plot.hclust: strange behaviour with "manufactured" hclust object - R-help

Wed, Feb 20, 2002 11:19 AM #

The problem seems to be that the original merge component is stored as int,
but the source()'d version is not.  Coercing that to int I think works.

Cheers,
Andy

-----Original Message-----
From: Hugh Chipman [mailto:hachipma at icarus.math.uwaterloo.ca]
Sent: Wednesday, February 20, 2002 1:32 PM
To: r-help at stat.math.ethz.ch
Cc: hachipma at icarus.math.uwaterloo.ca
Subject: [R] plot.hclust: strange behaviour with "manufactured" hclust
object

I've been trying to get plot.hclust to work with a hclust object I
created and have not had much success.  It seems that there is some
"hidden" characteristic of a hclust object that I can't see.  This is
most easily seen in the following example, where plot.hclust works on
one object, but when this object is "dumped" and then re-read,
plot.hclust no longer works.  Is this a scoping problem?

Script started on Wed Feb 20 13:17:37 2002
1>@icarus[101]% R

R : Copyright 2002, The R Development Core Team
Version 1.4.1  (2002-01-30)

......(stuff deleted)

set.seed(103)
library(mva)
x <- matrix(rnorm(5*2),ncol=2)
x.hc <- hclust(dist(x),method='average')     
plot.hclust(x.hc)

# the above works

dump('x.hc')
source('dumpdata.R')
plot.hclust(x.hc)

Error in plot.hclust(x.hc) : invalid dendrogram input

One hypothesis I had was that it might be something like the "call"
object that wasn't correctly being re-created by the dump & source,
but that doesn't seem to be it.  Below, I remove everything except
merge, order, and height, and plot.hclust still works on the original
object and fails on the dump + source object.

x.hc <- hclust(dist(x),method='average')
x.hc$call <- NULL
x.hc$dist.method <- NULL
x.hc$method <- NULL
x.hc$labels <- NULL
plot.hclust(x.hc)
dump('x.hc')
source('dumpdata.R')
plot.hclust(x.hc)

Error in plot.hclust(x.hc) : invalid dendrogram input

str(x.hc)

List of 3
 $ merge : num [1:4, 1:2] -2 -5 -1 -4 -3 1 2 3
 $ height: num [1:4] 0.873 1.257 1.633 2.430
 $ order : num [1:5] 4 1 5 2 3
 - attr(*, "class")= chr "hclust"

Any help would be greatly appreciated!

Hugh Chipman

-- 
-- Hugh Chipman -- Associate Professor, Statistics & 
Actuarial Science --
-- University of Waterloo, Ontario, Canada                    
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-- Visiting Stanford Statistics Department, January-March 
2002         --
-- (650) 725 6148                                   Fax (650) 
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-- Department of Statistics, Sequoia Hall, 390 Serra Mall     
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-- http://www.stats.uwaterloo.ca/~hachipma/     
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