packaging

effiken · Jul 26, 2018 · 85c9b12 · 85c9b12
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Showing 24 changed files with 47 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,10 @@
+Package: scDissector
+Title: Exploratory Data Analysis tool for single-cell RNA-seq data
+Version: 1.00
+Authors@R: person("Ephraim", "Kenigsberg", email = "effiken@gmail.com", role = c("aut", "cre"))
+Description: What the package does (one paragraph).
+Depends: R (>= 3.4.3),ggvis,dplyr,gplots,Matrix,Matrix.utils
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.1.0
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,3 @@
+# Generated by roxygen2: do not edit by hand
+
+export(runExample)
diff --git a/R/runExample.R b/R/runExample.R
@@ -0,0 +1,9 @@
+#' @export
+runExample <- function() {
+  appDir <- system.file("shiny", package = "scDissector")
+  if (appDir == "") {
+    stop("Could not find example directory. Try re-installing `scDissector`.", call. = FALSE)
+  }
+
+  shiny::runApp(appDir, display.mode = "normal")
+}
diff --git a/inst/.DS_Store b/inst/.DS_Store
diff --git a/colors_brewer_RdBu.txt → inst/extdata/colors_brewer_RdBu.txt b/colors_brewer_RdBu.txt → inst/extdata/colors_brewer_RdBu.txt
diff --git a/colors_paul.txt → inst/extdata/colors_paul.txt b/colors_paul.txt → inst/extdata/colors_paul.txt
diff --git a/colors_viridis.txt → inst/extdata/colors_viridis.txt b/colors_viridis.txt → inst/extdata/colors_viridis.txt
diff --git a/gene_sets.txt → inst/extdata/gene_sets.txt b/gene_sets.txt → inst/extdata/gene_sets.txt
diff --git a/hgnc_complete_set.txt → inst/extdata/hgnc_complete_set.txt b/hgnc_complete_set.txt → inst/extdata/hgnc_complete_set.txt
diff --git a/sample_colors.txt → inst/extdata/sample_colors.txt b/sample_colors.txt → inst/extdata/sample_colors.txt
diff --git a/surface_markers.csv → inst/extdata/surface_markers.csv b/surface_markers.csv → inst/extdata/surface_markers.csv
diff --git a/tfs.csv → inst/extdata/tfs.csv b/tfs.csv → inst/extdata/tfs.csv
diff --git a/inst/shiny/.DS_Store b/inst/shiny/.DS_Store
diff --git a/README.md → inst/shiny/README.md b/README.md → inst/shiny/README.md
diff --git a/gene_symbol_convertors.r → inst/shiny/gene_symbol_convertors.r b/gene_symbol_convertors.r → inst/shiny/gene_symbol_convertors.r
diff --git a/global.r → inst/shiny/global.r b/global.r → inst/shiny/global.r
diff --git a/load_dataset.R → inst/shiny/load_dataset.R b/load_dataset.R → inst/shiny/load_dataset.R
diff --git a/load_on_startup.r → inst/shiny/load_on_startup.r b/load_on_startup.r → inst/shiny/load_on_startup.r
diff --git a/projector.r → inst/shiny/projector.r b/projector.r → inst/shiny/projector.r
diff --git a/scPlots.r → inst/shiny/scPlots.r b/scPlots.r → inst/shiny/scPlots.r
diff --git a/server.R → inst/shiny/server.R b/server.R → inst/shiny/server.R
@@ -12,17 +12,17 @@ set.seed(3505)
 non_data_tabs=c("Gating","Basics","Clusters","Truth","QC","Clustering QC","Gene Modules","Samples")
 
 #write.table(file="~/Documents/GitHub/scDissector/viridis_colors.txt",viridis(100),quote=T,row.names=F,col.names=F)
-colgrad_abs<<-read.table("~/Documents/GitHub/scDissector/colors_viridis.txt",stringsAsFactors=F)[,1]
-colgrad_rel<<-read.table("~/Documents/GitHub/scDissector/colors_brewer_RdBu.txt",stringsAsFactors=F)[,1]
+colgrad_abs<<-read.table(system.file("extdata", "colors_viridis.txt", package="scDissector"),stringsAsFactors=F)[,1]
+colgrad_rel<<-read.table(system.file("extdata", "colors_brewer_RdBu.txt", package="scDissector"),stringsAsFactors=F)[,1]
 
-colgrad<<-read.table("~/Documents/GitHub/scDissector/colors_paul.txt",stringsAsFactors=F)[,1]
+colgrad<<-read.table(system.file("extdata", "colors_paul.txt", package="scDissector"),stringsAsFactors=F)[,1]
 #colgrad<<-c(colorRampPalette(c("white",colors()[378],"orange", "tomato","mediumorchid4"))(100))
 
-default_sample_colors<<-rep(paste("#",read.table("sample_colors.txt",stringsAsFactors = F)[,1],sep=""),10)
+default_sample_colors<<-rep(paste("#",read.table(system.file("extdata", "sample_colors.txt", package="scDissector"),stringsAsFactors = F)[,1],sep=""),10)
 
 
 print(getwd())
-genesetsfile<<-"gene_sets.txt"
+genesetsfile<<-system.file("extdata", "gene_sets.txt", package="scDissector")
 if (file.exists(genesetsfile)){
   geneList_tmp<-read.table(file=genesetsfile,header=T,stringsAsFactors = F,row.names =1)
   geneList<<-geneList_tmp[,1]
@@ -1151,6 +1151,9 @@ tab3_left_margin=12
 
   })
 
+
+
+
 #  output$avg_heatmap_interactive <-renderD3heatmap({
   output$avg_heatmap_interactive <-renderPlotly({
 
@@ -1177,6 +1180,7 @@ tab3_left_margin=12
       if (length(inclusts)==0){
         return()
       }
+
       zlim=input$inModelColorScale
       par(mar=c(7,tab3_left_margin,1,9))
       if (input$inModelOrAverage=="Model"){
@@ -1196,8 +1200,6 @@ tab3_left_margin=12
         numis_per_clust_mat=apply(session$userData$dataset$counts[insamples,,inclusts,drop=F],c(1,3),sum,na.rm=T)
         numis_per_clust_arr=aperm(array(numis_per_clust_mat,dim=c(length(insamples),length(inclusts),length(gene_match))),c(1,3,2))
     #    mat=t(t(mat)/numis_per_clust)
-
-        numis_per_sample=apply(session$userData$dataset$counts,1,sum)
 
         if (input$inModelOrAverage=="Batch-corrected Average"){
           if (!is.null(session$userData$dataset$noise_counts)){
@@ -1214,9 +1216,7 @@ tab3_left_margin=12
           counts=session$userData$dataset$counts[insamples,gene_match,inclusts,drop=F]
         }
         mat=avg_per_sample_cluster=apply(counts,2:3,sum,na.rm=T)/apply(numis_per_clust_arr,2:3,sum,na.rm=T)
-        #mat=apply(avg_per_sample_cluster,2:3,mean,na.rm=T)
         rownames(mat)=ingenes
-        #mat<-t(t(mat)/colSums(mat,na.rm=T))
       }
       isolate({
         mat1=mat

diff --git a/ui.R → inst/shiny/ui.R b/ui.R → inst/shiny/ui.R
diff --git a/www/sinai_logo.png → inst/shiny/www/sinai_logo.png b/www/sinai_logo.png → inst/shiny/www/sinai_logo.png
diff --git a/scDissector.Rproj b/scDissector.Rproj
@@ -0,0 +1,16 @@
+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+Encoding: UTF-8
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace