R (package superheat) - adding color (or rectangles) to the dendrograms

Question

Minimal example and package documentation (https://rlbarter.github.io/superheat/):

library(superheat)
superheat(mtcars,
          # scale the matrix columns
          scale = TRUE,
          left.label = "none",
          # add row dendrogram
          col.dendrogram = TRUE, 
          legend=F,
          )

I would like to achieve two things:

Color branches according to cluster (which necessarily I will have to determine k number of clusters) OR add rectangles on top of "chosen" clusters.
I would also be keen to extract and apply the same dendrogram to a different data set (with the same variables).

I believe the dendrogram is created used ggdendro (if that may assist).

Consequently these are example of what I wanna achieve:

score -1 · Answer 1 · answered Jul 30 '20 at 18:10

The ggdendro package does not support branch colors, and in general it is no longer supported. It was superseded by the dendextend package (which includes the ggdend object, which does support branch colors, lwd and lty). You can prepare your dendrograms using dendextend and feed them into a heatmap.2 function from gplots. Alternatively, you can look into the heatmaply package.

Good luck.

R (package superheat) - adding color (or rectangles) to the dendrograms

1 Answers1