cellxgene_census.get_anndata

cellxgene_census.get_anndata(census: Collection, organism: str, measurement_name: str = 'RNA', X_name: str = 'raw', X_layers: Sequence[str] | None = (), obsm_layers: Sequence[str] | None = (), obsp_layers: Sequence[str] | None = (), varm_layers: Sequence[str] | None = (), varp_layers: Sequence[str] | None = (), obs_value_filter: str | None = None, obs_coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = None, var_value_filter: str | None = None, var_coords: None | bytes | Slice[bytes] | Sequence[bytes] | float | Slice[float] | Sequence[float] | int | Slice[int] | Sequence[int] | slice | Slice[slice] | Sequence[slice] | str | Slice[str] | Sequence[str] | datetime64 | Slice[datetime64] | Sequence[datetime64] | TimestampType | Slice[TimestampType] | Sequence[TimestampType] | Array | ChunkedArray | ndarray[Any, dtype[integer]] | ndarray[Any, dtype[datetime64]] = None, column_names: AxisColumnNames | None = None, obs_embeddings: Sequence[str] | None = (), var_embeddings: Sequence[str] | None = ()) → AnnData

Convenience wrapper around tiledbsoma.Experiment query, to build and execute a query, and return it as an anndata.AnnData object.

Parameters:

  • census – The census object, usually returned by open_soma().

  • organism – The organism to query, usually one of "Homo sapiens or "Mus musculus".

  • measurement_name – The measurement object to query. Defaults to "RNA".

  • X_name – The X layer to query. Defaults to "raw".

  • X_layers – Additional layers to add to anndata.AnnData.layers.

  • obs_value_filter – Value filter for the obs metadata. Value is a filter query written in the SOMA value_filter syntax.

  • obs_coords – Coordinates for the obs axis, which is indexed by the soma_joinid value. May be an int, a list of int, or a slice. The default, None, selects all.

  • var_value_filter – Value filter for the var metadata. Value is a filter query written in the SOMA value_filter syntax.

  • var_coords – Coordinates for the var axis, which is indexed by the soma_joinid value. May be an int, a list of int, or a slice. The default, None, selects all.

  • column_names – Columns to fetch for obs and var dataframes.

  • obsm_layers – Additional obsm layers to read and return in the obsm slot.

  • obsp_layers – Additional obsp layers to read and return in the obsp slot.

  • varm_layers – Additional varm layers to read and return in the varm slot.

  • varp_layers – Additional varp layers to read and return in the varp slot.

  • obs_embeddings – Additional embeddings to be returned as part of the obsm slot. Use get_all_available_embeddings() to retrieve available embeddings for this Census version and organism.

  • var_embeddings – Additional embeddings to be returned as part of the varm slot. Use get_all_available_embeddings() to retrieve available embeddings for this Census version and organism.

Returns:

An anndata.AnnData object containing the census slice.

Lifecycle

experimental

Examples

>>> get_anndata(census, "Mus musculus", obs_value_filter="tissue_general in ['brain', 'lung']")

>>> get_anndata(census, "Homo sapiens", column_names={"obs": ["tissue"]})

>>> get_anndata(census, "Homo sapiens", obs_coords=slice(0, 1000))