[R] hclust graphics - plotting many points

From: Karin Lagesen <karin.lagesen_at_medisin.uio.no>
Date: Mon, 10 Mar 2008 10:54:19 +0100

Hello.

I have a distance matrix with lots of distances that I use hclust to organise. I then plot the results using the plot method of hclust.

However, the plot itself takes around 20 mins to make due to there being ~700 things in the matrix that I have distances for. I thus would like to dump this to some graphics format which will let me examine this further.

I tried dumping it to postscript:

postscript("myfile.ps", height = 50, pointsize=5) plot(my_hc_object)
dev.off()

What happens is that since most of the items in the matrix have a distance of zero to something everything just becomes a black smear on the bottom where I cannot distinguish anything from anything else. I thus tried increasing the heigth and/or width and also downscaling the pointsize. None of these improved anything much.

So, now I am wondering if any of you have any tips for how I can get something like I get in the x11() window which I can also store and potentially show other people.

Thanks!

Karin

-- 
Karin Lagesen, PhD student
karin.lagesen_at_medisin.uio.no
http://folk.uio.no/karinlag

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