From 21f17ab539cc37a289a95e8915323c0cd0c75100 Mon Sep 17 00:00:00 2001
From: Connor Thompson <connor.thompson@elembio.com>
Date: Fri, 7 Feb 2025 20:54:02 -0800
Subject: [PATCH] add scale

---
 src/python/cytoprofiling/cell_cycle_assignment.py | 4 ++++
 1 file changed, 4 insertions(+)

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