liana.multi.adata_to_views

liana.multi.adata_to_views(adata, groupby, sample_key, obs_keys=None, view_sep=':', keep_stats=False, verbose=False, psbulk_kwargs=None, filter_samples_kwargs=None, filter_by_expr_kwargs=None, filter_by_prop_kwargs=None)

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

Parameters:

• adata (AnnData) – Annotated data object.

• groupby (str) – Key to be used for grouping.

• sample_key (str) – key in adata.obs to use for grouping by sample or context.

• obs_keys (list[str] (default: None)) – Column names in adata.obs to merge with the MuData object

• view_sep (str (default: ':')) – Separator to use when assigning adata.var_names to views

• keep_stats (bool (default: False)) – If True, keep the pseudobulk statistics in mdata.uns['psbulk_stats']. Default is False.

• verbose (bool (default: False)) – Verbosity flag.

• psbulk_kwargs (dict (default: None)) – Arguments to pass to dc.pp.pseudobulk for pseudobulking. See decoupler documentation for more details.

• filter_samples_kwargs (dict (default: None)) – Arguments to pass to dc.pp.filter_samples for filtering samples. See decoupler documentation for more details. If None, won’t filter.

• filter_by_expr_kwargs (dict (default: None)) – Optional mapping of arguments to pass to dc.pp.filter_by_expr for gene filtering by expression. If None, won’t filter.

• filter_by_prop_kwargs (dict (default: None)) – Optional mapping of arguments to pass to dc.pp.filter_by_prop for gene filtering by proportion of cells that express the gene. If None, won’t filter.

Return type:

MuData

Returns:

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