How to make Co-phylogeny plot: easy tanglegram in R

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Tanglegram is a representation of co-phylogeny where two phylogenetic trees are linked. This method is super useful to visualize common traits shared by both trees. For example, it can be used to visualize host-pathogen (or host-symbiotic) evolution and visualize if there is any phylogenetic concordance between the two phylogenetic trees.

I was in need to visualize co-phylogeny of phylogenetic tree reconstructed from chromosomal and symbiotic genes. Surprisingly, I didn’t find any straight-forward solution in R that can be used for drawing tanglegram. Particularly I wanted to leverage the beautiful ggtree library. After trying out several methods, I found the following approach works well for me so far. I have released a small R package on it, which can be found on GitHub.

In this post, I’m going to use two toy trees with the following Newick format. Note that they have the same isolate, but different tree-topology (since supposedly different gene-set were used to reconstruct them).

Tree 1: (((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);
Tree 2: (((((((F:8,I:18,G:4):2,C:5):3,M:6):3,E:21):10,((A:2,B:2):4):3):13,((K:5,L:2):20,(H:18,J:11):2):17):4,D:56);

We might be interested to visualize one (or more) interesting feature(s) (i.e. genotype) associated with the isolates in both trees. Our meta-file looks like the following:

IsolateGenotype
AGreen
BGreen
CGreen
DGreen
ERed
FRed

Let’s load the necessary packages.

library(ggplot2)
library(ggtree)
library(phangorn)
library(dplyr)

The best thing about ggtree is you can attach any feature(s) associated with isolates using a simple CSV file. Just make sure that the first column of your metafile has the same isolate names as used in the tree. Let’s load the metafile and both phylogenetic tree to be used. I also like to do midpoint rooting at this point.

# Meta file
meta <- read.table('~/path/to/meta.csv', sep=',', header = T)

# Load tree 1
tree1 <- read.tree('~/path/to/tree1.nwk')
tree1 <- midpoint(tree1)

# Load tree 2
tree2 <- read.tree('~/path/to/tree2.nwk')
tree2 <- midpoint(tree2)

Let’s combine the meta feature dataset with both phylogenetic trees and visualize how they look.

t1 <-ggtree(tree1)  %<+%  meta + geom_tiplab()
t2 <- ggtree(tree2)  %<+%  meta + geom_tiplab()

t1
t2

Now we are going to draw both trees in a single figure. We also want to flip tree 2, for which we need to change the x-coordinates in that tree.

d1 <- t1$data
d2 <- t2$data

d1$tree <-'t1'
d2$tree <-'t2'

d2$x <- max(d2$x) - d2$x + max(d1$x) +  max(d1$x)*0.3
pp <- t1 + geom_tree(data=d2)
pp 

In the above code block, we are grabbing the backend data frame from both trees and updating the tree 2 data frame x-coordinate. We are using this equation for the update: max(d2$x) - d2$x + max(d1$x) + max(d1$x)*0.3. You can toy with different values depending on the branch length unit of your tree to get good visualization (I particularly suggest changing max(d1$x)*0.3 terms).

Two phylogenetic trees, face-to-face.

Let’s join d1 and d2 for dataset so that we can use the coordinates of the tips for making connections between both of the trees.

dd <- bind_rows(d1, d2) %>% 
  filter(isTip == TRUE)
dd1 <- as.data.frame(dd) 

Now, we are going to conditionally join the tips of both trees for the feature we are interested in. Connected tips will represent the same isolates.

green_tree <- dd1[which(dd1$Genotype == 'Green'), c('label', 'x', 'y', 'tree')]
pp + geom_line(aes(x, y, group=label), data=green_tree, color='#009E73') 

Connecting the isolates

Lily asked in the comment section if it is possible to connect all the tip labels from both trees. The previous code chunk actually connects the tips based on a subset from meta. In this case, we do not have to do any kind of subsetting. Using the following code we can connect all tips:

pp + geom_line(aes(x, y, group=label), data=dd1)

Here, label is the tip-label variable, which is already associated with cophylogeny. You can check it by head(pp$dd1)

This may look messy since I am using totally random trees. However, if your co-phylogeny trees have some particular pattern, the tanglegram will show that.

