R applying different colors to a phylogenetic tree branch

Question

I have a phylogenetic tree made with a Newick format

((a:1,b:1):2, (c:1, d:1):3):1;

The output will be

I have drawn this with http://etetoolkit.org/treeview/ , but output with R will be same.

What I want to do is apply colors to a certain branch.

That would be

Since the Newick input doesn't include any information other than the branch (c,d) has length 3, is there any way I can include multiple color information on the branch?

I usually use ggtree for making trees, but other suggestions can be helpful.

Answer 1

One solution would be to split the internal branches by adding extra non-bifurcating nodes.

library(ape)

## Creating the same tree with split branches
my_with_split_branch_tree <- read.tree(text = "((a:1,b:1):2, ((((c:1, d:1):1):1):1):1):1;")

## Set the edge colors and width
edge_colors <- rep("black", Nedge(my_with_split_branch_tree))
edge_width <- rep(1, Nedge(my_with_split_branch_tree))

## Color and width the edges of interest
edge_colors[c(5,6,7)] <- c("yellow", "orange", "red")
edge_width[c(5,6,7)] <- 3

## Plotting the tree with the colours
plot(my_with_split_branch_tree,
     edge.color = edge_colors,
     edge.width = edge_width)