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plot-aggregate

Plot the average cut-site signal around motif sites to inspect the shape of a footprint. Start with corrected bigWigs from atac-correct and motif results from match-motifs. Outputs can be static figures or an interactive HTML report.

Example command

plot-aggregate \
  --sample-table project/metadata/samples.tsv \
  --motifs SPIB CEBPB \
  --site-set bound \
  --outdir project

Primary inputs

  • --sample-table — TSV with sample and condition columns; the command reads corrected tracks and motif results from {project}/samples/{sample}/.
  • --motifs — motif names or identifiers to plot.
  • --site-set — sites to average; the example uses sites classified as bound in each sample.
  • --outdir — project directory containing motif results and receiving plots.

Replace SPIB CEBPB with motifs present in your motif results.

Main outputs

  • {project}/reports/plot_aggregate.html — default project-layout interactive aggregate report with motif-centered signal profiles.
  • the exact --output path — static PDF/PNG/SVG or interactive HTML in custom layout.
  • the exact --output-txt path — optional per-position aggregate values.
  • the exact --output_aggregated_signals, --output_aggregated_scores, and --output_aggregated_stats paths — optional source tables when requested.
  • the exact --output path in --motif-grid mode — multipage motif-by-comparison PDF built from a review bundle.

When both signal types are available, use footprint score bigWigs for motif statistics and bias-corrected cut-site signal bigWigs for observed aggregate profiles; label the chosen signal explicitly in figure captions.

Look for central cut-site depletion relative to the flanking signal. Also compare the number of sites and the sample-to-sample consistency. Bound-site plots can use different sites in each sample; choose --site-set all to inspect all matched motif sites instead.

For your own site sets, supply BED files with --TFBS. Use --regions to restrict or compare regions of interest.

Export a grid from a review report

plot-aggregate \
  --input-html project/reports/review_multi_comparisons/index.html \
  --motif-grid \
  --output project/reports/motif_aggregate_grid.pdf

See the Bulk output example and the complete plot-aggregate reference.