In the scripts/* folder you will find a set of python scripts for recreating results from Fig.1, Fig. 2, Fig.3, Fig. 4, Fig. 6 from our paper. The notebooks will show how Figs. 2 and 5 were obtained. All intermediate results are already present in this directory except for the following:
For example, python scripts/chng_between_sample.py
will regenerate the figures for the skin microbiome fungi result in our paper.
For files that are gzipped, you may have to ungzip.
- Look at
scripts/synthetic_pois_plot.py
- Look at
profile_analysis.ipynb
.
cd
intoreal_gut_results_v0.5
orreal_gut_results_v0.5/hadza
and look at thescripts
python scripts.
- Look at
scripts/diagonal_ani_nn.py
andscripts/mock_community_plot.py
- Look at
analysis.ipynb
for the MWAS statistical calculation andscripts/manhat.py
. - Look at
scripts/chng_between_sample.py
for the Chng et al analysis
- Look at
real_profile_analysis.ipynb
.
- Python 3 with the following libraries:
- matplotlib
- numpy
- seaborn
- natsort
- scipy
- statsmodels
- jupyter notebook if you want to rerun the MWAS results