[R] Saving heatmaps as PDFs

[dorothyc]

Hi,

I'm trying to save heatmaps as PDFs.  However, the PDF version of the  
heatmaps (Heatmap_CAFvsTNF_run2.pdf) is blurred when compared to its  
counterpart, which was saved manually by using the software  
"Grab" (Heatmap_CAFvsTNF_run2.tiff).

  -----R code--------
         sample_output <- "stroma_run2"
	filename <- "exp_limma_results_final_probesets_Pbelowpoint05.txt"

	# read in data
	my.data <- read.delim(filename, sep="\t")
	my.dataM <-my.data[,2:ncol(my.data)]

	hr <- hclust(as.dist(1-cor(t(my.dataM), method="pearson")),  
method="complete")
	hc <- hclust(as.dist(1-cor(my.dataM, method="spearman")),  
method="complete")

          # generate heat map
	library(gplots)

	if  (is.null(sample_output)) {
		pdf( "Heatmap.pdf")
	} else {
		pdf(file=paste("Heatmap_", sample_output, ".pdf", sep="")) } 	

	heatmap.2(as.matrix(my.dataM),Rowv=as.dendrogram(hr),  
Colv=as.dendrogram(hc),cexRow=0.01,
			cexCol=0.8, dendrogram="none", col=greenred(100),  
scale="row",key=TRUE, trace="none",density.info="none",
			symkey=FALSE, main=paste("Heatmap_", sample_output))

        dev.off()

--------------

Thanks,
Dorothy