cellxgene_census.get_obs

cellxgene_census.get_obs(census: Collection, organism: str, *, value_filter: str | None = None, 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]] = slice(None, None, None), column_names: Sequence[str] | None = None, modality: str = 'census_data') → DataFrame

Get the observation metadata for a query on the census.

Parameters:

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

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

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

  • 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.

  • column_names – Columns to fetch.

  • modality – Which modality to query, can be one of "census_data" or "census_spatial_sequencing". Defaults to "census_data".

Returns:

A pandas.DataFrame object containing metadata for the queried slice.