Try playing with the width, height of the pdf() Tal
On Tue, Aug 25, 2009 at 2:04 AM, dorothyc <[email protected]> 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 > > ______________________________________________ > [email protected] 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. > -- ---------------------------------------------- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs: http://www.r-statistics.com/ http://www.talgalili.com http://www.biostatistics.co.il [[alternative HTML version deleted]] ______________________________________________ [email protected] 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.
