[R] Analyzing dendrograms

Martin Maechler maechler at stat.math.ethz.ch
Fri Jan 9 18:58:11 CET 2004

>>>>> "Walton" == Walton A Green <walton.green at yale.edu>
>>>>>     on Wed, 7 Jan 2004 10:41:03 -0500 (EST) writes:

    Walton> Ladies and Gentlemen,

    Walton> As Johan Lindberg points out, the documentation for
    Walton> handling dendrograms is sparse....Does anyone know
    Walton> who is responsible for or working on development of
    Walton> tree methods and objects? I've written a couple of
    Walton> scripts for my own use to translate between
    Walton> parenthetical (A(B(CD))) or binary A00 B10 C11 D11
    Walton> tree formats and cluster objects in R, but as an
    Walton> inexperienced programmer have had difficulty
    Walton> integrating them with the existing framework--I'm
    Walton> trying to write some resampling routines and
    Walton> sensitivity tests for tree objects.

Well, the R-core team is responsible for some...
at least, some of us (mainly Fritz Leisch, then me) have defined
and used the "dendrogram" class.

where  help(dendrogram) says quite clearly

  >> The code is still in testing stage and the API may change in the
  >> future.

Then, there's the much more general S4 classes in Bioconductor's 
"graph" package (which has a maintainer as every addon package...)

    Walton> Perhaps this question should go to the r-devel list
    Walton> instead....

yes.  There you could also elaborate a bit about what you
wanted, what you did, and where your difficulties were.

    Walton> Yours, Walton Green

      >> Date: Tue, 06 Jan 2004 12:49:59 +0100
      >> From: Johan Lindberg <johanl at kiev.biotech.kth.se>
      >> Subject: RE: [R] Analyzing dendograms??

      >> ...dendograms/heatmaps/hclust in R in a proper way I ask
      >> myself, is there a way of doing this in R? or is this a
      >> limitation of the functions available today in the R
      >> programming language. I know there are some functions
      >> like cutree etc but the documentation is really, really
      >> sparse. Are there any tutorials out there of how to do
      >> these things? or should one turn to alternative programs
      >> like MEV from TIGR?

      >> / J

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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