$status <- "Attaching"
+    } else if(str_detect(tail(log, 1), "Successful")) {
+      Typing$multi_help <- TRUE
+      Typing$status <- "Successful"
+      show_toast(
+        title = paste0("Successful", sub(".*Successful", "", tail(log, 1))),
+        type = "success",
+        position = "bottom-end",
+        timer = 8000
+      )
+    } else if(str_detect(tail(log, 1), "failed")) {
+      Typing$status <- "Failed"
+      show_toast(
+        title = sub(".* - ", "", tail(log, 1)),
+        type = "error",
+        position = "bottom-end",
+        timer = 8000
+      )
+    } else if(str_detect(tail(log, 1), "Processing")) {
+      Typing$status <- "Processing"
+      
+      if(any(str_detect(tail(log, 2), "Successful"))) {
+        
+        if(!identical(Typing$last_success, tail(log, 2)[1])) {
+          Typing$multi_help <- TRUE
+          show_toast(
+            title = paste0("Successful", sub(".*Successful", "", tail(log, 2)[1])),
+            type = "success",
+            position = "bottom-end",
+            timer = 8000
+          )
+          
+          Typing$last_success <- tail(log, 2)[1]
+        }
+      } else if(any(str_detect(tail(log, 2), "failed"))) {
+        
+        if(!identical(Typing$last_failure, tail(log, 2)[1])) {
+          
+          show_toast(
+            title = sub(".* - ", "", tail(log, 2)[1]),
+            type = "error",
+            position = "bottom-end",
+            timer = 8000
+          )
+          
+          Typing$last_failure <- tail(log, 2)[1]
+        }
+      }
+    } else if(str_detect(tail(log, 1), "finalized")) {
+      Typing$multi_help <- TRUE
+      Typing$status <- "Finalized"
+      
+      if(Typing$pending == TRUE) {
+        show_toast(
+          title = "Typing finalized",
+          type = "success",
+          position = "bottom-end",
+          timer = 8000
+        )
+        
+        Typing$pending <- FALSE
+      }
+    }
+  })
+  
+  ##### Render Multi Typing UI Feedback ----
+  
+  observe({
+    if(!is.null(input$multi_results_picker)) {
+      Typing$multi_table_length <- nrow(Typing$result_list[[input$multi_results_picker]])
+    } else {
+      Typing$multi_table_length <- NULL
+    }
+  })
+  
+  observe({
+    if(!is.null(Typing$result_list)) {
+      if(length(Typing$result_list) > 0) {
+        if(is.null(Typing$multi_table_length)) {
+          output$multi_typing_result_table <- renderRHandsontable({
+            rhandsontable(Typing$result_list[[input$multi_results_picker]], 
+                          rowHeaders = NULL, stretchH = "all",
+                          readOnly = TRUE, contextMenu = FALSE) %>%
+              hot_rows(rowHeights = 25) %>%
+              hot_col(1:3, valign = "htMiddle", halign = "htCenter",
+                      cellWidths = list(100, 160, NULL)) %>%
+              hot_col("Value", renderer=htmlwidgets::JS(
+                "function(instance, td, row, col, prop, value, cellProperties) {
+                  if (value.length > 8) {
+                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                  }
+                  td.innerHTML = value;
+                  td.style.textAlign = 'center';
+                  return td;
+                 }"
+              ))
+            })
+          
+        } else {
+          if(Typing$multi_table_length > 15) {
+            output$multi_typing_result_table <- renderRHandsontable({
+              rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
+                            stretchH = "all", height = 500,
+                            readOnly = TRUE, contextMenu = FALSE) %>%
+                hot_rows(rowHeights = 25) %>%
+                hot_col(1:3, valign = "htMiddle", halign = "htCenter",
+                        cellWidths = list(100, 160, NULL)) %>%
+                hot_col("Value", renderer=htmlwidgets::JS(
+                  "function(instance, td, row, col, prop, value, cellProperties) {
+                  if (value.length > 8) {
+                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                  }
+                  td.innerHTML = value;
+                  td.style.textAlign = 'center';
+                  return td;
+                 }"
+                ))
+              })
+          } else {
+            output$multi_typing_result_table <- renderRHandsontable({
+              rhandsontable(Typing$result_list[[input$multi_results_picker]], rowHeaders = NULL, 
+                            stretchH = "all", readOnly = TRUE,
+                            contextMenu = FALSE) %>%
+                hot_rows(rowHeights = 25) %>%
+                hot_col(1:3, valign = "htMiddle", halign = "htCenter",
+                        cellWidths = list(100, 160, NULL)) %>%
+                hot_col("Value", renderer=htmlwidgets::JS(
+                  "function(instance, td, row, col, prop, value, cellProperties) {
+                  if (value.length > 8) {
+                    value = value.slice(0, 4) + '...' + value.slice(value.length - 4);
+                  }
+                  td.innerHTML = value;
+                  td.style.textAlign = 'center';
+                  return td;
+                 }"
+                ))
+              })
+          }
+        }
+      } else {
+        output$multi_typing_result_table <- NULL
+      }
+    } else {
+      output$multi_typing_result_table <- NULL
+    }
+  })
+  
+  observe({
+    if(!is.null(Typing$multi_result_status)) {
+      if(Typing$multi_result_status == "start" | Typing$multi_result_status == "finalized"){
+        
+        if(Typing$multi_help == TRUE) {
+          Typing$result_list <- readRDS(paste0(getwd(), "/execute/event_list.rds"))
+          Typing$multi_help <- FALSE
+        }
+      } 
+    }
+  })
+  
+  
+  observe({
+    #Render multi typing result feedback table
+    
+    if(!is.null(Typing$result_list)) {
+      if(length(Typing$result_list) > 0) {
