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plot-aggregate

Plot average signal around motif sites or other genomic regions as a static figure or interactive HTML report.

Multiple user-defined BED files are supported through --TFBS. Multiple --regions BED files can restrict or compare distinct regions of interest.

Example command

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

Primary inputs

  • --sample-table — samples, conditions, and bias-corrected cut-site signal bigWigs used for the aggregate profiles.
  • --motifs — motif names or identifiers to plot.
  • --site-set — motif-site set; the example uses bound sites.
  • --outdir — project directory containing motif results and receiving plots.

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.

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.