scib_metrics.benchmark.BatchCorrection

class scib_metrics.benchmark.BatchCorrection(silhouette_batch=True, ilisi_knn=True, kbet_per_label=True, graph_connectivity=True, pcr_comparison=True)

Specification of which batch correction metrics to run in the pipeline.

Metrics can be included using a boolean flag. Custom keyword args can be used by passing a dictionary here. Keyword args should not set data-related parameters, such as X or labels.

Attributes table

graph_connectivity
ilisi_knn
kbet_per_label
pcr_comparison
silhouette_batch

Methods table

Attributes

BatchCorrection.graph_connectivity: Union[bool, dict[str, Any]] = True

BatchCorrection.ilisi_knn: Union[bool, dict[str, Any]] = True

BatchCorrection.kbet_per_label: Union[bool, dict[str, Any]] = True

BatchCorrection.pcr_comparison: Union[bool, dict[str, Any]] = True

BatchCorrection.silhouette_batch: Union[bool, dict[str, Any]] = True

Methods