How to color the dendrogram labels of an additional factor variable in R

Question

I created the dendrogram after starting the hierarchical analysis of clustering in R using the code below. Now I'm trying to color the labels according to another factor variable, which is saved as a vector. The closest I came to achieve this is the color code of the branches using the ColourDendrogram function in the sparcl package. If possible, I would prefer to color the code with labels. I found answers to similar questions at the following links Colored branches of the dendrogram using an existing column and Coloring branches in the dendrogram to R , but I could not decide how to convert the sample code for my purpose. The following are some examples of data and code.

 > dput(df) structure(list(labs = c("a1", "a2", "a3", "a4", "a5", "a6", "a7", "a8", "b1", "b2", "b3", "b4", "b5", "b6", "b7"), var = c(1L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 2L), td = c(13.1, 14.5, 16.7, 12.9, 14.9, 15.6, 13.4, 15.3, 12.8, 14.5, 14.7, 13.1, 14.9, 15.6, 14.6), fd = c(2L, 3L, 3L, 1L, 2L, 3L, 2L, 3L, 2L, 4L, 2L, 1L, 4L, 3L, 3L)), .Names = c("labs", "var", "td", "fd" ), class = "data.frame", row.names = c(NA, -15L)) df.nw = df[,3:4] labs = df$labs d = dist(as.matrix(df.nw)) # find distance matrix hc = hclust(d, method="complete") # apply hierarchical clustering plot(hc, hang=-0.01, cex=0.6, labels=labs, xlab="") # plot the dendrogram hcd = as.dendrogram(hc) # convert hclust to dendrogram plot(hcd, cex=0.6) # plot using dendrogram object Var = df$var # factor variable for colours varCol = gsub("1","red",Var) # convert numbers to colours varCol = gsub("2","blue",varCol) # colour-code dendrogram branches by a factor library(sparcl) ColorDendrogram(hc, y=varCol, branchlength=0.9, labels=labs, xlab="", ylab="", sub="") 

Any advice on how to do this would be greatly appreciated.

Answer 1

Try

 # ... your code colLab <- function(n) { if(is.leaf(n)) { a <- attributes(n) attr(n, "label") <- labs[a$label] attr(n, "nodePar") <- c(a$nodePar, lab.col = varCol[a$label]) } n } plot(dendrapply(hcd, colLab)) 

( through )

Answer 2

To color your labels, it would be easiest to use the labels_colors function from the dendextend package. For example:

 # install.packages("dendextend") library(dendextend) small_iris <- iris[c(1, 51, 101, 2, 52, 102), ] dend <- as.dendrogram(hclust(dist(small_iris[,-5]))) # Like: # dend <- small_iris[,-5] %>% dist %>% hclust %>% as.dendrogram # By default, the dend has no colors to the labels labels_colors(dend) par(mfrow = c(1,2)) plot(dend, main = "Original dend") # let add some color: colors_to_use <- as.numeric(small_iris[,5]) colors_to_use # But sort them based on their order in dend: colors_to_use <- colors_to_use[order.dendrogram(dend)] colors_to_use # Now we can use them labels_colors(dend) <- colors_to_use # Now each state has a color labels_colors(dend) plot(dend, main = "A color for every Species") 

For more information about the package, you can look at your vignette .