--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/VolcanoPlotsScript.R	Fri Jun 26 09:35:11 2020 -0400
@@ -0,0 +1,426 @@
+# R script to plot volcanos through Galaxy based GIANT tool 
+# written by Jimmy Vandel
+#
+#
+initial.options <- commandArgs(trailingOnly = FALSE)
+file.arg.name <- "--file="
+script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
+script.basename <- dirname(script.name)
+source(file.path(script.basename, "utils.R"))
+source(file.path(script.basename, "getopt.R"))
+
+#addComment("Welcome R!")
+
+# setup R error handling to go to stderr
+options( show.error.messages=F, error = function () { cat(geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+loc <- Sys.setlocale("LC_NUMERIC", "C")
+
+#get starting time
+start.time <- Sys.time()
+
+options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
+args <- commandArgs()
+
+# get options, using the spec as defined by the enclosed list.
+# we read the options from the default: commandArgs(TRUE).
+spec <- matrix(c(
+  "statisticsFile", "i", 1, "character",
+  "volcanoName" , "n", 1, "character",
+  "pvalColumnName" , "p", 1, "character",
+  "fdrColumnName" , "m", 1, "character",
+  "fcColumnName" , "c", 1, "character",
+  "fcKind","d", 1, "character",
+  "fdrThreshold","s", 1, "double",
+  "fcThreshold","e", 1, "double",
+  "organismID","x",1,"character",
+  "rowNameType","y",1,"character",
+  "log", "l", 1, "character",
+  "outputFile" , "o", 1, "character",
+  "format", "f", 1, "character",
+  "quiet", "q", 0, "logical"),
+  byrow=TRUE, ncol=4)
+opt <- getopt(spec)
+
+# enforce the following required arguments
+if (is.null(opt$log)) {
+  addComment("[ERROR]'log file' is required\n")
+  q( "no", 1, F )
+}
+addComment("[INFO]Start of R script",T,opt$log,display=FALSE)
+if (is.null(opt$statisticsFile)) {
+  addComment("[ERROR]'statisticsFile' is required",T,opt$log)
+  q( "no", 1, F )
+}
+if (length(opt$pvalColumnName)==0 || length(opt$fdrColumnName)==0  || length(opt$fcColumnName)==0) {
+  addComment("[ERROR]no selected columns",T,opt$log)
+  q( "no", 1, F )
+}
+if (length(opt$pvalColumnName)!=length(opt$fcColumnName) || length(opt$pvalColumnName)!=length(opt$fdrColumnName)) {
+  addComment("[ERROR]different number of selected columns between p.val, adj-p.val and FC ",T,opt$log)
+  q( "no", 1, F )
+}
+if (is.null(opt$fcKind)) {
+  addComment("[ERROR]'fcKind' is required",T,opt$log)
+  q( "no", 1, F )
+}
+if (is.null(opt$fdrThreshold)) {
+  addComment("[ERROR]'FDR threshold' is required",T,opt$log)
+  q( "no", 1, F )
+}
+if (is.null(opt$fcThreshold)) {
+  addComment("[ERROR]'FC threshold' is required",T,opt$log)
+  q( "no", 1, F )
+}
+if (is.null(opt$outputFile)) {
+  addComment("[ERROR]'output file' is required",T,opt$log)
+  q( "no", 1, F )
+}
+if (is.null(opt$format)) {
+  addComment("[ERROR]'output format' is required",T,opt$log)
+  q( "no", 1, F )
+}
+
+#demande si le script sera bavard
+verbose <- if (is.null(opt$quiet)) {
+  TRUE
