luxiancao/tanglegram

Python wrapper for scipy and matplotlib to plot tanglegrams from two dendrograms

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+git://github.com/schlegelp/tanglegram@master

Attention: on Windows, the dependencies (i.e. Numpy, Pandas and SciPy) will likely fail to install automatically. Your best bet is to get a Python distribution that already includes them (e.g. Anaconda).

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

How it works

tanglegram exposes three functions:

1. tanglegram.plot plots a tanglegram (optionally untangling)
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()

Known Issues:

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

License:

This code is under GNU GPL V3