pvacview extra modules added

pvactools/tools/pvacview/anchor_and_helper_functions.R

@@ -83,7 +83,7 @@ peptide_coloring <- function(hla_allele, peptide_row) {
 #calculate anchor list for specific peptide length and HLA allele combo given contribution cutoff
 calculate_anchor <- function(hla_allele, peptide_length, anchor_contribution) {
   result <- tryCatch({
-      anchor_raw_data <- as.numeric(anchor_data[[peptide_length]][anchor_data[[peptide_length]]["HLA"] == hla_allele][2:(peptide_length + 1)])
+    anchor_raw_data <- as.numeric(anchor_data[[peptide_length]][anchor_data[[peptide_length]]["HLA"] == hla_allele][2:(peptide_length + 1)])
     if (any(is.na(anchor_raw_data))) {
       return("NA")
     }
@@ -100,7 +100,7 @@ calculate_anchor <- function(hla_allele, peptide_length, anchor_contribution) {
       }
     }
     return(anchor_list)
-    }, error = function(e) { return("NA") })
+  }, error = function(e) { return("NA") })
 }
 
 #converts string range (e.g. '2-4', '6') to associated list
@@ -224,7 +224,7 @@ tier <- function(variant_info, anchor_contribution, dna_cutoff, allele_expr_cuto
       return("Pass")
     }
   }
-
+  
   if ((mt_binding < binding_threshold) && allele_expr_pass && vaf_clonal_pass && tsl_pass && !anchor_residue_pass) {
     if (percentile_filter) {
       if (mt_percent <= percentile_threshold) {
@@ -275,7 +275,7 @@ tier_numbers <- function(variant_info, anchor_contribution, dna_cutoff, allele_e
   rna_depth <- as.numeric(variant_info["RNA Depth"])
   allele_expr <- as.numeric(variant_info["Allele Expr"])
   if (use_allele_specific_binding_thresholds && hla_allele %in% names(meta_data[["allele_specific_binding_thresholds"]][hla_allele])) {
-      binding_threshold <- as.numeric(meta_data[["allele_specific_binding_thresholds"]][hla_allele])
+    binding_threshold <- as.numeric(meta_data[["allele_specific_binding_thresholds"]][hla_allele])
   }
   trna_vaf <- as.numeric(meta_data["trna_vaf"])
   trna_cov <- as.numeric(meta_data["trna_cov"])
@@ -305,11 +305,11 @@ tier_numbers <- function(variant_info, anchor_contribution, dna_cutoff, allele_e
     range_stop <- as.numeric(strsplit(mutation_pos_list, "-")[[1]][2])
     mutation_pos_list <- c(range_start:range_stop)
     if (all(mutation_pos_list %in% anchor_list)) {
-        if (is.na(wt_binding)) {
-          anchor_residue_pass <- FALSE
-        }else if (wt_binding < binding_threshold) {
-          anchor_residue_pass <- FALSE
-        }
+      if (is.na(wt_binding)) {
+        anchor_residue_pass <- FALSE
+      }else if (wt_binding < binding_threshold) {
+        anchor_residue_pass <- FALSE
+      }
     }
   }else if (!is.na(mutation_pos_list)) {
     if (all(as.numeric(mutation_pos_list) %in% anchor_list)) {
@@ -354,7 +354,7 @@ tier_numbers <- function(variant_info, anchor_contribution, dna_cutoff, allele_e
         return(5)
       }
     }else {
-     return(5)
+      return(5)
     }
   }
   if ((mt_binding < binding_threshold) && allele_expr_pass && !vaf_clonal_pass && tsl_pass && anchor_residue_pass) {

pvactools/tools/pvacview/app.R

@@ -2,6 +2,8 @@ library(shiny)
 
 source(server.R)
 source(ui.R)
+source(neofox_ui.R)
+source(custom_ui.R)
 
 options(shiny.host = '127.0.0.1')
 options(shiny.port = 3333)

pvactools/tools/pvacview_dev_eve/custom_ui.R → pvactools/tools/pvacview/custom_ui.R

@@ -24,9 +24,16 @@ custom_tab <- tabItem("custom",
                         br(), br(),
                         uiOutput("custom_upload_ui")
                     ),
-                    uiOutput("custom_group_by_feature_ui"),
-                    uiOutput("custom_order_by_feature_ui"),
-                    uiOutput("custom_peptide_features_ui"),
+                    box(
+                      title = "Choose How to Visualize Data", status = "primary", solidHeader = TRUE, width = NULL,
+                      uiOutput("custom_group_by_feature_ui"),
+                      h5("Group peptides together by a certain feature. For example, grouping by variant would allow user to explore all proposed peptides for one variant at a time."),
+                      uiOutput("custom_order_by_feature_ui"),
+                      h5("Order peptides by a certain feature. For example, ordering peptides by binding scores to find the best binders."),
+                      uiOutput("custom_peptide_features_ui"),
+                      h5("Choose what features you would like to consider for each group of peptides.")
+                    ),
+
                     actionButton("visualize_custom", "Visualize")
                 ),
                 column(6,
@@ -59,14 +66,38 @@ custom_tab <- tabItem("custom",
                     enable_sidebar = TRUE, sidebar_width = 25, sidebar_start_open = TRUE,
                     DTOutput('customTable')%>% withSpinner(color="#8FCCFA"),
                     span("Currently investigating row: ", verbatimTextOutput("customSelected")),
-                    style = "overflow-x: scroll;font-size:100%")
+                    style = "overflow-x: scroll;font-size:100%"),
           ),
           fluidRow(
             box(width = 12, title = "Detailed Data", solidHeader = TRUE, collapsible = TRUE, status = "primary",
-                tabBox(width = 12, title = " ",
-                       tabPanel("Peptide candidates grouped by selected feature",
-                                DTOutput('customPeptideTable')%>% withSpinner(color="#8FCCFA"), style = "overflow-x: scroll;font-size:100%")
+                DTOutput('customPeptideTable')%>% withSpinner(color="#8FCCFA"), style = "overflow-x: scroll;font-size:100%"
+            )
+          ),
+          fluidRow(
+            box(width = 12,
+                title = "Dynamic Scatter Plot", status = "primary", solidHeader = TRUE, collapsible = TRUE,
+                h4("Scatter plot to explore characteristics of data"),
+                sidebarPanel(
+                  #variable selection for x-axis
+                  uiOutput("xvrbl_custom"),
+                  uiOutput("xvrbl_log_custom"),
+                  uiOutput("xvrbl_scale_custom"),
+                  # variable selection for y-axis
+                  uiOutput("yvrbl_custom"),
+                  uiOutput("yvrbl_log_custom"),
+                  uiOutput("yvrbl_scale_custom"),
+                  # color
+                  uiOutput("color_custom"),
+                  uiOutput("min_color_custom"),
+                  uiOutput("max_color_custom"),
+                  # size
+                  uiOutput("size_custom")
+                ),
+                mainPanel(
+                  align = "center",
+                  plotlyOutput(outputId = "scatter_custom", height = "800px") %>% withSpinner(color = "#8FCCFA"),
                 )
+
             )
           )
         )