fixed bugs for R4

CONDA/srp.yml

@@ -48,4 +48,5 @@ dependencies:
   - r-rcolorbrewer
   - r-tidyverse
   - r-ggiraph
+  - r-r.utils
   - pandoc

SCRIPTS/DE/annot.R

@@ -7,11 +7,7 @@ cond2=args[3]
 org=args[4]
 corresFile=args[5]
 
-library(GO.db)
-library(GSEABase)
 library(clusterProfiler)
-library(DOSE)
-library(fgsea)
 
 makeGeneList<-function(data,org){
 	pAdj=data[,"padj"]
@@ -31,13 +27,13 @@ makeGeneList<-function(data,org){
 	return(geneList)
 }
 
-corresIDorg=read.table(corresFile,header=T,row.names=1)
+corresIDorg=read.table(corresFile,header=T,row.names=1,stringsAsFactors=T)
 orgGO=as.character(corresIDorg[org,1])
 orgKegg=as.character(corresIDorg[org,2])
 
 comp=paste(cond1,cond2,sep="__vs__")
 
-data=read.csv(paste(paste(outputDir,comp,sep="/"),"DEseqResFiltered.tsv",sep="/"), header=TRUE, sep="\t") 
+data=read.csv(paste(paste(outputDir,comp,sep="/"),"DEseqResFiltered.tsv",sep="/"), header=TRUE, sep="\t",stringsAsFactors=T) 
 
 #Sys.setenv(http_proxy="http://cache.ha.univ-nantes.fr:3128")
 #Sys.setenv(https_proxy="https://cache.ha.univ-nantes.fr:3128")
@@ -60,10 +56,10 @@ if(dim(data)[1]>10){
 
 }
 
-dataTot=read.csv(paste(paste(outputDir,comp,sep="/"),"DEseqRes.tsv",sep="/"), header=TRUE, sep="\t")
+dataTot=read.csv(paste(paste(outputDir,comp,sep="/"),"DEseqRes.tsv",sep="/"), header=TRUE, sep="\t",stringsAsFactors=T)
 geneListTot=makeGeneList(dataTot,orgGO)
 
-ego2=gseGO(geneList=geneListTot,OrgDb=orgGO,ont="ALL",nPerm=1000,minGSSize=20,maxGSSize=500,pvalueCutoff=1,verbose=FALSE)
+ego2=gseGO(geneList=geneListTot,OrgDb=get(orgGO),ont="ALL",nPerm=1000,minGSSize=20,maxGSSize=500,pvalueCutoff=1,verbose=FALSE)
 ego2Symbol=setReadable(ego2,orgGO,keyType="ENTREZID")
 
 kk2=gseKEGG(geneList=geneListTot,organism=as.character(orgKegg),nPerm=1000,minGSSize=2,pvalueCutoff=1,verbose=FALSE)

SCRIPTS/DE/clusterHeatmap.R

@@ -33,9 +33,9 @@ outputDir=opt$outdir
 # usual functions
 lire<-function(x, character=FALSE){
         if(character){
-                d<-read.table(file = x,sep = "\t",header=T,row.names = 1,colClasses = "character",quote="",check.names=FALSE)
+                d<-read.table(file = x,sep = "\t",header=T,row.names = 1,colClasses = "character",quote="",check.names=FALSE,stringsAsFactors=T)
         }else{
-                d<-read.table(file = x,sep = "\t",header=T,row.names = 1,quote="",check.names=FALSE)
+                d<-read.table(file = x,sep = "\t",header=T,row.names = 1,quote="",check.names=FALSE,stringsAsFactors=T)
         }
         return(d)
 }

SCRIPTS/DE/deAnalysis.R

@@ -11,6 +11,8 @@ library("pvclust")
 library("circlize")
 library("RColorBrewer")
 library(optparse)
+library("R.utils")
+
 
 # Getting options from command line
 option_list = list(
@@ -270,11 +272,11 @@ ecrire(rbind(DE.sel$up,DE.sel$down),paste(paste(outputDir,comp,sep="/"),"DEseqRe
 
 #Volcano-plot
 p <- ggvulcano(DE, cond1, cond2, logFCthreshold=logFCthreshold, AdjPValthreshold=AdjPValthreshold, GenesInFig=GenesInFig)
-htmlwidgets::saveWidget(girafe(ggobj = p, pointsize = 12, width_svg = 17, height_svg = 14), paste(outputDir, comp, "Volcano-plot.html", sep="/"), selfcontained = FALSE)
+htmlwidgets::saveWidget(girafe(ggobj = p, pointsize = 12, width_svg = 17, height_svg = 14), getAbsolutePath(paste(outputDir, comp, "Volcano-plot.html", sep="/")), selfcontained = FALSE)
 
 #MA-plot
 p <- ggMA(DE, cond1, cond2, meanInCompThreshold=0.5, GenesInFig=GenesInFig)
-htmlwidgets::saveWidget(girafe(ggobj = p, pointsize = 12, width_svg = 17, height_svg = 14), paste(outputDir, comp, "MA-plot.html", sep="/"), selfcontained = FALSE)
+htmlwidgets::saveWidget(girafe(ggobj = p, pointsize = 12, width_svg = 17, height_svg = 14), getAbsolutePath(paste(outputDir, comp, "MA-plot.html", sep="/")), selfcontained = FALSE)
 
 #DE genes clustering
 if(nrow(DE.sel$isDE)>=10){