[R] how can I reorder a dendrogram?

From: Thomas Walter <Thomas.Walter_at_embl.de>
Date: Thu, 20 Mar 2008 11:23:44 +0100


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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