WATSON Mick
2012-Jul-10 08:48 UTC
[R] 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.
Uwe Ligges
2012-Jul-11 10:24 UTC
[R] identify.hclust() doesn't cut tree at the vertical position of the mouse pointer
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 >