[BioC] heatmap.2() get matrix after hierarchical clustering

James W. MacDonald jmacdon at uw.edu
Tue Oct 16 17:19:59 CEST 2012

Hi Whomever,

On 10/16/2012 10:32 AM, Guest [guest] wrote:
> Hi,
> Is there an easy way to obtain the matrix after the heatmap.2() function performs clustering. I'm plotting a matrix of fold change values with 359 genes. The names of the genes are not visible on the heatmap since there are so many. I want to view this matrix after the clustering is performed since the order of the genes from the input matrix is rearranged.
> Any input will be appreciated.

 From ?heatmap.2:


      Invisibly, a list with components

   rowInd: row index permutation vector as returned by
            order.dendrogram .

   colInd: column index permutation vector.

So if you assign the output of heatmap.2 you can get what you want.



> Thanks!
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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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