R help - Aug 2009 - Saving heatmaps as PDFs

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

Try playing with the
width, height
of the pdf()

Tal





On Tue, Aug 25, 2009 at 2:04 AM, dorothyc <dorothyc@bcgsc.ca> wrote:
> 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
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


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