diff --git a/tests/test_preprocessing.py b/tests/test_preprocessing.py index 7be5ff9..36a109b 100644 --- a/tests/test_preprocessing.py +++ b/tests/test_preprocessing.py @@ -61,3 +61,36 @@ def test_atac(adata_CP, tmp_path): fig_ncol=5, save_fig=True, fig_name='plot_pcs_features.png') + + +def test_genescores(adata_CP): + si.pp.filter_peaks(adata_CP, min_n_cells=5) + si.pp.cal_qc_atac(adata_CP) + si.pp.filter_cells_atac(adata_CP, min_n_peaks=5) + si.pp.pca(adata_CP, n_components=30) + si.pp.select_pcs(adata_CP, n_pcs=10) + si.pp.select_pcs_features(adata_CP) + + adata_CG_atac = si.tl.gene_scores(adata_CP, + genome='hg19', + use_gene_weigt=True, + use_top_pcs=True) + print(adata_CG_atac) + + +def test_integration(adata_CG): + si.pp.filter_genes(adata_CG, min_n_cells=3) + si.pp.cal_qc_rna(adata_CG) + si.pp.filter_cells_rna(adata_CG, min_n_genes=2) + si.pp.normalize(adata_CG, method='lib_size') + si.pp.log_transform(adata_CG) + si.pp.select_variable_genes(adata_CG, n_top_genes=2000) + adata_C1C2 = si.tl.infer_edges( + adata_CG, adata_CG, n_components=20, k=20) + si.pl.node_similarity(adata_C1C2, + cutoff=0.5, + save_fig=True) + si.pl.svd_nodes(adata_C1C2, + cutoff=0.5, + save_fig=True) + si.tl.trim_edges(adata_C1C2, cutoff=0.5)