anndata.AnnData.__getitem__

AnnData.__getitem__(index)

Slice AnnData object or retrieve an array using an accessor.

Overloads:

• index (MetaAcc) → DataFrame | Dataset2D

• index (LayerAcc | MultiAcc | GraphAcc) → AlignedArray

• index (AdRef) → InMemoryArray | ExtensionArray | Variable

• index (Index) → AnnData

Parameters:

index Index | AdRef | RefAcc | MapAcc

One of

• an Index along observations and variables, returning a view of the sliced object, e.g. adata[:, ["gene-1", "gene-2"]];

• an AdRef, returning the referenced 1D or 2D array, e.g. adata[A.obs["cell-type"]] or adata[A.layers["counts"][:, "gene-1"]];

• a reference accessor, returning the full element (see get()), e.g. adata[A.obs] or adata[A.obsm["pca"]].

Mapping accessors like A.obsm raise an IndexError, as they don’t refer to an array.