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python_mcl

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markov cluster algorithm - python

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# MCL algorithm

This module implements the Markov Cluster algorithm created by Stijn van Dongen and 
described in http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm.

This implementation is still in beta and is not yet optimized for large networks.

![example] (example.png)

##Installation

python setup.py install

##Usage

###Command line

Usage: mcl_clustering.py [options] <input_matrix>

Options
      -h, --help            show this help message and exit
      -e EXPAND_FACTOR, --expand_factor=EXPAND_FACTOR
                            expand factor (default: 2)
      -i INFLATE_FACTOR, --inflate_factor=INFLATE_FACTOR
                            inflate factor (default: 2)
      -m MULT_FACTOR, --mult_factor=MULT_FACTOR
                            multiply factor (default: 2)
      -l MAX_LOOP, --max_loops=MAX_LOOP
                            max loops (default: 60)
      -o FILE, --output=FILE
                            output (default: stdout)
      -v, --verbose         verbose (default: True)
      -d, --draw-graph      show graph with networkx (default: False)

The input matrix must be as comma-separated value file representing the 
adjacency matrix.

An example is the file example.csv in examples dir.

try: 
    mcl_clustering.py -d -e 3 <example_path>/example.csv

###Code
        
####Using numpy adjacency matrix

from mcl_clustering import mcl

A = <your matrix>

M, clusters = mcl(A, expand_factor = <expand_factor>,
                       inflate_factor = <inflate_factor>,
                       max_loop = <max_loop>,
                       mult_factor = <mult_factor>)

####Using a networkx graph

from mcl_clustering import networkx_mcl

G = <your graph>

M, clusters = networkx_mcl(G, expand_factor = <expand_factor>,
                       inflate_factor = <inflate_factor>,
                       max_loop = <max_loop>,
                       mult_factor = <mult_factor>)

Output
        M = otuput matrix
        clusters = dict with keys = [<cluster id>] values = [<vertex id>]

##Requirements
    
    numpy
    networkx

##References

* [1]   Stijn van Dongen, Graph Clustering by Flow Simulation.
      PhD thesis, University of Utrecht, May 2000.
      ( http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm )

* [2]   Stijn van Dongen. A cluster algorithm for graphs.  Technical Report
      INS-R0010, National Research Institute for Mathematics and Computer
      Science in the Netherlands, Amsterdam, May 2000.
      ( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z )

# license

MIT

python_mcl

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