scirpy.tl.alpha_diversity

scirpy.tl.alpha_diversity(adata, groupby, *, target_col='clone_id', inplace=True, key_added=None)

Computes the alpha diversity of clonotypes within a group.

Uses the Shannon Entropy as diversity measure. The Entrotpy gets normalized to group size.

Ignores NaN values.

Parameters

adata : AnnDataAnnData

Annotated data matrix

groupby : strstr

Column of obs by which the grouping will be performed.

target_col : strstr (default: 'clone_id')

Column on which to compute the alpha diversity

inplace : boolbool (default: True)

If True, add a column to obs. Otherwise return a DataFrame with the alpha diversities.

key_added : str | NoneOptional[str] (default: None)

Key under which the alpha diversity will be stored if inplace is True. Defaults to alpha_diversity_{target_col}.

Return type

DataFrameDataFrame

Returns

Depending on the value of inplace returns a DataFrame with the alpha diversity for each group or adds a column to adata.obs.