[R] plot.hclust with lots of objects
maechler at stat.math.ethz.ch
Wed Jun 19 17:25:50 CEST 2002
>>>>> "Michael" == Michael Dondrup <Michael.Dondrup at Genetik.Uni-Bielefeld.DE> writes:
Michael> I found that converting my hclust object to a
Michael> dendrogram and cutting it with cut.dendrogram, does
Michael> almost what I want, showing only a branch of the
Michael> tree. But now my labels in the plot are gone,
Michael> although they appear in the dendrogram object
Michael> itself, when printed. How can I bring them back?
plot.dendrogram() is still not as good as it should be.
R-devel has an improved version -- which still isn't good
But for hierarchical clustering results (hclust being one kind;
there are agnes(), diana() and others in the "cluster" package),
you shouldn't need the detour through dendrograms at all.
cutree() is the function to cut hclust objects; returning
grouping vectors only
but the `maptree' package has a prune.clust function (andmore).
Hoping this helps, yours,
Martin Maechler <maechler at stat.math.ethz.ch> http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228 <><
Michael> Laurent Gautier wrote:
>> On Sat, Jun 15, 2002 at 11:11:31PM +0200, Michael
>> Dondrup wrote: > Dear all,
>> > the default plotting method for hclust trees looks just
>> fine for few > objects like in the > example dataset. But
>> when it comes to many objects (some 1000 - I'm > trying
>> to visualize clustered microarray data) it renders a
>> tree, that > one cannot inspect, because of overlapping
>> text and lines. My question > is, is there a way or a
>> plotting parameter for plotting a tree which is > wide
>> enough to have all leaves separated and readable labels
>> even for > that many objects? > This would produce a
>> very big image, so I think scrolling is essential.
>> > I believe the answer is simple, but I'm unable to
>> figure it out.
>> > Thanks in advance > Michael
>> Dear Michael,
>> For the labels, you may want to try use smaller
>> characters to dsiplay them. This can be done using the
>> incantation: par(cex=0.5) # for example
>> For the overlapping lines, well I think there is not much
>> to do except magnifying. Did you try to save your plot in
>> a format like postscript or pdf then display it with a
>> wiever that let you zoom in ?
>> Ultimately, you can try to prune your tree and inspect
>> specific branches (I send you to R help files in this
>> Hopin' it helps,
>> Laurent Gautier CBS, Building 208, DTU PhD. Student
>> DK-2800 Lyngby,Denmark tel: +45 45 25 24 85
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