cycombinepy.evaluate.scib_metrics

cycombinepy.evaluate.scib_metrics(adata, batch_key, label_key=None, embedding_key='X_pca', layer=None)

Run selected scib-metrics batch-correction metrics on an AnnData.

Computes a PCA on adata.X (or adata.layers[layer] if supplied) and evaluates batch-mixing metrics from scib_metrics. To compare uncorrected and corrected data, call it once for each representation and compare the returned dictionaries.

Returns a dict of scalar scores. Metrics that require a biological label are skipped if label_key is None.

Return type:

dict

Parameters:

• adata (AnnData)

• batch_key (str)

• label_key (str | None)

• embedding_key (str)

• layer (str | None)