+}else{
+  FALSE
+}
+
+#paramètres internes
+addComment("[INFO]Parameters checked test mode !",T,opt$log,display=FALSE)
+
+addComment(c("[INFO]Working directory: ",getwd()),TRUE,opt$log,display=FALSE)
+addComment(c("[INFO]Command line: ",args),TRUE,opt$log,display=FALSE)
+
+#directory for plots
+dir.create(file.path(getwd(), "plotDir"))
+dir.create(file.path(getwd(), "plotLyDir"))
+
+#charge des packages silencieusement
+suppressPackageStartupMessages({
+  library("methods")
+  library("biomaRt")
+  library("ggplot2")
+  library("plotly")
+  library("stringr")
+})
+
+#define some usefull variable
+nbVolcanosToPlot=length(opt$pvalColumnName)
+
+#load input file
+statDataMatrix=read.csv(file=file.path(getwd(), opt$statisticsFile),header=F,sep="\t",colClasses="character")
+#remove first colum to convert it as rownames
+rownames(statDataMatrix)=statDataMatrix[,1]
+statDataMatrix=statDataMatrix[,-1]
+
+#identify lines without adjusted p-value info (should contain the same content as rownames) and replace them with NA values
+FDRinfo=rep(TRUE,nbVolcanosToPlot)
+for(iVolcano in 1:nbVolcanosToPlot){
+  #input parameter should be None when adjusted p-val are not available
+  if(opt$fdrColumnName[iVolcano]=="None"){
+    #content of the corresponding column should also be the same as rownames
+    if(!all(statDataMatrix[,(iVolcano-1)*3+2]==rownames(statDataMatrix))){
+      addComment(c("[ERROR]It seems that input stat matrix contains adjusted p-values for volcano",iVolcano,"whereas input parameter indicates that not."),T,opt$log)
+      q( "no", 1, F )
+    }
+    FDRinfo[iVolcano]=FALSE
+    statDataMatrix[,(iVolcano-1)*3+2]=NA
+  }
+}
+
+if(is.data.frame(statDataMatrix)){
+  statDataMatrix=data.matrix(statDataMatrix)
+}else{
+  statDataMatrix=data.matrix(as.numeric(statDataMatrix))
+}
+
+#check if available column number match with volcano requested number
+if(ncol(statDataMatrix)!=3*nbVolcanosToPlot){
+  addComment("[ERROR]Input file column number is different from requested volcano number",T,opt$log)
+  q( "no", 1, F )
+}
+
+#build global dataFrame with data and fill with p.val and log2(FC) and FDR
+dataFrame=data.frame(row.names = rownames(statDataMatrix))
+#start with p-value
+dataFrame$p.value=statDataMatrix[,seq(1,nbVolcanosToPlot*3,3),drop=FALSE]
+#compute FDR if needed or just get available info
+dataFrame$adj_p.value=dataFrame$p.value
+for(iVolcano in 1:nbVolcanosToPlot){
+  #adjusted p-value are already computed
+  if(FDRinfo[iVolcano]){
+    dataFrame$adj_p.value[,iVolcano]=statDataMatrix[,(iVolcano-1)*3+2,drop=FALSE]
+  }else{
+    #adjusted p-value should be computed based on p-val using FDR
+    dataFrame$adj_p.value[,iVolcano]=p.adjust(dataFrame$p.value[,iVolcano,drop=FALSE],"fdr")
+    addComment(c("[INFO]Adjusted p-values are not available in input for volcano",iVolcano,", FDR approach will be used on available raw p-values"),T,opt$log)
+  } 
+}
+if(opt$fcKind=="FC"){
+  #we should transform as Log2FC
