Thanks Sean, Initially I received the error "Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + : must have one more break than colour" when I included breaks = seq(-3,3,0.1), but I changed it to breaks = seq(-4,4,0.03125) to cover the 256 colors and it worked very nicely. Jeff -----Original Message----- From: Sean Davis [mailto:sdavis2@mail.nih.gov] Sent: Monday, March 27, 2006 3:46 PM To: Jeff Lande; Bioconductor Subject: Re: [BioC] Heatmap.2 color scheme Jeff, You may want to have a look at the "breaks" argument to heatmap.2. It will allow you to set the number of breaks above and below zero to be equal so that 0 is actually also the center of your color scale. Using something like breaks=seq(-3,3,0.1) is often helpful. Sean On 3/27/06 4:37 PM, "Jeff Lande" <land0038 at="" umn.edu=""> wrote: > > > I find heatmap.2 to be a very nice dynamic tool for cluster visualization. > I am having a little difficulty getting a good separation of colors in my > heatmap and I'm not sure how to tweak it. > > > > The accompanying color histogram in this package is a great feature. My > problem conceptually is that the distribution of colors is shifted to the > left in the histogram. I would like to revise the color scheme (or the > data) so that the color distribution spans the middle of the histogram. > I've played around using topo.colors(), heat.colors() and cm.colors(), but > there seems to always be a "leftward" shift so that I'm only using the > colors towards the left of the color vector. > > > > Here is the code I am using to create the heatmap > > > > -------------------------------------------------------------- > > hmcol <- colorRampPalette(brewer.pal(10, "RdBu"))(256) > > > > spcol <- ifelse(alldata$ABScore > 1,"red","blue") > > > > heatsub.2 <- function(myexprSet, genelist) { > > > > heatmap.2(exprs(myexprSet[genelist,]), col=hmcol, ColSideColors=spcol, > > labRow=mget(genelist,hgu133aGENENAME),trace="none", scale="row") > > } > > > > heatsub.2(alldata,mygenes[,1]) > > -------------------------------------------------------------- > > > > alldata is an exprSet and mygenes is the output from the pamr.listgenes > command (mygenes[,1] is just a vector of probe sets significant by PAM). > > > > > >> sessionInfo() > > R version 2.2.1, 2005-12-20, i386-pc-mingw32 > > > > attached base packages: > > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > "datasets" "base" > > > > other attached packages: > > gplots gdata gtools RColorBrewer pamr > hgu133a affy Biobase > > "2.3.0" "2.1.2" "2.2.3" "0.2-3" "1.28.0" > "1.10.0" "1.8.1" "1.8.0" > >> > > > > Any suggestions are appreciated. > > > > Thanks, > > > > Jeff Lande > > Post-Doctoral Associate > > University of Minnesota > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor