[R] identify.hclust() doesn't cut tree at the vertical position of the mouse pointer

[Uwe Ligges]

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
>