Hi, I am using the function heatmap(stats) to draw a microarray heatmap, columns are samples and rows are gene features. I did a 2D clustering during the heatmap drawing. The features and samples indeed cluster into several blocks both vertically and horizontally. I can get the index of re-ordered rows and columns after the heatmap drawing by typing the the return variable of the heatmap function. However, I cannot separate these index by the the dendro tree. All the indexes labeled at the bottom and right of the plot all jammed together. I cannot by looking at the plot to find where the borders are. Can someone help? Essentially I want the dendro tree of the genes which are grouped after the clustering so that, e.g., I want to check whether genes clustered together are in the same pathway etc. Thanks in advance. -- Waverley @ Palo Alto
Copied form the R-help messages' footer: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Uwe Ligges Waverley @ Palo Alto wrote:> Hi, > > I am using the function heatmap(stats) to draw a microarray heatmap, > columns are samples and rows are gene features. > > I did a 2D clustering during the heatmap drawing. The features and > samples indeed cluster into several blocks both vertically and > horizontally. > > I can get the index of re-ordered rows and columns after the heatmap > drawing by typing the the return variable of the heatmap function. > However, I cannot separate these index by the the dendro tree. All > the indexes labeled at the bottom and right of the plot all jammed > together. I cannot by looking at the plot to find where the borders > are. > > Can someone help? Essentially I want the dendro tree of the genes > which are grouped after the clustering so that, e.g., I want to check > whether genes clustered together are in the same pathway etc. > > Thanks in advance. >
On Tue, Nov 17, 2009 at 17:03, Waverley @ Palo Alto <waverley.paloalto at gmail.com> wrote:> Hi, > > I am using the function heatmap(stats) to draw a microarray heatmap, > columns are samples and rows are gene features. > > I did a 2D clustering during the heatmap drawing. ?The features and > samples indeed cluster into several blocks both vertically and > horizontally. > > I can get the index of re-ordered rows and columns after the heatmap > drawing by typing the the return variable of the heatmap function. > However, I cannot ?separate these index by the the dendro tree. All > the indexes labeled at the bottom and right of the plot all jammed > together. ?I cannot by looking at the plot to find where the borders > are. > > Can someone help? ?Essentially I want the dendro tree of the genes > which are grouped after the clustering so that, e.g., I want to check > whether genes clustered together are in the same pathway etc. > > Thanks in advance. > > -- > Waverley @ Palo Alto > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >The heatmap function does not return the full clustering information. If you look in the help, you'll see that the rows and columns are reordered by: dd <- as.dendrogram(hclustfun(distfun(X))) so you need to run your own clustering separately: x <- matrix(rnorm(100),ncol=10,dimnames=list(paste("gene",1:10),paste("sample",1:10))) x.hclust <- hclust(dist(x)) plot(as.dendrogram(x.hclust)) x.ident <- rect.hclust(x.hclust,k=2) x.ident To get the sample clusters, transpose the matrix for the distance calculation.