The main code for the PathFA method, which is implemented in pathfa/path_fa.py in lines
185 and 420 for the unimodal and multimodal variants. See the docstrings for more details.
- Python >= 3.7 with installed requirements.txt and rpy linked
- msigdb v7.2 pathways/genesets when re-running data preparation
- TuPro datasets for reproducing the corresponding experiments
The synthetic experiments use MSigDB Hallmark pathways and associations prepared in data_synth
to simulate example data.
To produce all commands that have to be run, execute python runscripts/synthetic_joblist_generate.py > runscripts/synthetic_joblist.sh.
Before executing each command, mkdir synthetic_results has to be executed as well.
Each line in the synthetic_joblist.sh corresponds to a command that has to be run.
For details on the synthetic experiment, see run_synthetic.py.
In notebooks/, use the ipynb notebook to produce figures.
The commands are generated with python runscripts/joblist_tupro_generate.py > runscripts/joblist_tupro.sh and each
line corresponds to a command that has to be executed.
Before executing all commands, make sure to create the directories tupro_results/ovarian and tupro_results/melanoma.
Further, make sure to set the variable TUPRO_PATH in pathfa/utils.py to the directory where to load TuPro data from (once it is released).
Afterwards, results are aggregated with python scripts/extract_tupro_results.py.
In notebooks/, use the ipynb notebook to produce figures.