[R] Analyzing dendograms??

Thomas W Blackwell tblackw at umich.edu
Sun Jan 4 19:31:48 CET 2004

Johan  -

Disclaimer:  I've never used  heatmap(), so probably I shouldn't
be answering this.

However ... the function  heatmap() probably calls either  plot()
or  image() (regular graphics) or  xyplot() (lattice graphics)  in
order to set up axes and initialize the actual plotting.  heatmap()
may also have a  "..."  argument which passes additional parameters
through to  plot(), unchanged.  If both of my guesses are correct
(use  help("heatmap")  to find out) then I would try calling
heatmap() again with an additional parameter  ylim=c(a,b),  where
"a" and "b" are two numbers, with  a < b,  which indicate plotting
coordinates which bracket the group of genes you wish to zoom in on.

It will take a bit of experimentation to figure out what internal
coordinate system  heatmap()  uses to do the plotting, but this
seems like a direct way to zoom in on just a part of the plot.

This is completely untested.  I leave it to you to read  help("heatmap")
and see whether any of this makes sense.  Hope this helps.

-  tom blackwell  -  u michigan medical school  -  ann arbor  -

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.
> Best regards.
> / Johan
> *******************************************************************************************
> Johan Lindberg
> Royal Institute of Technology
> AlbaNova University Center
> Stockholm Center for Physics, Astronomy and Biotechnology
> Department of Molecular Biotechnology
> 106 91 Stockholm, Sweden
> Phone (office): +46 8 553 783 45
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