scib.metrics.metrics_fast

scib.metrics.metrics_fast(adata, adata_int, batch_key, label_key, **kwargs)

Only metrics with minimal preprocessing and runtime

Biological conservation:

• HVG overlap hvg_overlap()

• Cell type ASW silhouette()

• Isolated label ASW isolated_labels()

Batch correction:

• Graph connectivity graph_connectivity()

• Batch ASW silhouette_batch()

• Principal component regression pcr_comparison()

Parameters:

• adata – unintegrated, preprocessed anndata object

• adata_int – integrated anndata object

• batch_key – name of batch column in adata.obs and adata_int.obs

• label_key – name of biological label (cell type) column in adata.obs and adata_int.obs

• kwargs –

  Parameters to pass on to metrics() function:

  • embed

  • si_metric

  • n_isolated