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`find-signature-fp`¶

Calculate and plot per-cell footprint signatures from completed pseudobulk or motif analyses.

Example command¶

find-signature-fp --annotations cell_annotations.tsv --fragments pbmc_fragments.tsv.gz --h5ad pbmc_embedding.h5ad \
  --tf-site-dir marker_motif_sites --all-motif-results project/pseudobulk/pseudobulk_diff_footprints_results.txt \
  --outdir project/pseudobulk/signature_fp

Primary inputs¶

--annotations — barcode-level cell annotation table.
--fragments — indexed single-cell fragment file.
--h5ad — single-cell object containing the spectral or UMAP embedding.
--tf-site-dir — motif-site directories from the footprint analysis.
--all-motif-results — completed motif-level differential result table.
--outdir — directory for per-cell scores, heatmaps, and UMAP figures.

Main outputs¶

Under {outdir} the default names include:

Path	Meaning
`knn_footprint_signature_scores.tsv`	Per-cell KNN-smoothed footprint protection scores for selected TFs.
`knn_footprint_orientation_summary.tsv`	Direction/orientation checks used to make marker scores comparable.
`chromvar_like_motif_activity_scores.tsv`	Companion accessibility-derived motif activity scores.
`knn_footprint_signature_umap.svg` and `.pdf`	Per-marker footprint-signature UMAP panels.
`per_cell_footprint_signature_heatmap.svg` and `.pdf`	Selected-marker per-cell heatmap.
`single_cell_footprinting_summary.svg` and `.pdf`	Combined heatmap and representative UMAP summary.
`all_motif_per_cell_footprint_signature_heatmap.tsv`	Optional all-motif score matrix and metadata when all-motif inputs are supplied.

Additional top-motif and all-TF review files use their requested output prefix.

See the Single-cell output example and the complete find-signature-fp reference.