liana.multi.adata_to_views

liana.multi.adata_to_views(adata: AnnData, groupby: str, sample_key: str, obs_keys: list | None = None, view_sep: str = ':', min_count: int = 10, min_total_count: int = 15, large_n: int = 10, min_prop: float = 0.1, keep_stats: bool = False, verbose: bool = False, **kwargs)

Converts an AnnData object to a MuData object with views that represent an aggregate for each entity in adata.obs[groupby].

Parameters:

adata

Annotated data object.

groupby

Key to be used for grouping.

sample_key

key in adata.obs to use for grouping by sample or context.

obs_keys:

Column names in adata.obs to merge with the MuData object

view_sep:

Separator to use when assigning adata.var_names to views

min_count:

Minimum number of counts per gene per sample to be included in the pseudobulk.

min_total_count:

Minimum number of counts per sample to be included in the pseudobulk.

large_n:

Number of samples per group that is considered to be “large”.

min_prop:

Minimum proportion of samples that must have a count for a gene to be included in the pseudobulk.

keep_stats:

If True, keep the pseudobulk statistics in mdata.uns[‘psbulk_stats’]. Default is False.

verbose

Verbosity flag.

**kwargs

Keyword arguments used to aggregate the values per cell into views. See dc.filter_by_expr for more details.

Returns:

Returns a MuData object with views that represent an aggregate for each entity in adata.obs[groupby].