Due to the popularity of this tutorial, I have released a small R package that can help you to draw simple tanglegram from two ggtree objects.

The R package called TangleR, currently released in GitHub.

You can download it in R using the following command:

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

Here’s how to use this TangleR package:

library(ggtree)
library(tangler)

# 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_tippoint(aes(color=species))

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

# Draw Tanglegram
simple.tanglegram(tree1, tree2, column_of_interest, value_in_column_that_you_want_to_connect, t2_pad=1, t2_y_pos = 100, t2_y_scale=22, tiplab = T)

I hope this is useful. Please let me know if you need any other features or find bugs! Thanks!


Comments

18 responses to “How to make Co-phylogeny plot: easy tanglegram in R”

  1. Jianshu Avatar

    Hi, in my case, I have several same names (tip label) in one tree, and the name is also in the second tree, I want to add link from all such names in tree 1 to tree 2. In the code provided, link within tree 1 are created (they are the same tip label), 2 same names in tree 1, only 1 are linked to tree 2, another linked each other in tree1. How should I adjust the code to have what I want?

    1. Arafat Avatar

      Hello! The strain names has to be unique in ggtree. But, you can add a second column in your meta where you can have the same names in the tip labels. You can use the geom_tiplab2 to show this column info. Then use the new column to connect the lines. This might work, please try!

  2. Rehemah Gwokyalya Avatar
    Rehemah Gwokyalya

    Hi, this is really great. Thanks for sharing it with us. I ma wondering if it is possible to subset basing on what is present in both data sets i.e., x > 0 in both A and B data sets?

    1. Hi, thanks for commenting. If I understand your question correctly, you can make a new column based on a condition of interest, and use the new column to subset and plot connected lines.

  3. Manuela Avatar

    Hi! Is there a way to rotate nodes on the trees? I rotate them before adding the meta data to the tree file but I keep getting the same tree order.

    Also, is there also a way to make the lines different colors, like make each clade a different color?

    Thank you

    1. Arafat Avatar

      I think this is possible.

      For rotation, you have to rotate them after adding meta data to the tree, or after you connect two trees side by side.

      To selectively colorize different clades, you can use this tutorial: https://yulab-smu.top/treedata-book/chapter6.html

  4. Dylan H. Cohen Avatar
    Dylan H. Cohen

    Is there anyway to connect the line from the end of the tip label to the other tree so the line does not cross thru the tip label? Thanks1

    1. Sorry for the late response. I think that is possible. I’ll try and come back to this. Thanks for the idea!

    2. Yes, if you check how it is plotting the line, geom_line(aes(x, y, group=label), data=green_tree, color='#009E73'), you just need to update the x coordinate in the green_tree data set.

      For each label, there are two entries here, one for tree 1 and another for tree 2.

      If you add some constant value to x-coordinate for tree 1 and subtract the same value from y-coordinate, that will do!

      Sorry for the late reply 🙁

  5. What if you have two different trees that do not have the same tip labels. For example a phylogenetic tree based on a core genome and then a protein based tree and then you want to show which genomes in the core tree that harbours the protein in the second tree. Thanks!

    1. That is definitely possible. Please give me some time, and I’ll update the main post. Sorry for the late reply. Best.

  6. Fernando Hayashi Avatar
    Fernando Hayashi

    I was not able to find how the variable dd1 was created. Could you please clarify?

    1. Arafat Avatar

      Sorry about that! I just added it to the main post:

      dd <- bind_rows(d1, d2) %>%
      filter(isTip == TRUE)
      dd1 <- as.data.frame(dd)

      1. Fernando Hayashi Avatar
        Fernando Hayashi

        Thank you very much!

  7. Hi, really clear description of how to draw tanglegrams within R. Would it be possible to extend this to more than two trees?

    1. Arafat Avatar

      That is really interesting idea. I think that is technically possible. Let me try that, I’ll come back to you soon! Thanks for reading 🙂

  8. Hi, this is great thanks. How would you edit your code to link the tips from the two trees not by your meta file, but by matching tiplabels? Thanks! Lily

    1. Arafat Avatar

      Yes you can do that. You do not need to do any subset, and use the following command in R instead:

      pp + geom_line(aes(x, y, group=label), data=dd1)

      Please check the article, I have updated it!

      Thanks for reading 🙂

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