R help - Sep 2003 - a. crossing branches with hclust, b. plot.dendrogram

Hello,

a. when I use hclust with the methods media, centroid, and mcquitty,
and plot the results,  the dendrograms have lines that are crossing each
other. Is this ok?

b. My next question refers to plot.dendrogram: How can I use parameters
as "hang" or "cex" here? E.g. for

st <- as.dendrogram(subtreeshc[[x]])

I would like to have something like this, where cex and hang would work:

plot(st, frame.plot=F, cex = 0.4, hang = 0, sub = "", xlab =
"",
ylab="", main = paste("Distance: ", me, " - Clustering
Method: ",
mecl, " - Subtree ", x, collapse="", sep=""))

Thanks and best regards,
Petra

--

  Petra Steiner
  International Computer Science Institute (ICSI)
  1947 Center Street, Berkeley, CA, 94704-1198, USA
  http://www.ICSI.berkeley.edu/~petra

>>>>> "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			<><