Hi, I'm trying to have a clear figure of gene clusters using heatmaps, but with more than 100-200 genes it's not possible to do it, with default options (and I would like to do that with 1500 genes or so...). Gene names (and branchs too) collapse together... I tried, setting new device dimensions (jpeg() or png() height and width), and modifying par() options (fin, etc..), to have long cluster figures (to be clear, dChip style). Well, it works for others high-level graphical functions, but it doesn't work for heatmaps(). I always obtain big figures, but with exactely the same squared heatmap inside. I spent long time on the documentation and searching the web, and when I found something, it was always some heatmaps for 50-100 genes at max I trust that someone working on gene clustering is confidential on this, and I will appreciate a lot any suggestion... I almost became crazy on that !!! Thanks in advance, Giulio

Hi There's a function called heatmap.2 in the gregmisc library that will resize properly when you send it to a long png() or jpg(). It's similar to, but not the same as, heatmap() so read the docs! Mick -----Original Message----- From: Giulio Di Giovanni [mailto:perimessaggini@hotmail.com] Sent: Tue 11/9/2004 3:37 PM To: bioconductor@stat.math.ethz.ch Cc: Subject: [BioC] Problems with heatmap on genes... Hi, I'm trying to have a clear figure of gene clusters using heatmaps, but with more than 100-200 genes it's not possible to do it, with default options (and I would like to do that with 1500 genes or so...). Gene names (and branchs too) collapse together... I tried, setting new device dimensions (jpeg() or png() height and width), and modifying par() options (fin, etc..), to have long cluster figures (to be clear, dChip style). Well, it works for others high-level graphical functions, but it doesn't work for heatmaps(). I always obtain big figures, but with exactely the same squared heatmap inside. I spent long time on the documentation and searching the web, and when I found something, it was always some heatmaps for 50-100 genes at max I trust that someone working on gene clustering is confidential on this, and I will appreciate a lot any suggestion... I almost became crazy on that !!! Thanks in advance, Giulio _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

Hi Giulio, If you have access to Adobe Illustrator, you could write your heatmap to a postscript file using postscript() and then open and edit the file in Illustrator. I've found that in many cases this is much easier than wrangling with the plotting parameters in R, in particular when it comes to fonts. Otherwise, trying to display > 50 genes on a heatmap becomes prohibitively difficult. Best, Jeff. On Tue, 9 Nov 2004, Giulio Di Giovanni wrote: > > Hi, > > I'm trying to have a clear figure of gene clusters using heatmaps, but with > more than 100-200 genes it's not possible to do it, with default options (and > I would like to do that with 1500 genes or so...). Gene names (and branchs > too) collapse together... > > I tried, setting new device dimensions (jpeg() or png() height and width), > and modifying par() options (fin, etc..), to have long cluster figures (to be > clear, dChip style). Well, it works for others high-level graphical > functions, but it doesn't work for heatmaps(). I always obtain big figures, > but with exactely the same squared heatmap inside. > > I spent long time on the documentation and searching the web, and when I > found something, it was always some heatmaps for 50-100 genes at max > > I trust that someone working on gene clustering is confidential on this, > and I will appreciate a lot any suggestion... I almost became crazy on that > !!! > > Thanks in advance, > > Giulio > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi Giulio. Heatmap is as you say a great tool if you have a small number of genes but NOT if you have a lot of genes. I was dealing with the same thing as you are doing now some 6 month ago and I found no good solution using Heatmap. Therefore we use the freeware (note freeware) MeV from TIGR at our department to do hierarchical clustering and similar things. http://www.tigr.org/software/tm4/mev.html What we have done is to write a script (exportMEV) that takes an MA-object (package Aroma in R) and export that object to MeV format and use it when doing clustering. http://www.biotech.kth.se/molbio/microarray/pages/kthpackagetransfer.h tm l Best regards // Johan Lindberg -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Giulio Di Giovanni Sent: Tuesday, November 09, 2004 4:38 PM To: bioconductor@stat.math.ethz.ch Subject: [BioC] Problems with heatmap on genes... Hi, I'm trying to have a clear figure of gene clusters using heatmaps, but with more than 100-200 genes it's not possible to do it, with default options (and I would like to do that with 1500 genes or so...). Gene names (and branchs too) collapse together... I tried, setting new device dimensions (jpeg() or png() height and width), and modifying par() options (fin, etc..), to have long cluster figures (to be clear, dChip style). Well, it works for others high-level graphical functions, but it doesn't work for heatmaps(). I always obtain big figures, but with exactely the same squared heatmap inside. I spent long time on the documentation and searching the web, and when I found something, it was always some heatmaps for 50-100 genes at max I trust that someone working on gene clustering is confidential on this, and I will appreciate a lot any suggestion... I almost became crazy on that !!! Thanks in advance, Giulio _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor