Gundala Viswanath
2013-Aug-22 02:05 UTC
[R] Interpreting the result of 'cutree' from hclust/heatmap.2
I have the following code that perform hiearchical clustering and plot them in heatmap. __ library(gplots) set.seed(538) # generate data y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""), paste("t", 1:5, sep=""))) # 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$rowDendrogram), 1:dim(y)[1]) But having problem in interpreting the result. What's the meaning of each value in the matrix? For example g9-9=8 . What does 8 mean here? 1 2 3 4 5 6 7 8 9 10 g1 1 1 1 1 1 1 1 1 1 1 g2 1 2 2 2 2 2 2 2 2 2 g3 1 2 2 3 3 3 3 3 3 3 g4 1 2 2 2 2 2 2 2 2 4 g5 1 1 1 1 1 1 1 4 4 5 g6 1 2 3 4 4 4 4 5 5 6 g7 1 2 2 2 2 5 5 6 6 7 g8 1 2 3 4 5 6 6 7 7 8 g9 1 2 3 4 4 4 7 8 8 9 g10 1 2 3 4 5 6 6 7 9 10 Your expert advice will be greatly appreciated. - G.V.
David Carlson
2013-Aug-22 14:20 UTC
[R] Interpreting the result of 'cutree' from hclust/heatmap.2
You specified 10 cuts to the dendrogram (all possible) so each column represents the cluster membership for that number of clusters. Column 1 is all ones because all rows belong to a single cluster and in column 10 all the rows belong to different clusters. For g9-9, 8 means that g9 belongs to cluster 8 when there are 9 clusters (g2 and g4 belong to the same cluster) in column 9. ------------------------------------- David L Carlson Associate Professor of Anthropology Texas A&M University College Station, TX 77840-4352 -----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Gundala Viswanath Sent: Wednesday, August 21, 2013 9:05 PM To: r-help at stat.math.ethz.ch Subject: [R] Interpreting the result of 'cutree' from hclust/heatmap.2 I have the following code that perform hiearchical clustering and plot them in heatmap. __ library(gplots) set.seed(538) # generate data y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""), paste("t", 1:5, sep=""))) # the actual data is much larger that the above # perform hiearchical clustering and plot heatmap test <- heatmap.2(y) __ What I want to do is to print the cluster member from each hierarchy of in the plot. I'm not sure what's the good way to do it. I tried this: cutree(as.hclust(test$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 1 1 4 4 5 g6 1 2 3 4 4 4 4 5 5 6 g7 1 2 2 2 2 5 5 6 6 7 g8 1 2 3 4 5 6 6 7 7 8 g9 1 2 3 4 4 4 7 8 8 9 g10 1 2 3 4 5 6 6 7 9 10 Your expert advice will be greatly appreciated. - G.V. ______________________________________________ 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.
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