Hi I would like to create a dendrogram in R which has colored branches, like the one shown below. <http://r.789695.n4.nabble.com/file/n4672993/dendrogram.png> So far I used following commands to create a standard dendrogram: 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 How should I modify this code to obtain a desired result ? Thanks in advance for your help. -- View this message in context: http://r.789695.n4.nabble.com/How-to-create-a-dendrogram-with-colored-branches-tp4672993.html Sent from the R help mailing list archive at Nabble.com.
How to create a dendrogram with colored branches
3 messages · beginner, Robin Cura, Dr Gregory Jefferis
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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
http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://www.neuroscience.cam.ac.uk/directory/profile.php?gsxej2
http://flybrain.stanford.edu