Fig 1. Extension Parameter

Run python3 extension_parameter.py

Fig 2. Shuffling Test

Run python3 shuffling_test.py

Fig 3. Precision-Recall

Run python3 precision_recall_plot_2022.py or use the notebook precision_recall_plot_2022.ipynb

Fig 4. Heatmap of Limb GO Terms

Run python3 term_comparison_heatmap_2022.py or use the notebook term_comparison_heatmap_2022.ipynb
Note: Default plot only considers terms with source of GO:BP. To plot terms of both GO:BP and GO:MF, use read_data(only_BP=False).

Fig 5. EnrichmentMap for UK Biobank GWAS Data (Basophil)

Open Cytoscape session file basophil_gobp_2022.cys with Cytoscape.Versions used:

• Cytoscape 3.9.1
• EnrichmentMap Pipeline Collection 1.1.0 (EnrichmentMap 3.3.3, AutoAnnotate 1.3.5, WordCloud 3.1.4, clusterMaker2 2.0)

The session file is generated using the two files in data/enrichment_map with default settings.
EnrichmentMap tutorial: https://baderlab.github.io/CBW_Pathways_2020/gprofiler-mod3.html#gprofiler_mod3