Metadata-Version: 1.2
Name: tanglegram
Version: 0.1.0
Summary: Plots simple tanglegrams from two dendrograms
Home-page: https://github.com/schlegelp/tanglegram
Author: Philipp Schlegel
Author-email: pms70@cam.ac.uk
License: GNU GPL V3
Description: tanglegram
        ==========
        Uses scipy and matplotlib to plot simple tanglegrams. Inspired by the amazing [dendextend](https://github.com/talgalili/dendextend) by Tal Galili.
        
        ## Installation
        I recommend using [Python Packaging Index (PIP)](https://pypi.python.org/pypi) to install the package.
        First, get [PIP](https://pip.pypa.io/en/stable/installing/) and then run in terminal:
        
        `pip install git+git://github.com/schlegelp/tanglegram@master`
        
        This command should also work to update the package.
        
        **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)).
        
        If your default distribution is Python 2, you have to explicitly tell [PIP](https://pip.pypa.io/en/stable/installing/) to install for Python 3:
        
        `pip3 install git+git://github.com/schlegelp/tanglegram@master`
        
        #### External libraries used:
        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)
        - [Tqdm](https://pypi.python.org/pypi/tqdm)
        
        ## Quickstart:
        
        ```python
        import tanglegram as tg
        import numpy as np
        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.gen_tangle(mat1, mat2, optimize_order=False)
        plt.show()
        
        # Plot again but this time try minimizing cross-over
        fig = tg.gen_tangle(mat1, mat2, optimize_order=1000)
        plt.show()
        ```
        
        <img src="https://user-images.githubusercontent.com/7161148/42809649-fde86b00-89ad-11e8-9ecd-051f40731bc1.png" width="650">
        
        ## Known Issues:
        * layout does not scale well, i.e. small dendrograms look weird
        
        ## License:
        This code is under GNU GPL V3
        
Keywords: python tanglegram dendrogram
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Requires-Python: >=3
