Random Modular Network Generator

This is the source code used for the following paper:

Sah, Pratha*, Lisa O. Singh, Aaron Clauset, and Shweta Bansal. "Exploring community structure in biological networks with random graphs." BMC Bioinformatics 2014, 15:220. doi:10.1186/1471-2105-15-220

This Python script generates undirected, simple, connected graphs with a specified degrees and pattern of communities, while maintaining a graph structure that is as random as possible.

email: ps875@georgetown.edu, sb753@georgetown.edu

Please cite the paper above, if you use our code in any form or create a derivative work.

Sample Output Graph

Modular random graphs with network size = 150, 375 edges, 3 modules (or communities) of size, s = 50 and degree distribution is power law with modularity values of: a) Q = 0.1; b) Q = 0.3; and c) Q = 0.6.

From Figure 2, Sah et al. (2014)

Dependencies

• Python 2.7
• Networkx 2.2

Link to install Networkx can be found here. The generator also requires sequence_generator.py script which is provided.

Usage

For a quick demo of the code, open the script "random_modular_generator_variable_modules.py" and scroll down to the main function. Adjust the model parameters, degree distribution function and module size distribution function and run in terminal using the command:

$ python random_modular_generator_variable_modules.py

Sample Code

For users unfamiliar to Python, I have uploadeded a sample code file (mock_code.py) demonstrating how the graph generator can be imported and used in a script. The mock code can be run using the command

$ python mock_code.py

Output

The code saves the the adjacency matrix of the generated random modular graph under the filename 'adjacency_matrix.txt'. The graph is also saved in a graphml format under the filename "random_modular_graph.graphml". The graphml file can be uploaded in Gephi (http://gephi.github.io/) for graph visualization. Note that Gephi currently does not have a layout plugin to visualize modular graphs. In the near future, I am planning to add a function in random-modular-network-generator.py code to assign each node a particular coordinate that allows easy visualization of modules (I have done this in Figure 2). Shoot us an email if you need this feature sooner than later.

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