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Pass embed through to LISI scores in metrics() - #437
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clisi_graph and ilisi_graph default to use_rep='X_emb', so metrics() computed LISI scores on X_emb regardless of the embed argument (default 'X_pca'). Fixes theislab#429.
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Closing and reopening to retrigger CI. The earlier run was canceled while building the louvain wheel during dependency install, before any tests ran. |
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Fixes #429.
metrics()acceptsembed(default"X_pca") and forwards it to everyrepresentation-dependent score except LISI:
clisi_graphandilisi_graphwere called withoutuse_repand always fell back totheir own
"X_emb"default. Whenembedis anything other than"X_emb", including the documented default, the kNN for LISI isrebuilt on a different representation than the caller asked for.
Nothing warned.
Both calls now pass
use_rep=embed, matching howembedis alreadyforwarded to
cluster_optimal_resolution,silhouette,pc_comparison,isolated_labels,kBETandcell_cyclein the same function.The regression test builds a small AnnData carrying
X_customand noX_emb, then callsmetrics(embed="X_custom", clisi_=True, ilisi_=True).Before the fix it fails looking for
X_emb. Afterwards both LISI scoresare finite.
blackreports both files clean.AI-assisted (Devin).