Jupyter notebooks and data - reproducible analysis from reassortment paper.
To re-run these analyses, run the code in the following notebooks:
Make Figure - Known Transmission Patterns.ipynb
Make Figure - Proportion Reassortant.ipynb
Make Figure - PWI Histogram.ipynb
Make Supplementary Data - Edge List and Node List.ipynb
For a tutorial on how to run Jupyter notebooks, see the Jupyter project website.
Software requirements:
- Python 3.4 (minimum)
networkx
pandas
numpy
seaborn
matplotlib
biopython
joblib
python-Levenshtein
To visualize lineage traces of the 2009 H1N1 or 2013 H7N9 viruses, do the following:
- Clone the repository to disk.
- Navigate to the directory
supp_data/viz
- Start a web server in the directory. One option is to use
python -m http.server 8000
. This starts a local web server in the directory with port 8000. - In your browser, type:
localhost:8000/h1n1.html
. Replace the port number accordingly; to visualize H7N9, useh7n9.html
instead.