Request - Technical Documentation

[cthoyt]

I'd like to use the HotNet2 algorithm/pipeline inside a Jupyter Notebook and be able to embed it in other Python scripts.

I have a couple questions which could be addressed with a bit of technical documentation:

• Is it possible for me to bring my own NetworkX (di)graph?
• If so, what schema its node and edge data dictionaries would need to follow to run the algorithm?
• What functions run the algorithm?
• Where do the results go?

If you have answers, I'd be happy to write it in Sphinx format and submit a PR :) I enjoyed your paper and thanks for making this code open source.

[matthewreyna]

Thank you for your questions, and apologies for the delayed response.

• Yes. HotNet2 takes a vertex-weighted graph as input, which we pass as an edge list to the makeNetworkFiles.py script and heat scores to the makeHeatFile.py script. Please see the paper folder for an example. However, note that the makeNetworkFiles.py script may take some time to run, so it may be better to run it offline.
• See above.
• The algorithm uses several functions, but the run_helper function in the hotnet2/run.py script drives much of HotNet2.
• The results go in the location given to the --output_directory argument for the HotNet2.py script.

The most expedient way to use HotNet2 in a Jupyter notebook is likely by calling or importing the makeNetworkFiles.py, makeHeatFile.py, and HotNet2.py scripts, but it depends, of course, on what you are trying to do.