diff --git a/scib/metrics/metrics.py b/scib/metrics/metrics.py index 8ede6ac3..98731c0f 100755 --- a/scib/metrics/metrics.py +++ b/scib/metrics/metrics.py @@ -4,7 +4,7 @@ from ..utils import check_adata, check_batch from .ari import ari from .cell_cycle import cell_cycle -from .clustering import opt_louvain +from .clustering import cluster_optimal_resolution from .graph_connectivity import graph_connectivity from .highly_variable_genes import hvg_overlap from .isolated_labels import isolated_labels @@ -290,16 +290,15 @@ def metrics( # clustering if nmi_ or ari_: - res_max, nmi_max, nmi_all = opt_louvain( + res_max, nmi_max, nmi_all = cluster_optimal_resolution( adata_int, label_key=label_key, cluster_key=cluster_key, + metric=nmi, use_rep=embed, - function=nmi, - plot=False, - verbose=verbose, - inplace=True, force=True, + verbose=verbose, + return_all=True, ) if cluster_nmi is not None: nmi_all.to_csv(cluster_nmi, header=False)