Function to color branches in dendrogram plot using base R

Question

I would like to write R function for coloring branches in dendrogram based on the given dendrogram object, specified number of clusters and vector of colors. I want to use base R instead of dendextend .

Using the exact code from this answer: https://stackoverflow.com/a/18036096/7064628 to similar question:

# Generate data
set.seed(12345)
desc.1 <- c(rnorm(10, 0, 1), rnorm(20, 10, 4))
desc.2 <- c(rnorm(5, 20, .5), rnorm(5, 5, 1.5), rnorm(20, 10, 2))
desc.3 <- c(rnorm(10, 3, .1), rnorm(15, 6, .2), rnorm(5, 5, .3))

data <- cbind(desc.1, desc.2, desc.3)

# Create dendrogram
d <- dist(data) 
hc <- as.dendrogram(hclust(d))

# Function to color branches
colbranches <- function(n, col)
  {
  a <- attributes(n) # Find the attributes of current node
  # Color edges with requested color
  attr(n, "edgePar") <- c(a$edgePar, list(col=col, lwd=2))
  n # Don't forget to return the node!
  }

# Color the first sub-branch of the first branch in red,
# the second sub-branch in orange and the second branch in blue
hc[[1]][[1]] = dendrapply(hc[[1]][[1]], colbranches, "red")
hc[[1]][[2]] = dendrapply(hc[[1]][[2]], colbranches, "orange")
hc[[2]] = dendrapply(hc[[2]], colbranches, "blue")

# Plot
plot(hc)

In the code above, you have to manually select the branches to recolor them. I would like to have a function which finds k highest branches and changes color for them (and all their sub-branches). So far I experimented with iteratively searching for the highest sub-branch, but it seems to be needlessly difficult. If there was a way to extract heights of all branches, find k highest, and change the edgePar for each of their sub-branches, would be awesome.

Answer 1

the dendextend R package is designed for these tasks. You can see the many options for changing a dendrogram branch color in the vignette .

For example:

par(mfrow = c(1,2))
dend <- USArrests %>% dist %>% hclust(method = "ave") %>% as.dendrogram
d1=color_branches(dend,k=5, col = c(3,1,1,4,1))
plot(d1) # selective coloring of branches :)
d2=color_branches(d1,5)
plot(d2)