Sc Velocity

---
name: sc-velocity
description: Load when computing RNA velocity vectors and latent time on a scRNA AnnData with spliced / unspliced layers via scVelo (stochastic / dynamical / steady-state). Skip when input lacks spliced+unspliced layers (run sc-velocity-prep first) or for trajectory pseudotime ordering (use sc-pseudotime).
version: 0.4.0
author: OmicsClaw
license: MIT
tags:
- singlecell
- scrna
- velocity
- rna-velocity
- scvelo
- latent-time
- kinetics
requires:
- anndata
- scanpy
- scvelo
- numpy
- pandas
---

# sc-velocity

## When to use

The user has a scRNA AnnData with `layers["spliced"]` and
`layers["unspliced"]` already populated (typically from
`sc-velocity-prep` running `velocyto` / `STARsolo` / `kb-python`) and
wants per-cell velocity vectors, magnitude maps, and optional latent
time. Three scVelo modes:

- `scvelo_stochastic` (default) — fast, robust to noise.
- `scvelo_dynamical` — full splicing-kinetics model + latent time
  (slower, more interpretable).
- `scvelo_steady_state` — simplest approximation, fastest.

For ordering cells along a trajectory without splicing kinetics use
`sc-pseudotime`. To **generate** the spliced/unspliced layers from raw
FASTQs / cellranger output, run `sc-velocity-prep` first.

## Inputs & Outputs

| Input | Format | Required |
|---|---|---|
| AnnData with spliced + unspliced layers | `.h5ad` | yes (unless `--demo`) |

| Output | Path | Notes |
|---|---|---|
| Annotated AnnData | `processed.h5ad` | adds `layers["velocity"]`, optional `obs["latent_time"]` (dynamical mode), velocity-graph in `obsp` |
| Run summary | `tables/velocity_summary.csv` | always |
| Per-cell summary | `tables/velocity_cells.csv` | velocity magnitude, latent time per cell |
| Top genes | `tables/top_velocity_genes.csv` | ranked by mean absolute velocity |
| Figures | `figures/velocity_stream.png`, `figures/velocity_magnitude_umap.png`, `figures/velocity_magnitude_distribution.png`, `figures/velocity_top_genes.png` | always |
| Latent time UMAP | `figures/latent_time_umap.png` | when `mode == scvelo_dynamical` (i.e., `has_latent_time = True`) |
| Report | `report.md` + `result.json` | always |

## Flow

1. Load AnnData (`--input`) or build a synthetic demo with spliced / unspliced layers.
2. Preflight `requires_layers=("spliced", "unspliced")` for the chosen method.
3. Run scVelo: filter & normalise → moments → velocity (mode-specific) → velocity graph.
4. If `scvelo_dynamical`: also compute latent time and gene-level dynamics.
5. Detect degenerate output (zero velocity genes / all-NaN) and emit a multi-action fix message in `result.json["suggested_actions"]` — does NOT raise.
6. Render figures, write tables, save `processed.h5ad`, `report.md`, `result.json`.

## Gotchas

- **Missing `spliced` / `unspliced` layers fail at preflight.** The METHOD_REGISTRY entries at `sc_velocity.py:112` / `:118` / `:124` declare `requires_layers=("spliced", "unspliced")`; the shared preflight aborts before scVelo runs. Generate the layers with `sc-velocity-prep` (`--method velocyto`, `starsolo`, or `kb-python`) first.
- **Degenerate velocity is a soft fail, not an exception.** When scVelo can't fit a meaningful kinetics model, `sc_velocity.py:795-806` records `result.json["degenerate"]=True`, `n_velocity_genes=0`, `all_zero_velocity=True` and writes `suggested_actions: [...]` — but the script returns 0. Always check `result.json["n_velocity_genes"]` before consuming the `velocity` layer downstream (e.g., before passing to `sc-pseudotime --method cellrank --cellrank-use-velocity`).
- **`--method` accepts both METHOD_REGISTRY names and `_MODE_ALIAS_MAP` keys.** `sc_velocity.py:656` builds `choices` as the union — passing a legacy alias (e.g., `--mode stochastic`) silently maps to `scvelo_stochastic`. The actual mode used is recorded in `result.json["mode"]`.
- **`scvelo_dynamical` is the only mode that produces `latent_time`.** `sc_velocity.py:818-822` writes `result.json["latent_time_range"]` only when `obs["latent_time"]` is populated. Stochastic / steady-state modes return velocity but no latent time — `figures/latent_time_umap.png` won't be written.
- **`--input` is mandatory unless `--demo` (parser.error, exit code 2).** `sc_velocity.py:682` calls `parser.error("--input required when not using --demo")`. Once `--input` is provided, `:685` raises `FileNotFoundError(f"Input file not found: {input_path}")` for a bad path.
- **All scVelo backends require the `scvelo` Python package.** All 3 METHOD_REGISTRY entries declare `dependencies=("scvelo",)`. The shared dependency manager raises `ImportError` if scvelo isn't installed.

## Key CLI

```bash
# Demo (synthetic spliced/unspliced)
python omicsclaw.py run sc-velocity --demo --output /tmp/sc_velocity_demo

# Default stochastic on real velocity-prepped data
python omicsclaw.py run sc-velocity \
  --input velocity_ready.h5ad --output results/

# Dynamical (full kinetics + latent time)
python omicsclaw.py run sc-velocity \
  --input velocity_ready.h5ad --output results/ \
  --method scvelo_dynamical --n-jobs 8

# Steady-state (fastest approximation)
python omicsclaw.py run sc-velocity \
  --input velocity_ready.h5ad --output results/ \
  --method scvelo_steady_state
```

## See also

- `references/parameters.md` — every CLI flag, per-mode notes
- `references/methodology.md` — when each scVelo mode wins; degenerate-output checklist
- `references/output_contract.md` — `layers["velocity"]` / `obs["latent_time"]` schema
- Adjacent skills: `sc-velocity-prep` (upstream — produces `layers["spliced"]` / `layers["unspliced"]`), `sc-pseudotime` (parallel — graph-based trajectory ordering, can consume velocity via `--cellrank-use-velocity`), `sc-clustering` (upstream — provides `obsm["X_umap"]` for the stream plot)