heatmap annotation

Question

[j_weld]

How to make pheatmap annotation in R, if I have cancer type and corresponding color for that? And also, the unique cancer types are 36 if it helps.

Answer 1

[seidel]

You simply have to put your custom colors in a List, and hand it to the pheatmap() function. It's explained pretty clearly in the help for pheatmap (type: ?pheatmap at your R prompt). There's an example below. 36 colors will be impossible to distinguish. You can see that starting with just a few from your table, some of the types can't be distinguished.

### Draw a heat map with Custom Color Annotations
library(pheatmap)

# create some data
dat <- matrix(rnorm(180), nrow=10, ncol=18)

# label rows
rownames(dat) <- paste0("g", 1:10)

# label columns
colnames(dat) <- paste0("e", 1:18)

# make up a table of cancer classifications, for the columns
cancer_types <- data.frame(CancerType=c(rep("CLL", 3), rep("BLCA", 3), rep("LUAD", 3), 
                                   rep("PRAD", 3), rep("STAD", 3), rep("GBM", 3)))

rownames(cancer_types) <- colnames(dat)

# Specify custom colors for our cancer types
ann_colors = list(
  CancerType=c(CLL="#FF0000", BLCA="#FF2A00", LUAD="#FF5500", 
                           PRAD="#FF8000", STAD="#FFAA00", GBM="#FFD500") 
)

# draw the heatmap with column annotations, and custom annotation colors
pheatmap(dat, annotation_col=cancer_types, annotation_colors=ann_colors, 
         main="toy heat map")