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muon.pl.embedding

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muon.pl.embedding#

muon.pl.embedding(data: AnnData | MuData, basis: str, color: str | Sequence[str] | None = None, use_raw: bool | None = None, layer: str | None = None, **kwargs)#

Scatter plot for .obs

Produce a scatter plot in the define basis, which can also be a basis inside any modality, e.g. "rna:X_pca".

See scanpy.pl.embedding() for details.

Parameters:

  • data (Union[AnnData, MuData]) – MuData or AnnData object

  • basis (str) – Name of the obsm basis to use

  • color (Optional[Union[str, Sequence[str]]], optional (default: None)) – Keys for variables or annotations of observations (.obs columns). Can be from any modality.

  • use_raw (Optional[bool], optional (default: None)) – Use .raw attribute of the modality where a feature (from color) is derived from. If None, defaults to True if .raw is present and a valid layer is not provided.

  • layer (Optional[str], optional (default: None)) – Name of the layer in the modality where a feature (from color) is derived from. No layer is used by default. If a valid layer is provided, this takes precedence over use_raw=True.

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