Nantes Université

Valider f96c1064 rédigé par Solenne DUMONT's avatar Solenne DUMONT
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modification of heatmap in report.html

parent 3897a6b6

SCRIPTS/DE/deAnalysis.R

+10 −5
Numéro de ligne d'origine Numéro de ligne de diff Ligne de diff
@@ -167,10 +167,10 @@ if(nrow(DE.sel$isDE)>=10){ 
        quantile.expr<-quantile(unlist(rowScaledExpr),seq(0,1,.01))

        colHA=colorRamp2(c(quantile.expr[2],0,quantile.expr[100]),c("blue","white","red"))



	png(paste(paste(outputDir,comp,sep="/"),"clustDEgene.png",sep="/"),width=25,height=22,units="cm",res=600,pointsize=3)

        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()

	#png(paste(paste(outputDir,comp,sep="/"),"clustDEgene.png",sep="/"),width=25,height=22,units="cm",res=600,pointsize=3)

        #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)

	print(Heatmap(exprDE.scaled,top_annotation = haByComp, row_names_gp = autoGparFontSizeMatrix(nrow(exprDE.scaled)),
@@ -199,6 +199,11 @@ if(nrow(DE.sel$isDE)>=10){ 
		hclustGeneDESelect<-unsupervisedClustering(exprDESelect.scaled,transpose = F,nboot=nboot,bootstrap = bootTemp)

        	hclustSampleDESelect<-unsupervisedClustering(exprDESelect.scaled,transpose = T,nboot=nboot,bootstrap = bootTemp,method.dist = "euclidean")

		

		png(paste(paste(outputDir,comp,sep="/"),"clustDEgene.png",sep="/"),width=25,height=22,units="cm",res=600,pointsize=3)

		print(Heatmap(exprDESelect.scaled,top_annotation = haByCompSelect, row_names_gp = autoGparFontSizeMatrix(nrow(exprDESelect.scaled)),

		cluster_rows = hclustGeneDESelect,col = colHA, cluster_columns = hclustSampleDESelect,name=comp,column_names_gp = autoGparFontSizeMatrix(ncol(exprDESelect.scaled)) ))	

		dev.off()



		print(Heatmap(exprDESelect.scaled,top_annotation = haByCompSelect, row_names_gp = autoGparFontSizeMatrix(nrow(exprDESelect.scaled)),

                cluster_rows = hclustGeneDESelect,col = colHA, cluster_columns = hclustSampleDESelect,name=comp,column_names_gp = autoGparFontSizeMatrix(ncol(exprDESelect.scaled)) ))