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Use scib.cl.cluster_optimal_resolution in metrics wrapper #405

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merged 4 commits into from
Apr 17, 2024
Merged

Use scib.cl.cluster_optimal_resolution in metrics wrapper #405

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c409c2b
use new clustering function in metrics function
mumichae Apr 1, 2024
904d876
Merge branch 'main' into update_clustering_default
mumichae Apr 17, 2024
6830279
Merge branch 'main' into update_clustering_default
mumichae Apr 17, 2024
c75926f
Merge branch 'main' into update_clustering_default
mumichae Apr 17, 2024
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11 changes: 5 additions & 6 deletions scib/metrics/metrics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand Down
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