[BioC] Fwd: heatmap.2 question

James W. MacDonald jmacdon at uw.edu
Thu May 24 17:18:17 CEST 2012

Hi Alyaa,

On 5/24/2012 11:04 AM, Alyaa Mahmoud wrote:
> Hi All
> How can I possibly extract the clusters by rows from a heatmap generated by
> heatmap.2 function. i.e. the heatmap is generated with colouring for every
> cluster of rows and I want to retrieve the members of each cluster.

Note that heatmap.2() uses hclust() to create the clusters. There is a 
function cutree() that can be used to get the groups from the output of 

Also note that heatmap.2() invisibly returns a list that includes both 
the row and column dendrograms (by returning the list invisibly, you 
don't get a bunch of junk printed out to your console. However, if you 
use the assignment function (<-) to assign the output to an object, you 
can then extract whichever dendrogram you want.).



> Any clue would be much appreciated
> Thank you very much
> Alyaa
> KAUST/AUC Marine Genomics Project
> American University in Cairo
> Egypt
> 2918

James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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