API reference

metalsinglecell mirrors the scanpy / squidpy namespaces: pp (preprocessing), tl (tools), gr (spatial graph). Import as:

import metalsinglecell as msc

Preprocessing — msc.pp

calculate_qc_metrics	Per-cell/per-gene QC metrics (sc.pp.calculate_qc_metrics).
filter_cells	Filter cells (sc.pp.filter_cells); subsets adata in place.
filter_genes	Filter genes (sc.pp.filter_genes); subsets adata in place.
normalize_total	Normalize counts per cell (sc.pp.normalize_total).
log1p	log(1 + x) (sc.pp.log1p); records adata.uns['log1p'].
normalize_pearson_residuals	Analytic Pearson residuals (sc.experimental.pp.normalize_pearson_residuals).
highly_variable_genes	Highly variable genes (sc.pp.highly_variable_genes); writes adata.var columns.
scale	Z-score genes then clip (sc.pp.scale).
regress_out	Regress out covariates in adata.obs[keys] (sc.pp.regress_out).
pca	PCA (sc.pp.pca); writes obsm['X_pca'], varm['PCs'], uns['pca'].
neighbors	kNN graph (sc.pp.neighbors); writes obsp['distances']/['connectivities'], uns['neighbors'].
bbknn	Batch-balanced kNN (sc.external.pp.bbknn); writes obsp + uns['neighbors'].
harmony_integrate	Harmony batch integration (sc.external.pp.harmony_integrate); writes obsm[adjusted_basis].
scrublet	Doublet detection (sc.pp.scrublet); writes obs['doublet_score']/['predicted_doublet'].

Tools — msc.tl

leiden	Leiden clustering (sc.tl.leiden); writes adata.obs[key_added] (categorical).
louvain	Louvain clustering (sc.tl.louvain); writes adata.obs[key_added] (categorical).
kmeans	k-means on an embedding; writes adata.obs[key_added] (categorical).
umap	UMAP embedding (sc.tl.umap); writes adata.obsm['X_umap'].
tsne	t-SNE (sc.tl.tsne); writes adata.obsm['X_tsne'].
diffmap	Diffusion map (sc.tl.diffmap); writes obsm['X_diffmap'] + uns['diffmap_evals'].
draw_graph	Force-directed layout (sc.tl.draw_graph); writes obsm[f'X_draw_graph_{layout}'].
embedding_density	Per-cell density in an embedding (sc.tl.embedding_density); writes obs[f'{basis}_density'].
rank_genes_groups	Marker genes per group (sc.tl.rank_genes_groups); writes scanpy-format adata.uns[key_added].
score_genes	Gene-set score (sc.tl.score_genes); writes adata.obs[score_name].
score_genes_cell_cycle	S/G2M scores + phase (sc.tl.score_genes_cell_cycle); writes obs['S_score'/'G2M_score'/'phase'].

Spatial graph — msc.gr

spatial_neighbors	Spatial graph from coordinates (sq.gr.spatial_neighbors); writes obsp['spatial_*'].
spatial_autocorr	Moran's I / Geary's C per gene (sq.gr.spatial_autocorr); writes uns['moranI']/['gearyC'].
co_occurrence	Cluster co-occurrence vs distance (sq.gr.co_occurrence); writes uns[f'{cluster_key}_co_occurrence'].
ligrec	Ligand-receptor permutation test (sq.gr.ligrec); writes uns[key_added] (means/pvalues).
calculate_niche	Spatial niches from neighborhood composition (sq.gr.calculate_niche); writes obs[key_added].