+  dataFrame$coefficients=log2(statDataMatrix[,seq(3,nbVolcanosToPlot*3,3),drop=FALSE])
+  addComment(c("[INFO]FC are converted in log2(FC) for plotting"),T,opt$log)
+}else{
+  dataFrame$coefficients=statDataMatrix[,seq(3,nbVolcanosToPlot*3,3),drop=FALSE]
+}
+
+addComment(c("[INFO]Input data available for",nbVolcanosToPlot,"volcano(s) with",nrow(statDataMatrix),"rows"),T,opt$log)
+
+
+#plot VOLCANOs
+volcanoPerPage=1
+logFCthreshold=log2(opt$fcThreshold)
+iToPlot=1
+plotVector=list()
+volcanoNameList=c()
+for (iVolcano in 1:nbVolcanosToPlot){
+  
+  if(nchar(opt$volcanoName[iVolcano])>0){
+    curentVolcanoName=opt$volcanoName[iVolcano]
+  }else{
+    curentVolcanoName=paste(iVolcano,opt$pvalColumnName[iVolcano],sep="_")
+  }
+  
+  #keep only rows without NA for p-val, adjusted p-val and coeff
+  pValToPlot=dataFrame$p.value[,iVolcano]
+  fdrToPlot=dataFrame$adj_p.value[,iVolcano]
+  coeffToPlot=dataFrame$coefficients[,iVolcano]
+
+  rowToRemove=unique(c(which(is.na(pValToPlot)),which(is.na(fdrToPlot)),which(is.na(coeffToPlot))))
+  if(length(rowToRemove)>0){
+    pValToPlot=pValToPlot[-rowToRemove]
+    fdrToPlot=fdrToPlot[-rowToRemove]
+    coeffToPlot=coeffToPlot[-rowToRemove]
+  }
+  addComment(c("[INFO]For",curentVolcanoName,"volcano,",length(rowToRemove),"rows are discarded due to NA values,",length(pValToPlot),"remaining rows."),T,opt$log)
+  
+  #save volcano name
+  volcanoNameList=c(volcanoNameList,curentVolcanoName)
+  
+  #remove characters possibly troubling
+  volcanoFileName=iVolcano
+  
+  #define the log10(p-val) threshold corresponding to FDR threshold fixed by user
+  probeWithLowFDR=-log10(pValToPlot[which(fdrToPlot<=opt$fdrThreshold)])
+  pvalThresholdFDR=NULL
+  if(length(probeWithLowFDR)>0)pvalThresholdFDR=min(probeWithLowFDR)
+  
+  #get significant points over FC and FDR thresholds
+  significativePoints=intersect(which(abs(coeffToPlot)>=logFCthreshold),which(fdrToPlot<=opt$fdrThreshold))
+  
+  #to reduce size of html plot, we keep 20000 points maximum sampled amongst genes with pval>=33%(pval) and abs(log2(FC))<=66%(abs(log2(FC)))
+  htmlPointsToRemove=intersect(which(abs(coeffToPlot)<=quantile(abs(coeffToPlot),c(0.66))),which(pValToPlot>=quantile(abs(pValToPlot),c(0.33))))
+  if(length(htmlPointsToRemove)>20000){
+    htmlPointsToRemove=setdiff(htmlPointsToRemove,sample(htmlPointsToRemove,20000))
+  }else{
+    htmlPointsToRemove=c() 
+  }
+
+  xMinLimPlot=min(coeffToPlot)-0.2
+  xMaxLimPlot=max(coeffToPlot)+0.2
+  yMaxLimPlot= max(-log10(pValToPlot))+0.2
+  
+  if(length(significativePoints)>0){
+    dataSignifToPlot=data.frame(pval=-log10(pValToPlot[significativePoints]),FC=coeffToPlot[significativePoints],description=paste(names(coeffToPlot[significativePoints]),"\n","FC: " , round(2^coeffToPlot[significativePoints],2) , " | Adjusted p-val: ",prettyNum(fdrToPlot[significativePoints],digits=4), sep=""))
+    #to test if remains any normal points to draw
