[R] How to create a dendrogram with colored branches

[Gregory Jefferis]

On 3 Aug 2013, at 16:47, beginner wrote:

> d <- dist(as.matrix(data[,29]))   # find distance matrix 
> hc <- hclust(d)                # apply hirarchical clustering 
> plot(hc,labels=data[,1], main="", xlab="") # plot the dendrogram

You haven't given a reproducible example (data is undefined), so we can't help you with your specific code.  But what you want can be achieved with the package dendroextras on CRAN.

install.packages("dendroextras")
library(dendroextras)
hc=hclust(dist(USArrests), "ave")
# nb you have to cut your dendrogram by number of groups (k) 
d5=colour_clusters(hc,k=5)
plot(d5)
#... or by height (h)
d5=colour_clusters(hc,h=75) 
plot(d5)

?colour_clusters

for more details.

Best wishes,

Greg Jefferis.

--
Gregory Jefferis, PhD                      
Division of Neurobiology
MRC Laboratory of Molecular Biology 
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK

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