+        output$multi_typing_results <- renderUI({
+          column(
+            width = 12,
+            fluidRow(
+              column(1),
+              column(
+                width = 9,
+                br(), br(),
+                br(), br(),
+                br(), 
+                div(
+                  class = "mult_res_sel",
+                  selectInput(
+                    "multi_results_picker",
+                    label = h5("Select Typing Results", style = "color:white"),
+                    choices = names(Typing$result_list),
+                    selected = names(Typing$result_list)[length(names(Typing$result_list))],
+                  )
+                ),
+                br(), br()
+              )
+            ),
+            rHandsontableOutput("multi_typing_result_table")
+          )
+        })
+      }
+    }
+  })
+  
+  observe({
+    
+    # Render log content
+    output$logText <- renderPrint({
+      cat(rev(paste0(tail(readLogFile(), 50), "\n")))
+    })
+    
+    output$logTextFull <- renderPrint({
+      cat(rev(paste0(readLines(paste0(getwd(), "/logs/script_log.txt")), "\n")))
+    })
+    
+    # Render Pending UI
+    if(!grepl("Multi Typing", tail(readLogFile(), n = 1)) & grepl("Start Multi Typing", head(readLogFile(), n = 1))) {
+      
+      Typing$multi_result_status <- "start"
+      
+      output$initiate_multi_typing_ui <- NULL
+      
+      output$pending_typing <- renderUI({
+        fluidRow(
+          fluidRow(
+            br(), br(),
+            column(width = 2),
+            column(
+              width = 4,
+              h3(p("Pending Typing ..."), style = "color:white"),
+              br(), br(),
+              fluidRow(
+                column(
+                  width = 5,
+                  HTML(paste('<i class="fa fa-spinner fa-spin" style="font-size:24px;color:white;margin-top:5px"></i>'))
+                ),
+                column(
+                  width = 6,
+                  align = "left",
+                  actionButton(
+                    "reset_multi",
+                    "Terminate",
+                    icon = icon("ban")
+                  )
+                )
+              ),
+            )
+          ),
+          br(), br(),
+          fluidRow(
+            column(width = 2),
+            column(
+              width = 10,
+              verbatimTextOutput("logText")
+            )  
+          )
+        )
+      })
+    } else if(grepl("Multi Typing finalized", tail(readLogFile(), n = 1))) {
+      
+      Typing$multi_result_status <- "finalized"
+      
+      Typing$last_scheme <- NULL
+      
+      output$initiate_multi_typing_ui <- NULL
+      
+      output$pending_typing <- renderUI({
+        
+        fluidRow(
+          fluidRow(
+            br(), br(),
+            column(width = 2),
+            column(
+              width = 4,
+              h3(p("Pending Multi Typing ..."), style = "color:white"),
+              br(), br(),
+              HTML(paste("<span style='color: white;'>", 
+                         paste("Typing of", sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "Processing")), "assemblies finalized."),
+                         paste(sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "Successful")), "successes."),
+                         paste(sum(str_detect(readLines(paste0(getwd(), "/logs/script_log.txt")), "failed")), "failures."),
+                         "Reset to start another typing process.", 
+                         sep = '<br/>')),
+              br(), br(),
+              fluidRow(
+                column(
+                  width = 5,
+                  actionButton(
+                    "reset_multi",
+                    "Reset",
+                    icon = icon("arrows-rotate")
+                  )
+                ),
+                column(
+                  width = 5,
+                  downloadButton(
+                    "print_log",
+                    "Logfile",
+                    icon = icon("floppy-disk")
+                  )
+                )
+              )
+            )
+          ),
+          br(), br(),
+          fluidRow(
+            column(width = 2),
+            column(
+              width = 10,
+              verbatimTextOutput("logTextFull"),
+            )
+          )
+        )
+      })
+    } else if (!grepl("Start Multi Typing", head(readLogFile(), n = 1))){
+      output$pending_typing <- NULL
+      Typing$multi_result_status <- "idle"
+    }
+  })
+  
+  observe({
+    # Get selected Genome in Multi Mode
+    shinyDirChoose(input,
+                   "hash_dir",
+                   roots = c(Home = path_home(), Root = "/"),
+                   defaultRoot = "Home",
+                   session = session,
+                   filetypes = c('', 'fasta', 'fna', 'fa'))
+  })
+  
+  observeEvent(input$hash_start, {
+    dir_path <- parseDirPath(roots = c(Home = path_home(), Root = "/"), input$hash_dir)
+    if (!is_empty(list.files(dir_path)) && all(endsWith(list.files(dir_path), ".fasta"))) {
+      log_print("Hashing directory using utilities")
+      shinyjs::hide("hash_start")
+      shinyjs::show("hash_loading")
+      show_toast(
+        title = "Hashing started!",
+        type = "success",
+        position = "bottom-end",
+        timer = 6000
+      )
+      hash_database(dir_path)
+      shinyjs::hide("hash_loading")
+      shinyjs::show("hash_start")
+      show_toast(
+        title = "Hashing completed!",
+        type = "success",
+        position = "bottom-end",
+        timer = 6000
+      )
+    } else {
+      show_toast(
+        title = "Incorrect folder selected!",
+        type = "error",
+        position = "bottom-end",
+        timer = 6000
+      )
+    }
+  })
+  
+} # end server
+
+# _______________________ ####
+
+# Shiny ----
+
+shinyApp(ui = ui, server = server)

