Analyzing dendograms??
Thanks for the ideas but I already tested to give the heatmapfunction the
argument ylim but I get the following error message:
Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + :
formal argument "ylim" matched by multiple actual arguments
So then I tried to adjust the function and changed the ylim argument when
the "heatmapfunction" calls "image". But this only makes it possible to
zoom in on the "picture" that is drawn in the heatmapfunction. The result
is that the function draws the full dendogram on a truncated picure.
Any ideas, anyone?
/ Johan
At 13:31 2004-01-04 -0500, you wrote:
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 Fax: + 46 8 553 784 81 Visiting adress: Roslagstullsbacken 21, Floor 3 Delivery adress: Roslagsv?gen 30B
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******************************************************************************************* 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 Fax: + 46 8 553 784 81 Visiting adress: Roslagstullsbacken 21, Floor 3 Delivery adress: Roslagsv?gen 30B