[R-sig-eco] Interpreting large clusters

[Nicholas Lewin-Koh]

Hi Phil,
Can you plot the dendorgam in pieces? if you look at 
example(hclust) the show an example where they plot the dendrogram
showing 10 aggregated groups from the centroids of a previous dendrogram
cut at 10 clusters. You could also do the opposite using as.dendrogram
example(hclust)
hcd<-as.dendrogram(hc)
hcc<-cut(hcd,2000)
par(ask=TRUE)
for(i in length(hcc$lower)) plot(hcc$lower[[i]])

dendrogram objects are a bit easier to manipulate than 
the output from hclust.

Cheers
Nicholas

> Message: 1
> Date: Tue, 14 Oct 2008 06:46:11 -0400
> From: Phil Novack-Gottshall <pnovackg at westga.edu>
> Subject: [R-sig-eco] Interpreting large clusters
> To: r-sig-ecology at r-project.org
> Message-ID: <200810141046.m9EAkNO5029369 at hypatia.math.ethz.ch>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
> 
> Hi all,
> 
> I have a related question concerning cluster analysis of large data 
> sets.  In my case, the matrix is reasonably small for R to work with, 
> but I have so many species (~2000) that it is not possible to read 
> labels on the resulting dendrogram.  I imagine that using an 
> ordination is a preferable method in this case, but I was wondering 
> whether anyone had any recommendations for producing a very large, 
> but still readable dendrogram.  (I've tried increasing the window 
> size and shrinking cex.text, but this still isn't sufficient.)
> 
> Cheers,
> Phil
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>    Phil 
> Novack-Gottshall                        pnovackg at westga.edu 
> 
> 
>    Assistant Professor
>    Department of Geosciences
>    University of West Georgia
>    Carrollton, GA 30118-3100
>    Phone: 678-839-4061
>    Fax: 678-839-4071
>    http://www.westga.edu/~pnovackg
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>