diff --git a/SCRIPTS/DE/deAnalysis.R b/SCRIPTS/DE/deAnalysis.R
index 70150a9388bf3d806207eb3dabafa4354cf097af..9904eac181dabdd0e12d66f67967c1315f1d6766 100644
--- a/SCRIPTS/DE/deAnalysis.R
+++ b/SCRIPTS/DE/deAnalysis.R
@@ -20,7 +20,7 @@ lire<-function(x, character=FALSE){
 }
 
 ecrire<-function(x,file="default.tsv",headRow="Name"){
-        options(warn=-1) #Supress unecessary warning about append 
+        options(warn=-1) #Supress unecessary warning about append
         write.table(x = paste0(headRow,"\t"),file = file,sep = "\t",eol="",quote=F,row.names=F,col.names=F)
         write.table(x=x,file=file,sep="\t", row.names = T, col.names = T, quote = FALSE,append=T)
         options(warn=0)
@@ -112,16 +112,42 @@ ecrire(rbind(DE.sel$up,DE.sel$down),paste(paste(outputDir,comp,sep="/"),"DEseqRe
 
 #Volcano-plot
 
+data <- cbind(DE, color = DE$DE)
+levels(data$color)[levels(data$color) == "DOWN"] <- "green"
+levels(data$color)[levels(data$color) == "NONE"] <- "grey75"
+levels(data$color)[levels(data$color) == "UP"] <- "red"
+data <- cbind(data, label = ifelse(data$DE != "NONE", rownames(data), ""))
+
+# removing NA for setting correct plot limits
+data <- data[!is.na(data$padj),]
+# limiting number of displayed genes
+data <- data[order(abs(data$padj)),]
+data[GenesInFig+1:nrow(data),]$label <- ""
+dataLabels <- subset(data, label != "")
+
 png(paste(paste(outputDir,comp,sep="/"),"Volcano-plot.png",sep="/"),width=10,height=10,units="cm",res=200)
-  
-plot(DE$log2FoldChange,-log10(DE$padj),type="n",ylab="-log10(DEseq padj)",xlab="log2(Fold-Change)",col="black",main=paste0("Volcano plot of comparison ",cond1," (pos FC) VS ",cond2," (neg FC)\nBenjamini & Hochberg method (",nrow(DE.sel$isDE),"/",nrow(DE)," DE genes)"),cex.main=0.5,cex.lab=0.8)
-abline(h=-log10(AdjPValthreshold))
-abline(v = -logFCthreshold)
-abline(v = logFCthreshold)
-if(nrow(DE.sel$up)>0) text(DE.sel$up$log2FoldChange,-log10(DE.sel$up$padj),labels = rownames(DE.sel$up),cex=.3,col="red")
-if(nrow(DE.sel$down)>0) text(DE.sel$down$log2FoldChange,-log10(DE.sel$down$padj),labels = rownames(DE.sel$down),cex=.3,col="green")
-points(DE.sel$notDE$log2FoldChange,-log10(DE.sel$notDE$padj),cex=.2,col="black",pch=16)
 
+p <- ggplot(data=data, aes(x=log2FoldChange, y=-log10(padj))) +
+    geom_point(size = 0.5, color = data$color) +
+    geom_hline(aes(yintercept=-log10(AdjPValthreshold))) +
+    geom_vline(aes(xintercept=logFCthreshold)) +
+    geom_vline(aes(xintercept=-logFCthreshold)) +
+    ylab("-log10(DEseq padj)") +
+    xlab("log2(Fold-Change)") +
+    ggtitle(paste0("Volcano plot of comparison\n", cond1," (pos FC) VS ",cond2," (neg FC)\nBenjamini & Hochberg method (",nrow(DE.sel$isDE),"/",nrow(DE)," DE genes)")) +
+    theme_bw() +
+    theme(plot.title = element_text(size=10),
+          axis.title = element_text(size=10))
+# put labels when existing
+if (nrow(dataLabels)>0) {
+	p <- p + geom_text_repel(
+	  data = dataLabels,
+	  aes(label = label, fontface="bold.italic"),
+	  size = 2,
+	  point.padding = unit(0.1, "lines")
+	)
+}
+print(p)
 dev.off()
 
 #MA-plot
@@ -151,7 +177,7 @@ if(nrow(DE.sel$isDE)>=10){
 
 	DEgenes.names=rownames(DE.sel$isDE)
 	colFun<-c(ggplotColours,rainbow)
-	
+
 	sampleHt<-colnames(exprDatT)
         haByComp<-ha
         exprDE=exprDatT[DEgenes.names,sampleHt,drop=FALSE]
@@ -171,7 +197,7 @@ if(nrow(DE.sel$isDE)>=10){
         #print(Heatmap(exprDE.scaled,top_annotation = haByComp, row_names_gp = autoGparFontSizeMatrix(nrow(exprDE.scaled)),
                # cluster_rows = hclustGeneDE,col = colHA, cluster_columns = hclustSampleDE,name=comp,column_names_gp = autoGparFontSizeMatrix(ncol(exprDE.scaled)) ))
         #dev.off()
-	
+
 	pdf(paste(paste(outputDir,comp,sep="/"),"clustDEgene.pdf",sep="/"),width=10,height=10)
 	p <- Heatmap(exprDE.scaled,top_annotation = haByComp, row_names_gp = autoGparFontSizeMatrix(nrow(exprDE.scaled)),
                 cluster_rows = hclustGeneDE,col = colHA, cluster_columns = hclustSampleDE,name=comp,column_names_gp = autoGparFontSizeMatrix(ncol(exprDE.scaled)) )
@@ -211,16 +237,14 @@ if(nrow(DE.sel$isDE)>=10){
   	}
   	else {	
 		png(paste(paste(outputDir,comp,sep="/"),"clustDEgene.png",sep="/"),width=25,height=22,units="cm",res=600,pointsize=3)
-        print(p)
+		print(p)
 		dev.off()
   	}
 	dev.off()
-		
+
 }else{
 	png(paste(paste(outputDir,comp,sep="/"),"clustDEgene.png",sep="/"))
 	plot.new()
 	text(0.5,0.5,"Less than 10 differential expressed gene for this comparison,\n clustering isn't relevant")
 	dev.off()
 }
-
-