On 10.07.2012 10:48, WATSON Mick wrote:
Dear All
According to the identify.hclust documentation the function "cuts the tree at the
vertical position of the pointer and highlights the cluster containing the horizontal
position of the pointer".
When I carry out this, the tree isn't cut where I click - in fact, there seems
to be a limit below which I cannot go.
Consider the following code:
mat <- matrix(rnorm(5000), ncol=5)
hc <- hclust(dist(mat))
plot(hc)
identify(hc)
No matter where I click on the tree, I cannot cut below around about 5. I can
cut above that value, but not below.
So time to read the help page:
?identify.hclust
tells you about an argument MAXCLUSTER
and hence
identify(hc, MAXCLUSTER=500)
will probably due the trick.
Best,
Uwe Ligges
Any help is much appreciated.
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] geneplotter_1.34.0 lattice_0.20-6 annotate_1.34.1
AnnotationDbi_1.18.1 Biobase_2.16.0 BiocGenerics_0.2.0
BiocInstaller_1.4.7 gplots_2.11.0 MASS_7.3-18
[10] KernSmooth_2.23-7 caTools_1.13 bitops_1.0-4.1
gdata_2.11.0 gtools_2.7.0
loaded via a namespace (and not attached):
[1] DBI_0.2-5 IRanges_1.14.4 RColorBrewer_1.0-5 RSQLite_0.11.1
stats4_2.15.1 tools_2.15.1 XML_3.9-4.1 xtable_1.7-0
Thanks
Mick
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