R help - Sep 2011 - hclust and cutree: identifying branches as classes

Good afternoon,


After cuting a hierarchical tree using cutree(), how to check correspondances
between classes and branches?
This is what we do:

srndpchc <- hclust(dist(srndpc$x[1:1000,1:3]),method="ward")
#creation of hierarchical tree
plclust(srndpchc,hmin=20000) #visualisation

srndpchc20000 = cutree(srndpchc,h=20000) #returns 4 classes
table(srndpchc20000 )

srndclass20000 = cbind(srnd@data[1:1000,],srndpchc20000) #assigning classes to
objects
srndcents20000 <- aggregate(srndclass20000, by=list(srndpchc20000),
FUN=median)
matplot(1:36,t(srndcents20000[,-c(1,38)]))


But how can we make sure that, for example, class 1 is the first branch in the
tree plotted  by plclust() ?


Regards
Laurent

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On Mon, Sep 12, 2011 at 4:59 AM, Laurent Fernandez Soldevila
<l.fernandez4 at yahoo.fr> wrote:
> Good afternoon,
>
>
> After cuting a hierarchical tree using cutree(), how to check
correspondances between classes and branches?
> This is what we do:
>
> srndpchc <- hclust(dist(srndpc$x[1:1000,1:3]),method="ward")
#creation of hierarchical tree
> plclust(srndpchc,hmin=20000) #visualisation
>
> srndpchc20000 = cutree(srndpchc,h=20000) #returns 4 classes
> table(srndpchc20000 )
>
> srndclass20000 = cbind(srnd at data[1:1000,],srndpchc20000) #assigning
classes to objects
> srndcents20000 <- aggregate(srndclass20000, by=list(srndpchc20000),
FUN=median)
> matplot(1:36,t(srndcents20000[,-c(1,38)]))
>
>
> But how can we make sure that, for example, class 1 is the first branch in
the tree plotted? by plclust() ?
Hi Laurent,

in the WGCNA package we have a function called plotDendroAndColors
that takes, as the minimum, the hierarchical clustering tree and the
clustering, and plots the tree with colors underneath.

you would use something along the lines of

plotDendroAndColors(srndpchc, srndpchc20000,
                                  "Classes", # Some label for the
classes,
                                   dendroLabels = FALSE # To not plot
labels for each leaf
                                  )

An example of the plot, with several different tree cuts, can be seen, e.g., at

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/Example-Dendrogram-10.png

HTH,

Peter