tanglegram
==========
Uses scipy and matplotlib to plot simple tanglegrams. Inspired by the amazing [dendextend](https://github.com/talgalili/dendextend) by Tal Galili.
## Installation
First, get [PIP](https://pip.pypa.io/en/stable/installing/) 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](https://www.continuum.io/downloads)).
#### Dependencies
Installing via [PIP](https://pip.pypa.io/en/stable/installing/) 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](https://raw.githubusercontent.com/schlegelp/PyMaid/master/setup.py) for version info):
- [Pandas](http://pandas.pydata.org/)
- [SciPy](http://www.scipy.org)
- [Numpy](http://www.scipy.org)
- [Matplotlib](http://www.matplotlib.org)
## 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
```Python
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()
```
<img src="https://user-images.githubusercontent.com/7161148/105351954-2ae19f80-5be5-11eb-9dad-2dd0fe83d44d.png" width="650">
```Python
# Plot again but this time try minimizing cross-over
fig = tg.plot(mat1, mat2, sort=True)
plt.show()
```
<img src="https://user-images.githubusercontent.com/7161148/105351772-e8b85e00-5be4-11eb-9343-db42f143ec68.png" width="650">
## Known Issues:
* layout does not scale well, i.e. small dendrograms look weird
## License:
This code is under GNU GPL V3
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