+    if(length(significativePoints)<length(pValToPlot)){
+      dataToPlot=data.frame(pval=-log10(pValToPlot[-significativePoints]),FC=coeffToPlot[-significativePoints],description=paste("FC: " , round(2^coeffToPlot[-significativePoints],2) , " | Adjusted p-val: ",prettyNum(fdrToPlot[-significativePoints],digits=4), sep=""))
+    }else{
+      dataToPlot=data.frame(pval=0,FC=0,description="null")
+    }
+  }else{
+    dataToPlot=data.frame(pval=-log10(pValToPlot),FC=coeffToPlot,description=paste("FC: " , round(2^coeffToPlot,2) , " | Adjusted p-val: ",prettyNum(fdrToPlot,digits=4), sep=""))
+  }
+  
+  ##traditional plot
+  
+  p <- ggplot(data=dataToPlot, aes(x=FC, y=pval)) + geom_point() + 
+    theme_bw() + ggtitle(curentVolcanoName) + ylab(label="-Log10(p-val)") + xlab(label="Log2 Fold Change") +
+    theme(panel.border=element_blank(),plot.title = element_text(hjust = 0.5),legend.position="none")
+  if(logFCthreshold!=0) p <- p + geom_vline(xintercept=-logFCthreshold, color="salmon",linetype="dotted", size=1) +  geom_vline(xintercept=logFCthreshold, color="salmon",linetype="dotted", size=1) + geom_text(data.frame(text=c(paste(c("log2(1/FC=",opt$fcThreshold,")"),collapse=""),paste(c("log2(FC=",opt$fcThreshold,")"),collapse="")),x=c(-logFCthreshold,logFCthreshold),y=c(0,0)),mapping=aes(x=x, y=y, label=text), size=4, angle=90, vjust=-0.4, hjust=0, color="salmon")
+  if(!is.null(pvalThresholdFDR)) p <- p + geom_hline(yintercept=pvalThresholdFDR, color="skyblue1",linetype="dotted", size=0.5) + geom_text(data.frame(text=c(paste(c("Adjusted pval limit(",opt$fdrThreshold,")"),collapse="")),x=c(xMinLimPlot),y=c(pvalThresholdFDR)),mapping=aes(x=x, y=y, label=text), size=4, vjust=0, hjust=0, color="skyblue3")
+  if(length(significativePoints)>0)p <- p + geom_point(data=dataSignifToPlot,aes(colour=description))
+  
+  ##interactive plot
+  
+  if(length(htmlPointsToRemove)>0){
+    pointToRemove=union(htmlPointsToRemove,significativePoints)
+    #to test if it remains any normal points to draw
+    if(length(pointToRemove)<length(pValToPlot)){
+      dataToPlot=data.frame(pval=-log10(pValToPlot[-pointToRemove]),FC=coeffToPlot[-pointToRemove],description=paste("FC: " , round(2^coeffToPlot[-pointToRemove],2) , " | Adjusted p-val: ", prettyNum(fdrToPlot[-pointToRemove],digits=4), sep=""))
+    }else{
+      dataToPlot=data.frame(pval=0,FC=0,description="null")
+    }
+  }
+  
+  if((nrow(dataToPlot)+length(significativePoints))>40000)addComment(c("[WARNING]For",curentVolcanoName,"volcano, numerous points to plot(",nrow(dataToPlot)+nrow(dataSignifToPlot),"), resulting volcano could be heavy, using more stringent thresholds could be helpful."),T,opt$log)
+  
+  phtml <- plot_ly(data=dataToPlot, x=~FC, y=~pval,type="scatter", mode="markers",showlegend = FALSE, marker = list(color="gray",opacity=0.5), text=~description, hoverinfo="text") %>%
+    layout(title = curentVolcanoName[iVolcano],xaxis=list(title="Log2 Fold Change",showgrid=TRUE, zeroline=FALSE),yaxis=list(title="-Log10(p-val)", showgrid=TRUE, zeroline=FALSE))
