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review-multi-comparisons

Combine differential-footprint reports as a scalable browser bundle or one self-contained HTML report.

Example command

review-multi-comparisons --inputs project/comparisons --output-dir project/reports/review_multi_comparisons \
  --default-comparison "HNF4A + FOXA2" "No HNF4A/FOXA2" \
  --default-aggregate-motifs MA1494.2 MA0484.3 MA0047.4 MA0148.5 MA0046.3 MA0153.2 MA0102.5 MA0466.4 \
  --default-aggregate-plots 8 --documentation-url https://oncologylab.github.io/fp-tools/

Primary inputs

  • --inputs — report files or directories containing differential reports.
  • --output-dir — destination for the complete static bundle.
  • --default-comparison — condition or region pair shown first.
  • --default-aggregate-motifs — ordered motif panel shown first.
  • --default-aggregate-plots — initial number of aggregate panels.
  • --documentation-url — optional link back to the documentation site.

Main outputs

{bundle} is the --output-dir:

Path Meaning
{bundle}/index.html Browser entry point; open or publish this file together with the full bundle.
{bundle}/app.js, {bundle}/plot_controls.js, and {bundle}/styles.css Local application code, shared plot behavior, and styling.
{bundle}/data/metadata.json Comparison index and payload checksums.
{bundle}/data/reports/{comparison}.json.gz Compact data for one comparison.
{bundle}/data/profiles/ Aggregate-profile shards loaded on demand.
{bundle}/data/logos/ Motif logo assets.

Project mode defaults to {project}/reports/review_multi_comparisons/index.html. The directory is a portable unit; copying only index.html produces a broken report.

Standalone output

Use --output-html instead of --output-dir. Aggregate profiles are optional, and --labels keeps repeated condition pairs distinct. The exact output is the path passed to --output-html; it is one portable HTML file with coordinated volcano, ranked-motif, logo, and SVG-export views. Aggregate controls appear only when profiles exist. One Comparison list selects the exact input record in --labels order, so repeated condition pairs remain distinct.

The ranked-motif waterfall has a compact switch between differential footprint score and -log10(p-value). Bar color and the printed row value show the other metric: blue/red preserves the direction in both modes, while color strength shows the active color metric. The volcano uses a stable square plotting area. The volcano highlight selector includes (none), and the Label TFs field accepts comma-separated TF names, motif IDs, or output prefixes. These controls work identically with and without aggregate profiles and are preserved in SVG exports. Waterfall, volcano, and combined-panel SVGs include the active comparison label inside the figure.

review-multi-comparisons --inputs baseline/report.html dose1/report.html dose2/report.html \
  --labels Baseline "Dose 1" "Dose 2" --output-html review.html

Continue with the --motif-grid mode of plot-aggregate, or see the complete review-multi-comparisons reference.