[R] heatmap color distribution

Wiener, Matthew matthew_wiener at merck.com
Thu Jul 21 16:09:32 CEST 2005

You can use the "breaks" argument in image to do this.  (You don't specify a
function you're using, but other heatmap functions probably have a similar
parameter.)  Look across all your data, figure out the ranges you want to
have different colors, and specify the appropriate break points in each call
to image.  Then you're using the same color set in each one.  You run the
risk, of course, that some of your images will have a very narrow color
range, which might obscure interesting features.  But nothing stops you from
making more than one plot.

Hope this helps.


Matt Wiener

-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Jacob Michaelson
Sent: Thursday, July 21, 2005 9:26 AM
To: r-help at stat.math.ethz.ch
Subject: [R] heatmap color distribution

Hi all,

I've got a set of gene expression data, and I'm plotting several  
heatmaps for subsets of the whole set.  I'd like the heatmaps to have  
the same color distribution, so that comparisons may be made  
(roughly) across heatmaps; this would require that the color  
distribution and distance functions be based on the entire dataset,  
rather than on individual subsets.  Does anyone know how to do this?

Thanks in advance,


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