+  if(length(significativePoints)>0) phtml=add_markers(phtml,data=dataSignifToPlot, x=~FC, y=~pval, mode="markers" , marker=list( color=log10(abs(dataSignifToPlot$FC)*dataSignifToPlot$pval),colorscale='Rainbow'), text=~description, hoverinfo="text", inherit = FALSE) %>% hide_colorbar()
+  if(logFCthreshold!=0){
+    phtml=add_trace(phtml,x=c(-logFCthreshold,-logFCthreshold), y=c(0,yMaxLimPlot), type="scatter", mode = "lines", line=list(color="coral",dash="dash"), hoverinfo='none', showlegend = FALSE,inherit = FALSE)
+    phtml=add_annotations(phtml,x=-logFCthreshold,y=0,xref = "x",yref = "y",text = paste(c("log2(1/FC=",opt$fcThreshold,")"),collapse=""),xanchor = 'right',showarrow = F,textangle=270,font=list(color="coral"))
+    phtml=add_trace(phtml,x=c(logFCthreshold,logFCthreshold), y=c(0, yMaxLimPlot), type="scatter",  mode = "lines", line=list(color="coral",dash="dash"), hoverinfo='none', showlegend = FALSE,inherit = FALSE)
+    phtml=add_annotations(phtml,x=logFCthreshold,y=0,xref = "x",yref = "y",text = paste(c("log2(FC=",opt$fcThreshold,")"),collapse=""),xanchor = 'right',showarrow = F,textangle=270,font=list(color="coral"))
+  }
+  if(!is.null(pvalThresholdFDR)){
+    phtml=add_trace(phtml,x=c(xMinLimPlot,xMaxLimPlot), y=c(pvalThresholdFDR,pvalThresholdFDR), type="scatter",  mode = "lines", line=list(color="cornflowerblue",dash="dash"), hoverinfo='none', showlegend = FALSE,inherit = FALSE)
+    phtml=add_annotations(phtml,x=xMinLimPlot,y=pvalThresholdFDR+0.1,xref = "x",yref = "y",text = paste(c("Adjusted pval limit(",opt$fdrThreshold,")"),collapse=""),xanchor = 'left',showarrow = F,font=list(color="cornflowerblue"))
+  }
+  plotVector[[length(plotVector)+1]]=p
+  
+  #save plotly files
+  pp <- ggplotly(phtml)
+  htmlwidgets::saveWidget(as_widget(pp), paste(c(file.path(getwd(), "plotLyDir"),"/Volcanos_",volcanoFileName,".html"),collapse=""),selfcontained = F)
+  
+  
+  if(iVolcano==nbVolcanosToPlot || length(plotVector)==volcanoPerPage){
+    #plot and close the actual plot
+    if(opt$format=="pdf"){
+      pdf(paste(c("./plotDir/Volcanos_",volcanoFileName,".pdf"),collapse=""))}else{
+        png(paste(c("./plotDir/Volcanos_",volcanoFileName,".png"),collapse=""))
+      }
+    multiplot(plotlist=plotVector,cols=1)
+    dev.off()
+    if(iVolcano<nbVolcanosToPlot){
+      #prepare for a new ploting file if necessary
+      plotVector=list()
+      iToPlot=iToPlot+1
+    }
+  }
+}
+remove(dataToPlot,dataSignifToPlot)
+addComment("[INFO]Volcanos drawn",T,opt$log,T,display=FALSE)
+
+
+#now add anotation infos about genes
+
+rowItemInfo=NULL
+if(!is.null(opt$rowNameType) && !is.null(opt$organismID)){
+  ##get gene information from BioMart
+  #if(!require("biomaRt")){
+  #    source("https://bioconductor.org/biocLite.R")
+  #    biocLite("biomaRt")
+  #}
+  
+  ensembl_hs_mart <- useMart(biomart="ensembl", dataset=opt$organismID)