From 131f476f77507926284d6077b65d80274b230323 Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Tue, 20 Aug 2024 19:17:08 +0200
Subject: [PATCH 73/75] Udpated type 2 clustering

---
 App.R | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/App.R b/App.R
index 5a25259..4df9e98 100644
--- a/App.R
+++ b/App.R
@@ -1443,12 +1443,12 @@ ui <- dashboardPage(
                               conditionalPanel(
                                 "input.mst_cluster_type=='Skeleton'",
                                 sliderInput(
-                                  "mst_cluster width",
+                                  "mst_cluster_width",
                                   label = h5("Skeleton Width", style = "color:white; margin-bottom: 0px;"),
-                                  value = 5,
+                                  value = 24,
                                   step = 1,
                                   min = 1,
-                                  max = 10,
+                                  max = 50,
                                   ticks = FALSE,
                                   width = "150px"
                                 )
@@ -18081,8 +18081,10 @@ server <- function(input, output, session) {
     if (input$mst_show_clusters) {
       if (input$mst_cluster_col_scale == "Viridis") {
         color_palette <- viridis(length(unique(data$nodes$group)))
+        color_edges <- viridis(length(unique(clusters$edges)))
       } else {
         color_palette <- rainbow(length(unique(data$nodes$group)))
+        color_edges <- rainbow(length(unique(clusters$edges)))
       }
       
       if (input$mst_cluster_type == "Area") {
@@ -18092,18 +18094,16 @@ server <- function(input, output, session) {
         }
       } else {
         thin_edges <- data$edges
-        thin_edges$width <- 1
+        thin_edges$width <- 2
         thin_edges$color <- "black"
         
         thick_edges <- data$edges
-        thick_edges$width <- 24
-        
+        thick_edges$width <- input$mst_cluster_width
         thick_edges$color <- rep("rgba(0, 0, 0, 0)", length(data$edges$from))
-        color_palette <- rainbow(length(unique(clusters$edges)))
+        
         for (i in 1:length(unique(clusters$edges))) {
-          print(clusters$edges)
           if (unique(clusters$edges)[i] != "0") {
-            edge_color <- paste(col2rgb(color_palette[i]), collapse=", ")
+            edge_color <- paste(col2rgb(color_edges[i]), collapse=", ")
             thick_edges$color[clusters$edges == unique(clusters$edges)[i]] <- paste0("rgba(", edge_color, ", 0.5)")
           }
         }

From 37359881931252b222b0fa74a21a2a70d488114c Mon Sep 17 00:00:00 2001
From: fpaskali <filip.paskali@gmail.com>
Date: Wed, 21 Aug 2024 13:04:55 +0200
Subject: [PATCH 74/75] One-node cluster color assignment

---
 App.R | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/App.R b/App.R
index 4df9e98..b3543c4 100644
--- a/App.R
+++ b/App.R
@@ -18089,8 +18089,13 @@ server <- function(input, output, session) {
       
       if (input$mst_cluster_type == "Area") {
         for (i in 1:length(unique(data$nodes$group))) {
-          visNetwork_graph <- visNetwork_graph %>% 
-            visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
+          if (sum(data$nodes$group == unique(data$nodes$group)[i]) > 1) { # Color only cluster with 2 or more nodes
+            visNetwork_graph <- visNetwork_graph %>% 
+              visGroups(groupname = unique(data$nodes$group)[i], color = color_palette[i])
+          } else {
+            visNetwork_graph <- visNetwork_graph %>% 
+              visGroups(groupname = unique(data$nodes$group)[i], color = mst_color_node())
+          }
         }
       } else {
         thin_edges <- data$edges

From 6119b6baa42df9382e2a9b20c2bce467ad8accbb Mon Sep 17 00:00:00 2001
From: Marian Freisleben <115372379+infinity-a11y@users.noreply.github.com>
Date: Wed, 21 Aug 2024 15:36:42 +0200
Subject: [PATCH 75/75] Removed insertion

---
 App.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/App.R b/App.R
index 90d4c13..bddf512 100644
--- a/App.R
+++ b/App.R
@@ -1430,7 +1430,7 @@ ui <- dashboardPage(
                                   width = "150px"
                                 )
                               )
-                            )f
+                            )
                           )
                         )
                       )