How do I change annotation color in pheatmap?-CodePudding

Consider the matrix:

test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)]   3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)]   2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)]   4
colnames(test) = paste("Test", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")

#creating group to divide

group_df = data.frame(Groups=rep(c("Control", "Treated"), c(5,5)))
rownames(group_df) <- colnames(test)

#Generating heatmap:

pheatmap(test, cluster_cols = FALSE, scale = 'row',
            annotation_col = group_df,
            show_colnames = FALSE,
            border_color = "white",
            colorRampPalette(c("#00FF00", "white", "#DC143C"))(75),
            gaps_col = cumsum(c(5,5)))

How do I change the color of Control and Treated from blue and red to different colors?

CodePudding user response：

Change group_df to a factor and specifying annotation_colors will work.

group_df = data.frame(Groups=as.factor(rep(c("Control", "Treated"), c(5,5))))

ann_colors = list(
  Groups = c(Control="black", Treated="white"))

rownames(group_df) <- colnames(dummy)
pheatmap(dummy, cluster_cols = FALSE, scale = 'row',
         annotation_col = group_df,
         annotation_colors = ann_colors,
         show_colnames = FALSE,
         border_color = "white",
         colorRampPalette(c("#00FF00", "white", "#DC143C"))(75),
         gaps_col = cumsum(c(5,5)))