TangleR

Tanglegram is a representation of co-phylogeny where two phylogenetic trees are linked. This package offers simple function to draw beautiful tanglegram. This is based on ggtree. You can annotate and illustrate the first ggtree object (main one), and then use a second ggtree to connect common tips based on any values shared by a defined column in their meta file.

History

I wrote a tutorial on how to create tanglegram on R in my website, which got some interest among peers: https://arftrhmn.net/how-to-make-cophylogeny/ Due to many comments, I decided to release my codes as a generic package in R.

Install from GitHub

library("devtools")
install_github('acarafat/tangler')

Use it

library(ggtree)

# Load meta
meta=read.csv('tree_meta.csv', header=T) 

# Load tree 1
t1 <- read.tree('tree1.nwk')

# Load tree 1 and use ggtree to annotate features
tree1 <- ggtree(t1)   %<+% meta +
  geom_tiplab() +
  geom_tippoint(aes(color=Genotype))

# Load tree 2
t2 <- read.tree("tree2.nwk")
tree2 <- ggtree(t2) %<+% meta

# Draw Tanglegram
simple.tanglegram(tree1, tree2, Genotype, Green, tiplab = T)

# Update the connecting line x-position so that it do not overlap with tip-labels.
simple.tanglegram(tree1, tree2, Genotype, Green,
                  tiplab = T, lab_pad = 3, x_hjust = 1)

Now you can update the x-position of the lines' beginning and ending by lab_pad, which will introduce equidistant padding. t2_tiplab_size has been introduced to control Tree 2 tip labels.

simple.tanglegram(t1, t2, sample_type, clinical, t2_pad = 0.5,
                           tiplab = T, lab_pad = 0, x_hjust = 1, 
                           t2_y_pos = 0, t2_y_scale = 1.5, t2_branch_scale = 0.3)

Output

Feature Request and Bug Reports

Please use this GitHub repo's Issues :)