`review-multi-comparisons`¶

Review several diff-footprints comparisons in one place. Combine the existing reports into a browser bundle or a single HTML file, then switch between comparisons to explore motif statistics and aggregate profiles.

Example command¶

review-multi-comparisons \
  --inputs project/comparisons \
  --output-dir project/reports/review_multi_comparisons

Primary inputs¶

--inputs — report files or directories containing differential reports.
--output-dir — destination for the complete static bundle.

Main outputs¶

{bundle} is the --output-dir:

Path	Meaning
`{bundle}/index.html`	Report entry page, served together with the other bundle files.
`{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. Keep the entire directory together when copying or publishing a bundle.

Open the bundle¶

The bundle loads its data through a web server. To view it locally, run:

python -m http.server 8000 --bind 127.0.0.1 \
  --directory project/reports/review_multi_comparisons

Open http://127.0.0.1:8000/ in your browser. Stop the server with Ctrl+C when you finish. To open a report directly without a server, use the standalone output below.

To choose the bundle's opening view, add --default-comparison with the two condition or region labels, --default-aggregate-motifs with the motif names or IDs in display order, and --default-aggregate-plots with the number of panels. The selected labels and motifs must exist in the input reports. Use --documentation-url to add a documentation link.

Standalone output¶

Use --output-html instead of --output-dir to create one HTML file that you can open directly or share. It includes volcano plots, ranked motifs, logos, and SVG exports. Aggregate controls appear when the input reports contain profiles. Use --labels to give each input report a distinct name in the Comparison list, especially when reports compare the same condition pair.

In the ranked-motif plot, switch between differential footprint score and -log10(p-value) to change the ranking view. Use the legend to interpret the color scale and direction of change. In the volcano plot, use Label TFs to label selected TF names, motif IDs, or output prefixes, separated by commas. Select (none) in the highlight control to clear highlighting. SVG exports retain the selected comparison label and plot settings.

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.

review-multi-comparisons¶