diff --git a/src/python/cytoprofiling/cell_cycle_assignment.py b/src/python/cytoprofiling/cell_cycle_assignment.py index acc7cca..1f02aa9 100644 --- a/src/python/cytoprofiling/cell_cycle_assignment.py +++ b/src/python/cytoprofiling/cell_cycle_assignment.py @@ -43,6 +43,8 @@ def cluster_cells(adata, targets="all", do_log=True, do_norm=True, resolution=1) if do_log: sc.pp.log1p(adata) + sc.pp.scale(adata) + sc.tl.pca(adata) sc.pp.neighbors(adata) @@ -73,6 +75,8 @@ def assign_cell_phase(adata, s_genes=S_GENES, g2m_genes=G2M_GENES, do_log=True, if do_log: sc.pp.log1p(adata) + sc.pp.scale(adata) + sc.tl.score_genes_cell_cycle(adata, s_genes=s_genes, g2m_genes=g2m_genes) return adata \ No newline at end of file