[BioC] Extracting dendogram information from Heatmaps

[James W. MacDonald]

Hi Alison,

alison waller wrote:
> Hello Everyone,
> 
>  
> 
> I've been using heatmap and heatmap.2 to draw heatmaps for my experiments.  
> 
>  
> 
> I have a heatmap of the M values of 6 arrays for the spots with pvalues were
> <0.005 (from eBayes).
> 
> However, I would like to see which spots it has grouped together in the row
> dendogram.  Is there a way I can extract the information about the spots
> that are clustered together.  I cannot read the row names, and even if I
> could I was hoping there would be some way to list the clusters and save it
> to a file.

There are two ways to do this that I know of. And either can be a pain, 
depending on how big the dendrogram is.

Both methods require you to construct your dendrogram first. You can 
then choose the clusters with the mouse. This might be more difficult if 
you have some gigantic dendrogram and have ingested too much coffee ;-D.

Normally, one would simply do

heatmap(mymatrix, otherargs)

and accept the default clustering method. However, you can always 
pre-construct the dendrograms and then feed those to heatmap().

Rowv <- as.dendrogram(hclust(dist(mymatrix)))
Colv <- as.dendrogram(hclust(dist(t(mymatrix))))

heatmap(mymatrix, Rowv=Rowv, Colv=Colv, otherargs)

Now if you do something like that, then you can try

plot(Rowv)
a.cluster <- identify(Rowv)

and then use your mouse to choose the upper left corner of a rectangle 
that encompasses the cluster you are interested in. Here is where the 
size of the dendrogram and the amount of coffee comes in. If the 
dendrogram is really large then identify() may not be able to figure out 
what you are trying to select, or may decide you are choosing the upper 
right corner.

You can choose as many clusters as you want, and they will be in the 
list a.cluster, in the order you selected.

A more programmatic method is to use rect.hclust() and either choose the 
height at which to make the cuts, or the number of clusters, etc. Again, 
depending on the size of your dendrogram, this may work well or it may 
be painful.

Best,

Jim


> 
>  
> 
> Thanks,
> 
>  
> 
> Alison  
> 
>  
> 
> ******************************************
> Alison S. Waller  M.A.Sc.
> Doctoral Candidate
> awaller at chem-eng.utoronto.ca
> 416-978-4222 (lab)
> Department of Chemical Engineering
> Wallberg Building
> 200 College st.
> Toronto, ON
> M5S 3E5
> 
>   
> 
>  
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623