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Web Based Visualizations using NeoPredViz

Additional Dependencies For Visualizations

  1. bokeh

  2. holoviews (pip install holoviews)

Executing NeoPredViz

You can use NeoPredViz to visualize some or all of the information in the output files consistent with the modularity of execution.

python NeoPredViz.py --help
usage: NeoPredViz.py [-h] [-s SUMMARYFILE] [-o OUTPUT] [-n NEOSFILE]
                     [-r NEORECOFILE]

optional arguments:
  -h, --help      show this help message and exit

Required arguments:
  -s SUMMARYFILE  Neoantigens Summary File
  -o OUTPUT       Output Directory Path

Optional Arguments:
  -n NEOSFILE     Neoantigen Predictions Output File. Default: None.
  -r NEORECOFILE  Neoantigen Recognition Potentials Output File. Default:
                  None.

The NeoPredViz output will produce a simple web based visualization for you to explore outputs quickly. The use all of the information that NeoPredPipe can output simply run:

python NeoPredViz.py -o NeoantigenVizDashboard.html -s SummaryTable.txt -n NeoantigensOutput.txt -r NeoRecoPoTable.txt

Finally, in order to visualize, open the output file (NeoantigenVizDashboard.html) with your preferred web browser. This file can also be shared as an html with others.

It's possible to export these plots, but for this, please refer to bokeh documentation.

Troubleshooting:

Updated versions and new machines (M1-4 Macs) might require different dependencies. If encountering issues, try the set-up detailed here: #47 (comment)