monkeybread.calc.neighborhood_profile

monkeybread.calc.neighborhood_profile(adata, groupby, basis='X_spatial', subset_output_features=None, subset_cells_by_group=None, radius=None, n_neighbors=None, normalize_counts=True, standard_scale=True, clip_min=None, clip_max=None)

Calculates a neighborhood profile for each cell.

The resulting AnnData object will have the same index corresponding to rows/cells, but a new index corresponding to columns, one column for each category in adata.obs[groupby]. Instead of a gene expression profile, each column corresponds to the proportion of cells in the surrounding radius that belong to the respective category.

Parameters:

  • adata (AnnData) – Annotated data matrix.

  • groupby (str) – A categorical column in obs to use for neighborhood profile calculations.

  • basis (Optional[str] (default: 'X_spatial')) – Coordinates in adata.obsm[{basis}] to use. Defaults to spatial.

  • subset_output_features (Optional[Sequence[str]] (default: None)) – A list of groups from adata.obs[groupby] to include in the resulting adata.var_names. Will not affect the calculations themselves, only which results are provided.

  • subset_cells_by_group (Optional[Sequence[str]] (default: None)) – A list of groups in adata.obs[groupby] to restrict the resulting AnnData object to. Only cells in those groups will be included in the resulting adata.obs_names.

  • radius (Optional[float] (default: None)) – Radius in coordinate space to include nearby cells for neighborhood profile calculation.

  • n_neighbors (Optional[int] (default: None)) – Number of neighbors to consider for the neighborhood profile calculations.

  • normalize_counts (Optional[bool] (default: True)) – Normalize neighborhood counts to proportions instead of raw counts. Note, if subset_output_features is provided and normalize_counts = True, the normalization step will be performed before removing groups, so proportions will not sum to 1.

  • standard_scale (Optional[bool] (default: True)) – Compute z-score of neighborhood values by subtracting the mean and dividing by the standard deviation.

  • clip_min (Optional[float] (default: None)) – Clip values that are less than clip_min to clip_min

  • clip_max (Optional[float] (default: None)) – Clip values that are greater than clip_max to clip_max

Return type:

AnnData

Returns:

: A new AnnData object where columns now correspond to neighborhood profile proportions. All .obs columns will be carried over from the provided AnnData object, and they will share an index.