BFF-PXF-PLOT

bff-pxf-plot creates a self-contained HTML report from BFF or PXF records. From v1.09, HTML replaces PNG output.

The report shows entry distributions (including the mean and median), section coverage, and phenotype and disease frequencies with searchable term tables. Excluded phenotypes are shown separately. Counts describe available annotations, not necessarily disease complexity or annotation quality. All charts and tables work offline.

Example reports

These reports were generated with v1.09 from the repository's BFF example and 100 simulated PXF records. Open either report to explore its summary table, distributions, section coverage and searchable terms.

Open BFF report · Open PXF report

Preview the BFF report

Usage

Desktop

Open Tools > Phenotype summary plot, select BFF or PXF records from a file or previous run, then run the utility. Open the HTML report in the results panel; expand it to explore the charts and searchable tables. Generic JSON and binary analysis exports are not supported as summary inputs.

CLI

The tool, bff-pxf-plot, is found in the utils directory (if downloaded from GitHub or Docker).

View source README

HOW TO RUN

usage: bff-pxf-plot [-h] -i INPUT [-o OUTPUT] [-v]

Process BFF/PXF (JSON or YAML) data and generate a self-contained HTML report.

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input JSON or YAML file path (e.g., "data.json" or "data.yaml").
  -o OUTPUT, --output OUTPUT
                        Output HTML file path (default: "output_plots.html")
  -v, --verbose         Increase output verbosity

Example:

./bff-pxf-plot -i individuals.json

INSTALLATION

It should work out of the box with the containerized version. Otherwise:

pip install matplotlib PyYAML

AUTHOR

Written by Manuel Rueda, PhD. Info about CNAG can be found at https://www.cnag.eu.

COPYRIGHT AND LICENSE

This Python file is copyrighted. See the LICENSE file included in this distribution.