mudata.acc.MuAcc

class mudata.acc.MuAcc(ref_class=<class 'anndata.acc.AdRef'>, layer_cls=<class 'anndata.acc.LayerAcc'>, meta_cls=<class 'anndata.acc.MetaAcc'>, multi_cls=<class 'anndata.acc.MultiAcc'>, graph_cls=<class 'anndata.acc.GraphAcc'>, mod_cls=<class 'mudata.acc.ModAcc'>)

Bases: AdAcc

Accessor to create AdRefs (A).

Attributes

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

mod: MultiModAcc[AdRef[Hashable, MuData]]

Access modalities.

obsmap: ModMapAcc[AdRef[Hashable, MuData]]

Access mappings of observation indices in the MuData to indices in individual modalities.

varmap: ModMapAcc[AdRef[Hashable, MuData]]

Access mappings of variable indices in the MuData to indices in individual modalities.

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

from_json(data)

Create a AdRef from a JSON sequence.

Schema: acc-schema-v1.json

Return type:

TypeVar(R, bound= AdRef)

resolve(spec, *, strict=True)

Create AdRef from a simplified string.

Return type:

TypeVar(R, bound= AdRef) | None

to_json(ref)

Serialize AdRef to a JSON-compatible list.

Schema: acc-schema-v1.json

Return type:

list[str | int | None]