R Pheatmap: Change Annotation Colors and Prevent Graphics Window from Popping Up

How do I change annotation color in pheatmap?

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)))

Pheatmap annotation colors and border

I use grid functions to edit the relevant grob:

library(pheatmap)   
set.seed(123)
df<-data.frame( matrix(sample(30), ncol = 5))
colnames(df)<-LETTERS[1:5]
subj<-c("P1", "P2","P3", "T1", "T2","T3")
rownames(df)<-subj
aka2 = data.frame(ID = factor(rep(c("Pat","Trea"), each=3)))
rownames(aka2)<-subj
aka3 = list(ID = c(Pat = "white", Trea="blue"))

pheatmap(t(scale(df)),
         annotation_col = aka2, 
         annotation_colors = aka3[1],
         annotation_legend = FALSE,
         gaps_col =  3,
         show_colnames = T, show_rownames = T, cluster_rows = F, 
         cluster_cols = F, legend = TRUE, 
         clustering_distance_rows = "euclidean", border_color = FALSE)

# Edit the relevant grob
library(grid)
grid.ls(grid.force()) # "col_annotation" looks like it's the one to edit
grid.gedit("col_annotation", gp = gpar(col="grey70"))

Applying grid.gget("col_annotation")$gp to the original heatmap shows that col_annotation does have a gp slot with fill set but no col. After the edit, both fill and col are set.

Change colors in multiple annotations

Specify annotation_colors:

# Specify colors
annotation_colors = list(
  Var1 = c(Exp1="black", None="white"),
  Var1.1 = c(Exp1="black", None="white"))
pheatmap(test, annotation = annotation, annotation_colors = annotation_colors)

pheatmap: change text color

Here's the answer. The code modifies the color and font size of the x and y labels as well as the color and linewidth of the dendrogram. The colors are set to white, but you can change it to other colors.

p = pheatmap(heat_data, cluster_rows=F,  gaps_row = 3, 
            cellwidth=45, cellheight=45, fontsize = 20, angle_col = "90", legend=TRUE,legend_breaks=c(40, 20, 0, -20, -40, -60),
             legend_labels=c(40, 20, " 0", -20, -40, -60), annotation_row = NULL,
            annotation_legend = FALSE, labels_row = NULL, labels_col=NULL, 
            annotation_names_row = F, annotation_names_col = F, annotation_colors  = ann_colors, dist="euclidean", 
            col=COLS, scale="none", show_rownames = T, show_colnames = T)
my_gtable = p$gtable

my_gtable$grobs[[3]]$gp=gpar(col="#ffffff", fontsize=20)# assuming that the xlabels are in the third grob
my_gtable$grobs[[4]]$gp=gpar(col="#ffffff", fontsize=20)# assuming that the ylabels are in the fourth grob
my_gtable$grobs[[1]]$gp=gpar(col="#ffffff", lwd=2) # change the color of the dendrogram and set the linewidth to 2
my_gtable$grobs[[5]]$gp=gpar(col="#ffffff", fontsize="20", just="center") # legend

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