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

Kasoji, Manjula (NIH/NCI) [C] manjula.kasoji at nih.gov
Tue Oct 16 17:51:40 CEST 2012

Hey, that's a pretty neat trick!

I was going to use the reorder() function and re-order my input matrix
based on the values returned by rowInd, but I think is may be more

Thank you Thomas and Jim!

On 10/16/12 11:42AM, "Thomas Girke" <thomas.girke at ucr.edu> wrote:

>## Some input sample matrix
>y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""),
>paste("t", 1:5, sep="")))
>## Run heatmap.2 on this matrix
>test <- heatmap.2(y)
>y[rev(test$rowInd), test$colInd]
>Now try to understand why y[rev(test$rowInd), test$colInd] does the
>trick of returning the row names/labels in the proper order, which is
>just some basic R syntax of accessing a list-like object and then
>using an index for sorting.
>Another way of doing this is to separate the clustering with hclust from
>heatmap plotting, where you want to learn how to access the hclust object
>you need. 
>For instance:
>## Row clustering (adjust here distance/linkage methods to what you need!)
>hr <- hclust(as.dist(1-cor(t(y), method="pearson")), method="complete")
>## Column clustering (adjust here distance/linkage methods to what you
>hc <- hclust(as.dist(1-cor(y, method="spearman")), method="complete")
>## Plot heatmap
>heatmap.2(y, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), scale="row",
>density.info="none", trace="none")
>## Return matrix with row/column sorting as in heatmap
>y[rev(hr$labels[hr$order]), hc$labels[hc$order]]
>On Tue, Oct 16, 2012 at 02:32:35PM +0000, 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.
>> Thanks!
>>  -- output of sessionInfo():
>> N/A
>> --
>> Sent via the guest posting facility at bioconductor.org.
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