[R] Analyzing dendograms??

Sean Davis sdavis2 at mail.nih.gov
Mon Jan 5 17:38:11 CET 2004

I think that for heatmap, one needs to "preprocess" the data before passing
it to heatmap.  In particular, if you know the row indices of the genes of
interest, you may pass just those rows with or without the row dendrogram.
If one has a dendrogram object, using "cutree" (see ?cutree)  will give
indices of genes in k clusters or with splits above a certain height; the
resulting indices can then be passed to heatmap.


On 1/5/04 10:20, "Simon Fear" <Simon.Fear at synequanon.com> wrote:

> Post script: I'm afraid my `solution` was no good, because
> I forgot the need to change nc and nr. (I got bogged down
> in passing ylim and lost track of your real question.)
> Hopefully someone with a deeper understanding of the
> original problem will come to the rescue. If not there may
> be milage on restricting your matrix[,] to matrix[<cond1>,<cond2>]
> according to information in sclus and gclus. But I am in
> over my depth here.
>>> On Sun, 4 Jan 2004, Johan Lindberg wrote:
>>>> I have used heatmap to visualize my microarray data. I
>> have a matrix of
>>>> M-values. I do the following.
>>>> #The distance between the columns.
>>>> sampdist <- dist(t(matrix[,]), method="euclidean")
>>>> sclus <- hclust(sampdist, method="average")
>>>> #The distance between the rows.
>>>> genedist <- dist(matrix[,], method="euclidean")
>>>> gclus <- hclust(genedist, method="average")
>> heatmap(matrix[,],Rowv=as.dendrogram(gclus),Colv=as.dendrogram
>> (sclus), 
>>> col=rbg)
>>>> So far so good. But what if I want to look at a group of
>> genes that appear
>>>> to have the same expression pattern in the heatmap? How
>> do I zoom in on a
>>>> dendogram in a heatmap to look at which genes that are forming the
>>>> interesting clusters? I would really appreciate if
>> someone could give me a
>>>> pointer.  
> Simon Fear 
> Senior Statistician
> Syne qua non Ltd 
> Tel: +44 (0) 1379 644449
> Fax: +44 (0) 1379 644445
> email: Simon.Fear at synequanon.com
> web: http://www.synequanon.com
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