anndata.acc.AdAcc

class anndata.acc.AdAcc(*, ref_class)

Bases: LayerAcc

Accessor to create AdRefs (A).

See examples below and in anndata.acc.

Attributes

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

k: None = None

A[:, :] is equivalent to A.layers[None][:, :].

layers: LayerMapAcc[AdRef[Hashable]]

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]]

Access 1D arrays along observations.

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

var: MetaAcc[AdRef[Hashable]]

Access 1D arrays along variables.

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

obsm: MultiMapAcc[AdRef[Hashable]]

Access 1D vectors along observations.

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

varm: MultiMapAcc[AdRef[Hashable]]

Access 1D vectors along variables.

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

obsp: GraphMapAcc[AdRef[Hashable]]

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]]

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'}

ref_class: type[AdRef[Hashable]]

Methods

from_json(data)

Create AdRef from a JSON sequence.

Schema: acc-schema-v1.json

Raises:

ValueError – If parsing fails.

Return type:

AdRef[Hashable]

resolve(spec, *, strict=True)

Create AdRef from a simplified string.

Return type:

AdRef[Hashable] | None

Examples

>>> A.resolve("X[:,:]")
A[:, :]
>>> A.resolve("layers.y[c,:]")
A.layers['y']['c', :]
>>> A.resolve("layers.y[:,g]")
A.layers['y'][:, 'g']
>>> A.resolve("obs.a")
A.obs['a']
>>> A.resolve("var.b")
A.var['b']
>>> A.resolve("obsm.c.0")
A.obsm['c'][:, 0]
>>> A.resolve("varm.d.1")
A.varm['d'][:, 1]
>>> A.resolve("obsp.g[c1,:]")
A.obsp['g']['c1', :]
>>> A.resolve("obsp.g[:,c2]")
A.obsp['g'][:, 'c2']

to_json(ref)

Serialize AdRef to a JSON-compatible list.

Schema: acc-schema-v1.json

Return type:

list[str | int | None]