Merge pull request #1 from Nanostring-Biostats/updates-for-release

update to point to new repos

R/download_profile_matrix.R

@@ -77,9 +77,8 @@ download_profile_matrix <- function(matrixname) {
     warning(paste0(matrixname, " is not an expected cell profile matrix name."))
   }
 
-  # X = as.matrix(utils::read.csv(paste0("https://github.com/Nanostring-Biostats/Extensions/blob/refactor/cell-profile-library/",
   X <- as.matrix(utils::read.csv(paste0(
-    "https://raw.githubusercontent.com/patrickjdanaher/cell-profile-library/master/profile_matrices/",
+    "https://raw.githubusercontent.com/Nanostring-Biostats/CellProfileLibrary/master/", 
     matrixname, ".csv"
   ), row.names = 1))
 

README.md

@@ -47,8 +47,9 @@ These include:
 ## Installation
 
 ``` r
-devtools::install_github("Nanostring-Biostats/Extensions",
-subdir="SpatialDecon", ref = "refactor", build_vignettes = TRUE)
+devtools::install_github("Nanostring-Biostats/SpatialDecon",
+                         ref = "master", 
+                         build_vignettes = TRUE)
 ```
 
 ## Getting started

code for creating SpatialDecon.R

@@ -0,0 +1,82 @@
+##### this script contains the code used to build the package.
+rm(list=ls())
+
+### strategy for shiny-in-a-package deployment: taken from https://www.r-bloggers.com/packaging-shiny-applications-a-deep-dive/
+### code written to emulate: https://github.com/MangoTheCat/shinyAppDemo
+
+
+#### package building code: from https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/
+
+
+library("devtools")
+library(roxygen2)
+library(qpdf)
+library(BiocCheck)
+library("styler")
+#library("formatR")
+library("lintr")
+
+setwd("SpatialDecon")
+#usethis::use_tidy_style(indent_by = 4)
+#styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
+
+devtools::document()
+devtools::test() # run unit tests
+devtools::check()
+setwd("..")
+BiocCheck("SpatialDecon")
+BiocCheckGitClone("SpatialDecon")
+setwd("SpatialDecon")
+devtools::build()
+devtools::build(binary = TRUE)
+setwd("..")
+install("SpatialDecon")
+#setwd("SpatialDecon")
+library("SpatialDecon")
+
+
+#########################################
+#### Creating data objects for SpatialDecon   ####
+#########################################
+
+# create colors:
+cellcols = c()
+cellcols["CD4.T.cells"] = "red"
+cellcols["CD8.T.cells"] = "firebrick"
+cellcols["Treg"] = "#FF66FF"
+
+cellcols["T.CD4.naive"] = "#CC0000"
+cellcols["T.CD4.memory"] = "#FF0000"
+cellcols["T.CD8.naive"] = "#FF6633"
+cellcols["T.CD8.memory"] = "#FF9900"
+
+cellcols["NK"] = "grey10"
+cellcols["B"] = "darkblue"
+cellcols["B.naive"] = "#000099"
+cellcols["B.memory"] = "#0000FF"
+cellcols["plasma"] = "#3399CC"
+cellcols["pDC"] = "#00FFFF"
+cellcols["pDCs"] = "#00FFFF"
+cellcols["macrophages"] = "#006600"
+cellcols["monocytes"] = "#33CC00"
+cellcols["monocytes.C"] = "#66CC66"
+cellcols["monocytes.NC.I"] = "#33CC00"
+cellcols["mDCs"] = "#00FF00"
+cellcols["neutrophils"] = "#9966CC"
+cellcols["mast"] = "#FFFF00"
+cellcols["fibroblasts"] = "#999999"
+cellcols["endothelial.cells"] = "#996633"
+cellcols["tumor"] = "#333333"
+
+# see how they look:
+tempb = rep(1, length(cellcols))
+names(tempb) = names(cellcols)
+barplot(tempb, las = 2, col = cellcols)
+
+
+
+save(cellcols, file = "SpatialDecon/data/cellcols.RData")
+# create test dataset:
+#source("create test results.R")
+
+