R help - Aug 2013 - 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.

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.

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