R-help Digest, Vol 28, Issue 28

  
Message: 37
Date: Tue, 28 Jun 2005 09:08:24 +0800
From: "Mulholland, Tom" <Tom.Mulholland at dpi.wa.gov.au>
Subject: Re: [R] A. Mani : colours in Silhouette
To: <a_mani_sc_gs at vsnl.net>, <r-help at stat.math.ethz.ch>
Message-ID:
 <4702645135092E4497088F71D9C8F51A128BAF at afhex01.dpi.wa.gov.au>
Content-Type: text/plain; charset="iso-8859-1"

It's not so much a problem, as not working the way you expected.
cluster:::plot.partition is used to do the plotting. If you look at the
code for this you can see the difficulty in putting every possible
permutation into the code. If for example you want the silhouette plot to
be red using col = "red" is not intuitive as the cluster plot (which comes
up first) has more than one colour. If you have a look at methods(plot)
(assuming that you have loaded the cluster package) you will see that there
is a specific piece of code in the form of plot.silhouette. It has an
asterisk next to it so you need to use cluster:::plot.silhouette to see the
code. It has what you need.

args(cluster:::plot.silhouette)

function (x, nmax.lab = 40, max.strlen = 5, main = NULL, sub = NULL,

    xlab = expression("Silhouette width " * s[i]), col = "gray",
    do.col.sort = length(col) > 1, border = 0, cex.names = par("cex.axis"),
    do.n.k = TRUE, do.clus.stat = TRUE, ...)


 data(ruspini)
      pr4 <- pam(ruspini, 4)
      si <- silhouette(pr4)
      plot(si,col = "red")

The issue is that whenever code is written there is always a choice as to
what functionality is put in place. Just because something can be done,
does not mean it will or in some cases should be done. In this case the
help for plot.partition notes that "For more flexibility, use
'plot(silhouette(x), ...)', see 'plot.silhouette'."

Tom

Thanks for that I found out something I will find useful in the future.

-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch]On Behalf Of A. Mani
Sent: Tuesday, 28 June 2005 4:30 AM
To: r-help at stat.math.ethz.ch
Subject: [R] A. Mani : colours in Silhouette


Hello,
       In cluster analysis with cluster, how does one colour
the silhouette
plots ? For example in using pam. There seems to be some
problem there.
Everything else can be coloured.

Thanks,