 

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


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