Tree cut and Rectangles around clusters for a horizontal dendrogram in R

Question

I am trying to plot the results of a hierarchical clustering in R as a dendrogram, with rectangles identifying clusters.

The following code does the trick for a vertical dendrogram, but for a horizontal dendrogram, (horiz=TRUE), the rectangles are not drawn. Is there any way to do the same for horizontal dendrograms too.

library("cluster")
dst <- daisy(iris, metric = c("gower"), stand = FALSE)
hca <- hclust(dst, method = "average")
plot(as.dendrogram(hca), horiz = FALSE)
rect.hclust(hca, k = 3, border = "red")

Moreover I would like to plot a line to cut the tree at a desired distance value. How to plot that in R. The cutree function returns the clusters, but is it possible to plot it as well.

cutree(hca, k = 3)

The desired output that I am looking for is like this.

How to get this done in R?

Answer 1

Both jlhoward and Backlin answers are good.

What you could also try is using the dendextend package, designed exactly for this sort of thing. It has a rect.dendrogram function which works like rect.hclust, but with a horiz parameter (plus some more control over the location of the edge of the rect). For finding the relevant height you can use the heights_per_k.dendrogram function (which is much faster when also using the dendextendRcpp package)

Here is a simple example for how you would get the same result as in the above examples (with an added bonus of colored branches, just for fun):

install.packages("dendextend")
install.packages("dendextendRcpp")

library("dendextend")
library("dendextendRcpp")

# using piping to get the dend
dend <- iris[,-5] %>% dist %>% hclust %>% as.dendrogram

# plot + color the dend's branches before, based on 3 clusters:
dend %>% color_branches(k=3) %>% plot(horiz=TRUE, main = "The dendextend package \n Gives extended functionality to R's dendrogram object")

# add horiz rect
dend %>% rect.dendrogram(k=3,horiz=TRUE)

# add horiz (well, vertical) line:
abline(v = heights_per_k.dendrogram(dend)["3"] + .6, lwd = 2, lty = 2, col = "blue")