[R] heatmap.2 adapting the colour scale and text overlay

[David Winsemius]

On Nov 23, 2009, at 10:02 AM, Daniel Brewer wrote:

> Hello,
>
> I am using heatmap.2 from the gplots library to plot a small  
> symmetrical matrix.
>
> This is the command:
>
> heatmap. 
> 2 
> (tempHeat 
> ,symm 
> = 
> T 
> ,trace 
> ="none",cexRow=0.7,cexCol=0.7,col="redgreen",density.info="none")
>
> I have a couple of questions:
> 1) The range is from -0.2 to 0.4 and the colour scheme I am using is  
> redgreen.  What I would like is that a zero value to be black, 0.4  
> strong green and -0.2 red.  Is this possible?  At the moment around  
> 0.1 is black.

Perhaps:
color.palette = colorRampPalette(c("green", "black", "pink", "red"))
  heatmap.2(tempHeat,symm=T,trace="none",cexRow=0.7,cexCol=0.7,  
col=color.palette, density.info="none")

> 2) Is it possible to overlay text on the squares of colour?  How  
> ould one go about doing that.
>
> I am happy to use another heatmap function if ti would be better.  I  
> am not using the original heatmap as it does not provide a colour key.
>
> Thanks
>
> Dan
> -- 
> **************************************************************
> Daniel Brewer, Ph.D.
>
> Institute of Cancer Research
> Molecular Carcinogenesis
> Email: daniel.brewer at icr.ac.uk
> **************************************************************
>
> The Institute of Cancer Research: Royal Cancer Hospital, a  
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> Company No. 534147 with its Registered Office at 123 Old Brompton  
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>
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT