[R] hclust graphics - plotting many points

[Hans Ekbrand]

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: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
> On Behalf Of Karin Lagesen
> Sent: 10 March 2008 09:54
> To: r-help at r-project.org
> 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("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.

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)
dev.off()

-- 
Hans Ekbrand (http://sociologi.cjb.net) <hans at sociologi.cjb.net>
GPG Fingerprint: 1408 C8D5 1E7D 4C9C C27E 014F 7C2C 872A 7050 614E
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