Oups ... sorry, actually I found the problem. The problem lies not with the reordering but with the construction of the dendrogram: if a hierarchical method is used, there are never more than 2 branches for a node. Therefore, the reordering does not give the expected result. I will have to try something different ...
Thanks anyway. Thomas. Thomas Walter wrote: >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. > >______________________________________________ >R-help@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. > > > -- ------------------------- Thomas Walter EMBL Heidelberg Meyerhofstrasse 1 69117 Heidelberg Germany Tel: +49 (0)6221 387-8857 ______________________________________________ R-help@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.