tanglegram

Uses scipy and matplotlib to plot simple tanglegrams. Inspired by the amazing dendextend by Tal Galili.

Installation

First, get PIP and then run in terminal:

pip3 install tanglegram -U

To install the bleeding-edge version from Github you can run:

pip3 install git+https://github.com/schlegelp/tanglegram@master

Dependencies

Installing via PIP should install all external dependencies. You may run into problems on Windows though. In that case, you need to install dependencies manually, here is a list of dependencies (check out install_requires in setup.py for version info):

• Pandas
• SciPy
• Numpy
• Matplotlib
• tqdm
• networkx

How it works

tanglegram exposes three functions:

1. tanglegram.plot plots a tanglegram (untangling optionally)
2. tanglegram.entanglement measures the entanglement between two linkages
3. tanglegram.untangle rotates dendrograms to minimize entanglement

import tanglegram as tg
import matplotlib.pyplot as plt
import pandas as pd

# Generate two distance matrices and just switch labels in one
labelsA= ['A', 'B', 'C', 'D']
labelsB= ['B', 'A', 'C', 'D']
data = [[ 0,  .1,  .4, .3],
        [.1,   0,  .5, .6],
        [.4,  .5,   0, .2],
        [.3,  .6,  .2,  0]]

mat1 = pd.DataFrame(data,
                    columns=labelsA,
                    index=labelsA)

mat2 = pd.DataFrame(data,
                    columns=labelsB,
                    index=labelsB)

# Plot tanglegram
fig = tg.plot(mat1, mat2, sort=False)
plt.show()

# Plot again but this time try minimizing cross-over
fig = tg.plot(mat1, mat2, sort=True)
plt.show()

# Alternatively, you can also explicitly provide the edges to plot and untangle  
# Note how in this case the labels don't have to match anymore
fig = tg.plot(mat1, mat2, sort=True, edges=[('A', 'A'), ('C', 'D')])
plt.show()

Known Issues:

• layout does not scale well, i.e. small dendrograms look weird

License:

This code is under GNU GPL V3