search for: rowdendrogram

Hi, I am a beginner for R. I had use gplots to generate a heatmap as following: >heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE, trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2, cexCol=0.6) It work well. It generate heatmap whith rcolumn clustering dendrogram and I can export a very nice graph. But I don not know how

...the actual data is much larger that the above # perform hiearchical clustering and plot heatmap test <- heatmap.2(y) __ What I want to do is to print the cluster member from each hierarchy of in the plot. I'm not sure what's the good way to do it. I tried this: cutree(as.hclust(test$rowDendrogram), 1:dim(y)[1]) But having problem in interpreting the result. What's the meaning of each value in the matrix? For example g9-9=8 . What does 8 mean here? 1 2 3 4 5 6 7 8 9 10 g1 1 1 1 1 1 1 1 1 1 1 g2 1 2 2 2 2 2 2 2 2 2 g3 1 2 2 3 3 3 3 3 3 3 g4 1 2 2 2 2 2 2 2 2 4 g5 1 1 1 1 1...

Hello R-Helpers, I have a question about extracting the clusters of genes after we make the heatmap (say ht4) using the heatmap.2 function. Basically, I want to get the clusters which are shown as row dendrogram in the heatmap. I understand that ht4$rowDendrogram is an object of dendrogram and it containes details of all the nodes and branches, but lets say I want to know the number of clusters and the genes in each cluster if I terminated the tree (dendrogram) at a particular height. Also, if I know that I want 12 clusters, how do I know which height I sho...