diff --git a/pertpy/tools/_milo.py b/pertpy/tools/_milo.py index 8b3c59e9..494ef2fa 100644 --- a/pertpy/tools/_milo.py +++ b/pertpy/tools/_milo.py @@ -73,8 +73,8 @@ def make_nhoods( Args: data: AnnData object with KNN graph defined in `obsp` or MuData object with a modality with KNN graph defined in `obsp` neighbors_key: The key in `adata.obsp` or `mdata[feature_key].obsp` to use as KNN graph. - If not specified, `make_nhoods` looks .obsp[‘connectivities’] for connectivities (default storage places for `scanpy.pp.neighbors`). - If specified, it looks at .obsp[.uns[neighbors_key][‘connectivities_key’]] for connectivities. + If not specified, `make_nhoods` looks at `.obsp['connectivities']` for connectivities. + If specified, looks at `.obsp[neighbors_key + '_connectivities']` for connectivities. feature_key: If input data is MuData, specify key to cell-level AnnData object. prop: Fraction of cells to sample for neighbourhood index search. seed: Random seed for cell sampling. @@ -540,7 +540,9 @@ def annotate_nhoods( sample_adata.var["nhood_annotation_frac"] = anno_frac_dataframe.max(axis=1) def annotate_nhoods_continuous(self, mdata: MuData, anno_col: str, feature_key: str | None = "rna"): - """Assigns a continuous value to neighbourhoods, based on mean cell level covariate stored in adata.obs. This can be useful to correlate DA log-foldChanges with continuous covariates such as pseudotime, gene expression scores etc... + """Assigns a continuous value to neighbourhoods, based on mean cell level covariate stored in adata.obs. + + This can be useful to correlate DA log-foldChanges with continuous covariates such as pseudotime, gene expression scores etc... Args: mdata: MuData object