[R] dendrogram again

[Gavin Simpson]

On Fri, 2007-03-09 at 12:17 +0100, bunny , lautloscrew.com wrote:
> Hi all,
> 
> ok, i know i can cut a dendrogram, which i did.
> all i get is three objects that a dendrograms itself.
> 
> for example:
> myd$upper, myd$lower[[1]], myd$lower[[2]]
> and so on. of course i can plot them seperately now.
> 
> but the lower parts still have hundreds of branches. i´ll need a 30 "  
> widescreen to watch the whole picture.
> what i´d like to is group the lower branches , so that i get a  
> dendrogram with a few branches, splitting only in the upper levels.  
> In terms of the cluster analysis, i just want to have a few bigger  
> clusters.
> 
> thx,
> 
> m.
> 
> P.S.:
> putting parts of a cutted dendrogram back into to one could be an  
> idea ? is it somehow possible ?

Again, perhaps I'm missing something, but if I understand you correctly
(again no example I can follow - what is myd and how did you create
it?), you only want to plot the upper part of the dendrogram and not the
lower branches. If so, then this /is/ on ?dendrogram and you /do/ use
cut() to do it ...:

'cut.dendrogram()' returns a list with components '$upper' and
     '$lower', the first is a truncated version of the original tree,
     also of class 'dendrogram', the latter a list with the branches
     obtained from cutting the tree, each a 'dendrogram'.

So to only show the pruned tree, you just plot $upper - it does say that
$upper is a dendrogram and that it is the truncated version of the
original tree - which is what I understand you to be asking for. This
example shows it in action - this is what I mean by a reproducible
example - (I'm using package vegan as I am familiar with this data set):

require(vegan) ## if false install it
data(varespec)

hc <- hclust(vegdist(varespec, "bray"), method = "ward")
hc <- as.dendrogram(hc)

## this is the full dendrogram - too many nodes, so prune
plot(hc)

## lets take four clusters and prune it back
hc.pruned <- cut(hc, h = 1) # can't specify k so read height of first
                            # plot - cutting at h = 1 gives 4 clusters

# plot only the upper part of the tree showing only the 4 clusters
plot(hc.pruned$upper, center = TRUE)

Is this what you want? If not, using the example I provide above, tell
us exactly what you want to achieve.

HTH

G

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