[R] Is there a way to print branch distances for hclust function?
kbrownk at gmail.com
Tue Dec 13 07:05:48 CET 2011
Never mind on my reply post (hasn't posted yet, but assuming it does).
I found a way to use the merge and height values with Excel to
subtract out the lower level distance. Thanks for the help!
On Dec 12, 1:38 am, Peter Langfelder <peter.langfel... at gmail.com>
> On Sun, Dec 11, 2011 at 8:43 PM,kbrownk<kbro... at gmail.com> wrote:
> > The R function hclust is used to do cluster analysis, but based on R
> > help I see no way to print the actual fusion distances (that is, the
> > vertical distances for each connected branch pairs seen in the cluster
> > dendrogram).
> > Any ideas? I'd like to use them test for significant differences from
> > the mean fusion distance (i.e. The Best Cut Test).
> > To perform a cluster analysis I'm using:
> > x <- dist(mydata, method = "euclidean") # distance matrix
> > y <- hclust(x, method="ward") #clustering (i.e. fusion) method
> > plot(y) # display dendogram
> > Thanks,
> You need to dig a bit deeper in the help file :) The return value is a
> list that contains, among others, components
> 'merge' and 'height'. The 'merge' component tells you which objects
> were merged at each particular step, and the 'height' component tells
> you what the merging height at that step was. The (slightly) tricky
> part is to relate the merge component to actual objects - AFAIK there
> is no function for that. The function cutree() using the argument k
> and varying it between 2 and n should basically do it for you but you
> need to match it to the entries in 'merge'. Maybe someone else knows a
> better way to do this.
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