+  ensembl_df <- getBM(attributes=c(opt$rowNameType,"description"),mart=ensembl_hs_mart)
+  rowItemInfo=ensembl_df[which(ensembl_df[,1]!=""),2]
+  rowItemInfo=unlist(lapply(rowItemInfo,function(x)substr(unlist(strsplit(x," \\[Source"))[1],1,30)))
+  names(rowItemInfo)=ensembl_df[which(ensembl_df[,1]!=""),1]
+}
+
+#filter out genes with higher p-values for all comparisons
+genesToKeep=names(which(apply(dataFrame$adj_p.value,1,function(x)length(which(x<=opt$fdrThreshold))>0)))
+#filter out genes with lower FC for all comparisons
+genesToKeep=intersect(genesToKeep,names(which(apply(dataFrame$coefficients,1,function(x)length(which(abs(x)>=logFCthreshold))>0))))
+
+if(length(genesToKeep)>0){
+  dataFrameNew=data.frame(row.names=genesToKeep)
+  
+  dataFrameNew$adj_p.value=matrix(dataFrame$adj_p.value[genesToKeep,,drop=FALSE],ncol=ncol(dataFrame$adj_p.value))
+  rownames(dataFrameNew$adj_p.value)=genesToKeep
+  colnames(dataFrameNew$adj_p.value)=colnames(dataFrame$p.value)
+  
+  dataFrameNew$p.value=matrix(dataFrame$p.value[genesToKeep,,drop=FALSE],ncol=ncol(dataFrame$p.value))
+  rownames(dataFrameNew$p.value)=genesToKeep
+  colnames(dataFrameNew$p.value)=colnames(dataFrame$adj_p.value)
+  
+  dataFrameNew$coefficients=matrix(dataFrame$coefficients[genesToKeep,,drop=FALSE],ncol=ncol(dataFrame$coefficients))
+  rownames(dataFrameNew$coefficients)=genesToKeep
+  colnames(dataFrameNew$coefficients)=colnames(dataFrame$adj_p.value)
+  
+  dataFrame=dataFrameNew
+  rm(dataFrameNew)
+}else{
+  addComment("[WARNING]No significative genes",T,opt$log,display=FALSE)
+}
+
+addComment("[INFO]Significant genes filtering done",T,opt$log,T,display=FALSE)
+
+
+#plot VennDiagramm for genes below threshold between comparisons
+#t=apply(dataFrame$adj_p.value[,1:4],2,function(x)names(which(x<=opt$threshold)))
+#get.venn.partitions(t)
+#vennCounts(dataFrame$adj_p.value[,1:4]<=opt$threshold)
+
+#make a simple sort genes based only on the first comparison
+#newOrder=order(dataFrame$adj_p.value[,1])
+#dataFrame$adj_p.value=dataFrame$adj_p.value[newOrder,]
+
+#alternative sorting strategy based on the mean gene rank over all comparisons
+if(length(genesToKeep)>1){
+  currentRank=rep(0,nrow(dataFrame$adj_p.value))
+  for(iVolcano in 1:ncol(dataFrame$adj_p.value)){
+    currentRank=currentRank+rank(dataFrame$adj_p.value[,iVolcano])
+  }
+  currentRank=currentRank/ncol(dataFrame$adj_p.value)
+  newOrder=order(currentRank)
+  rownames(dataFrame)=rownames(dataFrame)[newOrder]
+  
+  dataFrame$adj_p.value=matrix(dataFrame$adj_p.value[newOrder,],ncol=ncol(dataFrame$adj_p.value))
+  rownames(dataFrame$adj_p.value)=rownames(dataFrame$p.value)[newOrder]
+  colnames(dataFrame$adj_p.value)=colnames(dataFrame$p.value)
+  
+  dataFrame$p.value=matrix(dataFrame$p.value[newOrder,],ncol=ncol(dataFrame$p.value))
+  rownames(dataFrame$p.value)=rownames(dataFrame$adj_p.value)
+  colnames(dataFrame$p.value)=colnames(dataFrame$adj_p.value)
+  
