Skip to content

Latest commit

 

History

History
executable file
·
26 lines (18 loc) · 1.01 KB

Visualization.md

File metadata and controls

executable file
·
26 lines (18 loc) · 1.01 KB

ProteinGraphML : Visualization

The initial visualization code was developed by Danny Byrd, to visualize the evidence subgraph representing XGBoost feature importance results.

Visualize

MakeVis.py generates HTML/JS files, with feature importance, for visualization via web browser. ProteinGraphML/Analysis/ contains code for graph and feature visualization. Visualize has code for creating HTML/JS graphs, and featureLabel has code for taking a dictionary of feature importance, and giving it human readable labels.

Command-line parameters:

  • --disease : Disease name.
  • --featurefile : full path to the pickled features file produced by TrainModelML.py, e.g. results/104300/featImportance_XGBCrossVal.pkl.
  • --num : number of top important features selected.
  • --kgfile : Pickled KG file, produced by BuildKG_OlegDb.py (default: ProteinDisease_GRAPH.pkl).

Example command:

MakeVis.py --disease 104300 --featurefile results/104300/featImportance_XGBCrossVal.pkl --num 2

Notes