INNER CODE UNIT · Python
signature
antigenomics/vdjtools · python/vdjtools/cli/__init__.py:480
def signature(
samples: Optional[list[Path]] = _SAMPLES, metadata: Optional[Path] = _META,
base_dir: Optional[Path] = _BASE, sample_col: str = _SCOL, file_template: str = _TMPL,
fmt: str = _FMT,
corpus: str = typer.Option(..., "--corpus",
help="Corpus to rotate through: a published name (blood, tissue, "
"deep-tcr, blood-uncapped, tissue-uncapped, synthetic-blood, "
"synthetic-tissue, naive, memory) or a path to an artifact. "
"A published name is fetched on first use and cached. "
"REQUIRED -- a silently chosen rotation makes two matrices "
"look comparable when they are not."),
winsorize: str = typer.Option("features", "--winsorize",
help="features (clamp raw features, then rotate) | pcs (rotate, "
"then clamp PC scores) | none. Whatever is clamped is "
"reported in vsig:qc:-:winsor_frac -- never silently."),
winsor_p: Optional[float] = typer.Option(None, "--winsor-p",
help="Which stored percentile to clamp at: 0.01 or "
"0.05. Default: the one the corpus was fitted "