R help - Jan 2009 - heatmap.2 color issue

Dear All:

I tried to use heatmap.2 to generate hierarchical clustering using the following
command:

heatmap.2(datamatrix, scale="row", trace="none",
col=greenred(256), labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE)

datamatrix is subset of a RMA normalized data subset by a genelist. 

The problem is a lot of times, the z-score in key are from, like -5 to 15 or -15
to 5, as a result, the zero of z distribution are are either green region or red
region of
the key, the resulting heatmap are either generally greenish or redish.

I wonder if there is a way to make the heatmap more balanced between red and
green, I tried to read the heatmap.2 help but could not get a clear idea.

Thanks
Hao


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the heatmapCol function of package MKmisc might help ... try:
library(MKmisc)
example("heatmapCol")

Best
Matthias

Liu, Hao [CNTUS] wrote:
> Dear All:
>
> I tried to use heatmap.2 to generate hierarchical clustering using the
following command:
>
> heatmap.2(datamatrix, scale="row", trace="none",
col=greenred(256), labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE)
>
> datamatrix is subset of a RMA normalized data subset by a genelist. 
>
> The problem is a lot of times, the z-score in key are from, like -5 to 15
or -15 to 5, as a result, the zero of z distribution are are either green region
or red region of
> the key, the resulting heatmap are either generally greenish or redish.
>
> I wonder if there is a way to make the heatmap more balanced between red
and green, I tried to read the heatmap.2 help but could not get a clear idea.
>
> Thanks
> Hao
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
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>   
-- 
Dr. Matthias Kohl
www.stamats.de