mudata.acc.ModAcc

class mudata.acc.ModAcc(ref_class=<class 'anndata.acc.AdRef'>, *, layer_cls=<class 'mudata.acc.ModLayerAcc'>, meta_cls=<class 'mudata.acc.ModMetaAcc'>, multi_cls=<class 'mudata.acc.ModMultiAcc'>, graph_cls=<class 'mudata.acc.ModGraphAcc'>, mod)

Bases: AdAcc

Accessor to create AdRefs (A) for modalities (mod).

Attributes

ATTRS: ClassVar = frozenset({'layers', 'obs', 'obsm', 'obsp', 'var', 'varm', 'varp'})

mod: str

Modality this accessor refers to.

X: LayerAcc[AdRef[Hashable, MuData | AnnData]]

Access data matrix (shortcut for A.layers[None]).

>>> A.X[:, :]
>>> A.X["cell-1", :]
>>> A.X[:, "gene-5"]

layers: LayerMapAcc[AdRef[Hashable, MuData | AnnData]]

Access complete layers or 1D vectors across observations or variables.

>>> A.layers["counts"][:, :]
>>> A.layers["counts"]["cell-1", :]
>>> A.layers["counts"][:, "gene-5"]

obs: MetaAcc[AdRef[Hashable, MuData | AnnData]]

Access 1D arrays along observations.

>>> A.obs["cell-type"]
>>> A.obs.index

var: MetaAcc[AdRef[Hashable, MuData | AnnData]]

Access 1D arrays along variables.

>>> A.var["symbols"]
>>> A.obs.index

obsm: MultiMapAcc[AdRef[Hashable, MuData | AnnData]]

Access 1D vectors along observations.

>>> A.obsm["pca"][:, 0].idx
0

varm: MultiMapAcc[AdRef[Hashable, MuData | AnnData]]

Access 1D vectors along variables.

>>> A.varm["loadings"][:, 0].idx
0

obsp: GraphMapAcc[AdRef[Hashable, MuData | AnnData]]

Access 1D or 2D vectors along observations.

>>> A.layers["x"][:, :].dims
('obs', 'obs')
>>> A.layers["x"]["cell-1", :].dims
{'obs'}
>>> A.layers["x"][:, "cell-1"].dims
{'obs'}

varp: GraphMapAcc[AdRef[Hashable, MuData | AnnData]]

Access 1D or 2D vectors along variables.

>>> A.layers["x"][:, :].dims
('var', 'var')
>>> A.layers["x"]["gene-1", :].dims
{'var'}
>>> A.layers["x"][:, "gene-1"].dims
{'var'}

Methods

get(mdata)

Get the referenced modality from the MuData object.

Return type:

AnnData

isin(mdata)

Check if the referenced modality is in the MuData object.

Return type:

bool

to_json(ref)

Serialize AdRef to a JSON-compatible list.

Return type:

list[str | int | None]