grassp.tl.calinski_habarasz_score#

calinski_habarasz_score(data, gt_col, use_rep='X_umap', key_added='ch_score', class_balance=False, inplace=True, seed=42)[source]#

Calculate Calinski-Harabasz score for clustered data.

Parameters:

data AnnData

Annotated data matrix.

gt_col str

Column name in data.obs containing cluster labels.

use_rep str, optional

Key for representation in data.obsm to use for score calculation. Defaults to ‘X_umap’.

key_added str, optional

Key under which to add the score. Defaults to ‘ch_score’.

inplace bool, optional

If True, store results in data, else return score. Defaults to True.

Return type:

None | float

Returns:

None or float If inplace=True, returns None and stores result in data. If inplace=False, returns the Calinski-Harabasz score.