[R] plot.hclust with lots of objects

Laurent Gautier laurent at cbs.dtu.dk
Sun Jun 16 11:33:38 CEST 2002

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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