Label and color leaf dendrogram

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Here is a solution for this question using a new package called “dendextend“, built exactly for this sort of thing.

You can see many examples in the presentations and vignettes of the package, in the “usage” section in the following URL: https://github.com/talgalili/dendextend

Here is the solution for this question: (notice the importance of how to re-order the colors to first fit the data, and then to fit the new order of the dendrogram)

####################
## Getting the data:

sample = data.frame(matrix(floor(abs(rnorm(20000)*100)),ncol=200))
groupCodes <- c(rep("Cont",25), rep("Tre1",25), rep("Tre2",25), rep("Tre3",25))
rownames(sample) <- make.unique(groupCodes)

colorCodes <- c(Cont="red", Tre1="green", Tre2="blue", Tre3="yellow")

distSamples <- dist(sample)
hc <- hclust(distSamples)
dend <- as.dendrogram(hc)

####################
## installing dendextend for the first time:

install.packages('dendextend')

####################
## Solving the question:

# loading the package
library(dendextend)
# Assigning the labels of dendrogram object with new colors:
labels_colors(dend) <- colorCodes[groupCodes][order.dendrogram(dend)]
# Plotting the new dendrogram
plot(dend)


####################
## A sub tree - so we can see better what we got:
par(cex = 1)
plot(dend[[1]], horiz = TRUE)

enter image description here

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