Re: [R] hclust graphics - plotting many points

From: Hans Ekbrand <>
Date: Tue, 11 Mar 2008 10:43:23 +0100

On Mon, Mar 10, 2008 at 10:19:01AM -0000, michael watson (IAH-C) wrote:
> I'd recommend outputting either as pdf or as a windows metafile
> -----Original Message-----
> From: []
> On Behalf Of Karin Lagesen
> Sent: 10 March 2008 09:54
> To:
> Subject: [R] hclust graphics - plotting many points
> 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("", height = 50, pointsize=5)
> plot(my_hc_object)
> 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.

Don't you have the problem of too small distances in the X11() window?

I've had similar problems with a graph in graphviz, where I found it easier to get what I wanted using a png-driver instead of postscript driver.

Png doesn't scale well, but it might be worth a try.

png(file="myfile.png", width=3000, height=2250) plot(my_hc_object)

Hans Ekbrand ( <>
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