Generates diagnostic figures from a finished training run.
mosa plot --config <your-config>.yaml
| Flag | Type | Required | Description |
|---|---|---|---|
-c, --config |
path | yes | Path to YAML config file |
-o, --output-dir |
path | no | Path to training output directory (defaults to model.output_dir in config) |
-d, --debug |
flag | no | Add artifact paths, per-plot timings, skip reasons and tracebacks |
Description¶
Reads the parquets and the Lightning metrics log written by train, plus the
dataset itself at data.path, since the input values are needed for the
reconstruction scatter plots and the sample metadata for colouring. Figures go
to <output_dir>/plots/, and clustering_metrics.csv to
<output_dir>/metrics/. Nothing is plotted during training itself.
Embedding figures use tissue for colour and model_type for source markers.
The command requires a tissue column even when some figures, such as loss curves, do not use it.
Latent representations are read from the full/ split, falling back to
train/. Loss curves come from lightning_logs/version_*/metrics.csv, using
the latest version directory.
What each figure shows is described in Plots.
Limitations¶
- It does not train, and does not load the model. A run directory with no outputs in it produces an error naming the paths that were searched.
--output-dirchanges where outputs are read from as well as written to; it points the whole command at a different run.