pheatmap: Color for NA

Question

Using R package pheatmap to draw heatmaps. Is there a way to assign a color to NAs in the input matrix? It seems NA gets colored in white by default. E.g.:

libra         


        

Answer 1

You can enable assigning a colour by using the developer version of pheatmap from github. You can do this using devtools:

#this part loads the dev pheatmap package from github
if (!require("devtools")) {
  install.packages("devtools", dependencies = TRUE)
  library(devtools)
}
install_github("raivokolde/pheatmap")

Now you can use the parameter "na_col" in the pheatmap function:

pheatmap(..., na_col = "grey", ...)

(edit) Don't forget to load it afterwards. Once it is installed, you can treat it as any other installed package.