I have the following code that perform hiearchical clustering and plot them in heatmap.
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.
Column j tells you how your gs should be grouped if you wanted exactly j groups.
Columns 1 and 10 are not very useful, but maybe column 2 is a good example. It is telling you that if you wanted exactly two groups then they would be:
group1: {g1, g5}
group2: {g2, g3, g4, g6, g7, g8, g9, g10}