R help - Jul 2012 - identify.hclust() doesn't cut tree at the vertical position of the mouse pointer

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.

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

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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
>