Analyzing dendograms??
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. Sean
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 Number of attachments included with this message: 0 This message (and any associated files) is confidential and\...{{dropped}}
______________________________________________ R-help at stat.math.ethz.ch mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html