[R] how can I reorder a dendrogram?
Thomas Walter
Thomas.Walter at embl.de
Thu Mar 20 11:23:44 CET 2008
Hi!
I am trying to reorder a dendrogram via reorder.dendrogram. However, I
observed some problems with this, and I will illustrate them with an
example.
Take the following clustering problem:
datamatrix <- matrix(c(2,2,2.5,2,1.5,2,2,1.5,2,2.5,
6,2,6.5,2,5.5,2,6,1.5,6,2.5, 4,4,4.5,4,3.5,4,4,3.5,4,4.5), ncol=2,
byrow=TRUE)
distmatrix <- dist(datamatrix, method="manhattan")
hc <- hclust(distmatrix, method="single")
dendro <- as.dendrogram(hc)
The datamatrix contains three equidistant (for manhattan distance)
clusters, each of which contains 5 points.
Now, I want to impose an order:
weights <- c(2.0, 2.0, 2.0, 2.0, 2.0, 6.0, 6.0, 6.0, 6.0, 6.0, 4.0, 4.0,
4.0, 4.0, 4.0)
ddd <- reorder(dendro, weights, agglo.FUN=mean)
but if you compare the order of ddd with dendro, you see no change:
unlist(ddd)
[1] 15 14 13 11 12 5 4 3 1 2 10 9 8 6 7
unlist(dendro)
[1] 15 14 13 11 12 5 4 3 1 2 10 9 8 6 7
I would have expected something like:
5 4 3 1 2 15 14 13 11 12 10 9 8 6 7
or something of the sort. (I still do not know, if the order should be
ascending or descending, but in the obtained result, it is neither nor).
I do not see, where my mistake is ...
Thanks for your advice!
Thomas.
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