[R] plot.hclust with lots of objects
Michael.Dondrup at Genetik.Uni-Bielefeld.DE
Sun Jun 16 17:11:07 CEST 2002
I found that converting my hclust object to a dendrogram and cutting it
cut.dendrogram, does almost what I want, showing only a branch of the
But now my labels in the plot are gone, although they appear in the
dendrogram object itself, when printed.
How can I bring them back?
Thanks for your help
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 case)
> Hopin' it helps,
> Laurent Gautier CBS, Building 208, DTU
> PhD. Student DK-2800 Lyngby,Denmark
> tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent
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