+  dataFrame$coefficients=matrix(dataFrame$coefficients[newOrder,],ncol=ncol(dataFrame$coefficients))
+  rownames(dataFrame$coefficients)=rownames(dataFrame$adj_p.value)
+  colnames(dataFrame$coefficients)=colnames(dataFrame$adj_p.value)
+}
+
+#formating output matrix depending on genes to keep
+if(length(genesToKeep)==0){
+  outputData=matrix(0,ncol=ncol(dataFrame$adj_p.value)*4+2,nrow=3)
+  outputData[1,]=c("X","X",rep(volcanoNameList,each=4))
+  outputData[2,]=c("X","X",rep(c("p-val","Adjusted.p-val","FC","log2(FC)"),ncol(dataFrame$adj_p.value)))
+  outputData[,1]=c("Volcano","Gene","noGene")
+  outputData[,2]=c("Comparison","Info","noInfo")
+}else{
+  if(length(genesToKeep)==1){
+    outputData=matrix(0,ncol=ncol(dataFrame$adj_p.value)*4+2,nrow=3)
+    outputData[1,]=c("X","X",rep(volcanoNameList,each=4))
+    outputData[2,]=c("X","X",rep(c("p-val","Adjusted.p-val","FC","log2(FC)"),ncol(dataFrame$adj_p.value)))
+    outputData[,1]=c("Volcano","Gene",genesToKeep)
+    outputData[,2]=c("Comparison","Info","na")
+    if(!is.null(rowItemInfo))outputData[3,2]=rowItemInfo[genesToKeep]
+    outputData[3,seq(3,ncol(outputData),4)]=prettyNum(dataFrame$p.value,digits=4)
+    outputData[3,seq(4,ncol(outputData),4)]=prettyNum(dataFrame$adj_p.value,digits=4)
+    outputData[3,seq(5,ncol(outputData),4)]=prettyNum(2^dataFrame$coefficients,digits=4)
+    outputData[3,seq(6,ncol(outputData),4)]=prettyNum(dataFrame$coefficients,digits=4)
+  }else{
+    #format matrix to be correctly read by galaxy (move headers in first column and row)
+    outputData=matrix(0,ncol=ncol(dataFrame$adj_p.value)*4+2,nrow=nrow(dataFrame$adj_p.value)+2)
+    outputData[1,]=c("X","X",rep(volcanoNameList,each=4))
+    outputData[2,]=c("X","X",rep(c("p-val","Adjusted.p-val","FC","log2(FC)"),ncol(dataFrame$adj_p.value)))
+    outputData[,1]=c("Volcano","Gene",rownames(dataFrame$adj_p.value))
+    outputData[,2]=c("Comparison","Info",rep("na",nrow(dataFrame$adj_p.value)))
+    if(!is.null(rowItemInfo))outputData[3:nrow(outputData),2]=rowItemInfo[rownames(dataFrame$adj_p.value)]
+    outputData[3:nrow(outputData),seq(3,ncol(outputData),4)]=prettyNum(dataFrame$p.value,digits=4)
+    outputData[3:nrow(outputData),seq(4,ncol(outputData),4)]=prettyNum(dataFrame$adj_p.value,digits=4)
+    outputData[3:nrow(outputData),seq(5,ncol(outputData),4)]=prettyNum(2^dataFrame$coefficients,digits=4)
+    outputData[3:nrow(outputData),seq(6,ncol(outputData),4)]=prettyNum(dataFrame$coefficients,digits=4)
+  }
+}
+addComment("[INFO]Formated output",T,opt$log,display=FALSE) 
+
+#write output results
+write.table(outputData,file=opt$outputFile,quote=FALSE,sep="\t",col.names = F,row.names = F)
+
+
+end.time <- Sys.time()
+addComment(c("[INFO]Total execution time for R script:",as.numeric(end.time - start.time,units="mins"),"mins"),T,opt$log,display=FALSE)
+
+addComment("[INFO]End of R script",T,opt$log,display=FALSE)
+
+printSessionInfo(opt$log)
+
+#sessionInfo()
\ No newline at end of file