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_