Metadata-Version: 1.1
Name: tanglegram
Version: 0.0.2
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
        from tanglegram import tangle
        import numpy as np
        import matplotlib.pyplot as plt
        
        # Quick test: 
        # Generate two distance matrices and just switch labels in one
        labelsA= ['A','B','C','D']
        labelsB= ['B','A','C','D']
        data = np.array( [ [ 1, .1,  0, 0],
                         [.1,  1, .5, 0],
                         [ 0, .5,  1, 0],
                         [ 0,  0,  0, 1]
                        ])
        
        mat1 = pd.DataFrame( data,
                             columns=labelsA,
                             index=labelsA)
        
        mat2 = pd.DataFrame( data,
                             columns=labelsB,
                             index=labelsB)
        
        # Plot tanglegram
        fig = tangle.plot(mat1,mat2)
        plt.show()
        ```
        
        <img src="https://user-images.githubusercontent.com/7161148/29683302-c2cc22e0-8905-11e7-9091-97e55bce1ddb.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
