[BioC] qustion on heatmap

James W. MacDonald jmacdon at med.umich.edu
Tue Jul 20 23:02:45 CEST 2010


Hi B.S.,

On 7/20/2010 6:18 AM, sidahmed BENABDERRAHMANE wrote:
> Hello
>
> I have a similarity matrix between a set of genes with which I want to
> generate a heatmap, for this reason let me ask some questions:
>
> - Is it possible to change the color of a cell of the heatmap after its
> creation? because I want to keep the upper triangle of the heatmap to
> display the color assigned to the similarity measure between genes, and
> in the lower triangle of the heatmap I want to use its cells to display
> other information.

When you use the term 'heatmap', the connotation is that you want to do 
some sort of clustering rather than a simple similarity matrix, and that 
is what the various heatmap functions in R are designed to do. So, no it 
isn't possible to use any of the heatmap functions to do what you want.

That said, the heatmap functions are all pretty much just wrappers 
around the image() function, and as R is a scripting language it 
wouldn't be that difficult to write a function to do what you want. Just 
make a matrix of the data you want to create an image of, and then plot. 
The image() function is a bit tricky as to the orientation of the 
resulting image, so you should look at the help file. The code for the 
heatmap() function might also be useful.

Best,

Jim


>
> thank you in advance
>
> ------
> B.S. (benabdsi at loria.fr)
> INRIA France.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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