scib.metrics.metrics_all

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

All metrics

Biological conservation:

• HVG overlap hvg_overlap()

• Cell type ASW silhouette()

• Isolated label ASW isolated_labels()

• Isolated label F1 isolated_labels()

• NMI cluster/label nmi()

• ARI cluster/label ari()

• Cell cycle conservation cell_cycle()

• cLISI (cell type Local Inverse Simpson’s Index) clisi_graph()

• Trajectory conservation trajectory_conservation()

Batch correction:

• Graph connectivity graph_connectivity()

• Batch ASW silhouette_batch()

• Principal component regression pcr_comparison()

• kBET (k-nearest neighbour batch effect test) kBET()

• iLISI (integration Local Inverse Simpson’s Index) ilisi_graph()

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

  • cluster_key

  • cluster_nmi

  • nmi_method

  • nmi_dir

  • si_metric

  • organism

  • n_isolated

  • subsample

  • type_