sc-gene-programs

name	sc-gene-programs
description	Load when extracting gene programs (NMF / cNMF factorisation) and per-cell program usage scores from a non-negative scRNA AnnData. Skip when ranking marker genes per cluster (use sc-markers) or for inferring TF → target regulons (use sc-grn).
version	0.2.0
author	OmicsClaw
license	MIT
tags	["singlecell","scrna","gene-programs","nmf","cnmf","factorisation"]
requires	["anndata","scanpy","numpy","pandas","scikit-learn"]

sc-gene-programs

When to use

The user has a non-negative scRNA AnnData (raw counts or log-normalised expression) and wants to decompose it into K gene programs (latent factors) plus a per-cell usage matrix. Two methods:

• cnmf (default) — consensus NMF (multiple runs + clustering of factors) for stable programs. Auto-falls back to nmf if the cnmf package isn't installed.
• nmf — sklearn NMF, single run.

Output: tables/program_usage.csv (cells × K), tables/program_weights.csv (genes × K), tables/top_program_genes.csv (top-N genes per program).

For per-cluster marker discovery use sc-markers; for TF → target regulons use sc-grn; for per-cell pathway scores against curated gene sets use sc-pathway-scoring.

Inputs & Outputs

Input	Format	Required
Non-negative AnnData	.h5ad (raw counts in layers["counts"] or log-normalised in .X)	yes (unless --demo)

Output	Path	Notes
Annotated AnnData	processed.h5ad	adds obsm["X_gene_programs"] (cells × K usage matrix; sc_gene_programs.py:469). The program_usage name only applies to the tables/program_usage.csv file, NOT to the obsm key.
Per-cell usage	tables/program_usage.csv	cells × K matrix
Gene weights	tables/program_weights.csv	genes × K matrix
Top genes	tables/top_program_genes.csv	top---top-genes per program
Figures	figures/mean_program_usage.png, figures/program_correlation.png	always
Report	report.md + result.json	always

Flow

1. Auto-fallback check: try import cnmf; if it fails, silently switch --method to nmf.
2. Load AnnData (--input) or build a demo.
3. Preflight: pick source matrix per --layer (auto-prefer layers["counts"] for cnmf when --layer is unset); reject negative values; warn if n_genes < 50 or running NMF on raw counts without --layer counts.
4. Run cNMF (consensus NMF with --n-iter runs) or sklearn NMF (single run, --seed).
5. Build top-genes-per-program table; compute per-program correlation matrix.
6. Detect degenerate output → record diagnostics; do NOT raise.
7. Save tables, figures, processed.h5ad, report.md, result.json.

Gotchas

• cnmf silently auto-falls back to nmf if cnmf is not installed. sc_gene_programs.py:407-409 catches ImportError from import cnmf, logs a warning, sets args.method = "nmf" (so summary["method"] at :527 already reflects the post-fallback value). summary["backend"] at :528 records the same. Inspect either before quoting "we used cNMF".
• Negative values reject the run. sc_gene_programs.py:132 raises SystemExit("NMF/cNMF requires non-negative input, but the data matrix contains negative values. This usually means the data has been z-score scaled. ...") with a multi-option fix message. Most common cause: feeding a sc.pp.scale-d AnnData where .X is mean-centred. Pass --layer counts or re-run sc-preprocessing without scaling.
• cnmf auto-prefers layers["counts"]; nmf doesn't. sc_gene_programs.py:111-112 switches to layers["counts"] for cnmf if --layer is unset and the layer exists. nmf without --layer uses .X directly. If your raw counts live elsewhere, pass --layer <name> explicitly to avoid silent fallback to .X.
• Missing --layer value also SystemExits. sc_gene_programs.py:118 raises SystemExit("Layer '<name>' not found in adata.layers. Available layers: <list>. ...") when an explicit --layer doesn't resolve. Wrappers expecting ValueError need to catch SystemExit.
• --input mandatory unless --demo. sc_gene_programs.py:418 raises SystemExit("Provide --input or use --demo").
• Degenerate output is a soft fail. When the factorisation collapses to fewer effective programs than --n-programs, sc_gene_programs.py:533-534 records summary["degenerate_output"] = True and lists degenerate_issues — but the script returns 0. Always inspect (line 529, the count) before chaining downstream.

Key CLI

# Demo (cNMF on synthetic data, falls back to NMF if cnmf missing)
python omicsclaw.py run sc-gene-programs --demo --output /tmp/sc_gp_demo

# cNMF with 8 programs on raw counts
python omicsclaw.py run sc-gene-programs \
  --input clustered.h5ad --output results/ \
  --method cnmf --n-programs 8 --n-iter 200 --layer counts

# NMF on log-normalised .X (faster, less stable)
python omicsclaw.py run sc-gene-programs \
  --input normalized.h5ad --output results/ \
  --method nmf --n-programs 10 --top-genes 50

See also

• references/parameters.md — every CLI flag, NMF / cNMF tunables
• references/methodology.md — when consensus NMF wins; layer-selection guide
• references/output_contract.md — obsm["X_gene_programs"] / tables/program_*.csv schemas
• Adjacent skills: sc-preprocessing (upstream — produces a non-negative .X or layers["counts"]), sc-markers (parallel — cluster markers, NOT latent factors), sc-pathway-scoring (parallel — supervised program scoring against curated gene sets), sc-grn (parallel — TF → target regulons; complementary to gene programs)