scglue.data.get_metacells

scglue.data.get_metacells(*adatas, use_rep=None, n_meta=None, common=True, seed=0, agg_kws=None)

Aggregate datasets into metacells

Parameters:

• *adatas (AnnData) – Datasets to be correlated

• use_rep (typing.Optional[str]) – Data representation based on which to cluster meta-cells

• n_meta (typing.Optional[int]) – Number of metacells to use

• common (bool) – Whether to return only metacells common to all datasets

• seed (int) – Random seed for k-Means clustering

• agg_kws (typing.Optional[typing.List[typing.Optional[typing.Mapping[str, typing.Any]]]]) – Keyword arguments per dataset passed to aggregate_obs()

Return type:

typing.List[AnnData]

Returns:

adatas – A list of AnnData objects containing the metacells

Note

When a single dataset is provided, the metacells are clustered with the dataset itself. When multiple datasets are provided, the metacells are clustered jointly with all datasets.