[R] a. crossing branches with hclust, b. plot.dendrogram
Martin Maechler
maechler at stat.math.ethz.ch
Mon Sep 29 09:24:35 CEST 2003
>>>>> "Petra" == Petra Steiner <petra at icsi.berkeley.edu>
>>>>> on Fri, 26 Sep 2003 15:06:59 -0700 writes:
Petra> Hello, a. when I use hclust with the methods media,
"median"
Petra> centroid, and mcquitty, and plot the results, the
Petra> dendrograms have lines that are crossing each
Petra> other. Is this ok?
yes. It is known in the litterature that only some methods
(those that are `monotone') are guaranteed to produce
dendrograms without "reversal"s or "inversion"s. I don't have
the complete theory handy, but I know that "centroid" is known
*not* to fulfill the property and "single", "complete" and
"average" linkage *are*.
Petra> b. My next question refers to plot.dendrogram: How
Petra> can I use parameters as "hang" or "cex" here?
Petra> E.g. for
Petra> st <- as.dendrogram(subtreeshc[[x]])
The vertical position of nodes is part of the dendrogram
definition,
hence use
st <- as.dendrogram(subtreeshc[[x]], hang = ...)
Where as "cex" can be specified using `nodePar', see the
examples on help(plot.dendrogram).
Petra> I would like to have something like this, where cex
Petra> and hang would work:
Petra> plot(st, frame.plot=F, cex = 0.4, hang = 0, sub = "",
Petra> xlab = "", ylab="", main = paste("Distance: ", me, "
Petra> - Clustering Method: ", mecl, " - Subtree ", x,
Petra> collapse="", sep=""))
Petra> Thanks and best regards, Petra
You're welcome.
--
Martin Maechler <maechler at stat.math.ethz.ch> http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228 <><
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