How can I add pie charts to the tip of a ggplot phylogenetic tree?

Question

I'm trying to make a phylogenetic tree with pie charts at the tips of the tree, but I'm really stuck with how to do it.

Here's a simple fabricated example

library("treeio")
library("ggtree")

nwk <- system.file("extdata", "sample.nwk", package="treeio")
tree <- read.tree(nwk)

ggplot(tree, aes(x, y)) + geom_tree() + theme_tree() + geom_tiplab()

If I now want to include a small pie chart at each tip to the right of the label names (hence the label names with letters should still be there), how should I do?

Answer 1

This code should work, using ggplot with ggtree

library(ggtree)
library(reshape2)
library(ggplot2)

set.seed(2020-12-18)

## generate random data with 15 tips
num_tips = 15
tr <- rtree(num_tips)
p <- ggtree(tr)

a <- runif(num_tips, 0, 0.33)
b <- runif(num_tips, 0, 0.33)
c <- runif(num_tips, 0, 0.33)
d <- 1 - a - b - c
dat <- data.frame(a=a, b=b, c=c, d=d)

## melt the dataframe to create pie-charts
dat.m = melt(dat, id.vars = "tip")

## create list to hold all pie charts
pies = list()
for (i in 1:num_tips) {
  curr_dat = melt(dat[i,])
  ## create a ggplot object for each pie chart
  pies[[i]] =  ggplot(curr_dat, aes(y = value, fill = variable, x="")) + 
    geom_bar(stat = "identity") +
    coord_polar("y", start=0) +
    theme_void() + scale_fill_brewer(palette = "Set1", guide = F)
}
# give them the appropriate names and plot on tree
names(pies) = 1:15
inset(p, pies, width=0.1, height=0.1, hjust=0)