Add layer argument to score_genes() (#2921)

Co-authored-by: Isaac Virshup <[email protected]>
Co-authored-by: Philipp A <[email protected]>

Author: 3 people

docs/release-notes/1.11.0.md

@@ -3,6 +3,8 @@
 ```{rubric} Features
 ```
 
+* Add layer argument to {func}`scanpy.tl.score_genes` and {func}`scanpy.tl.score_genes_cell_cycle` {pr}`2921` {smaller}`L Zappia`
+
 ```{rubric} Docs
 ```
 

scanpy/tests/test_score_genes.py

@@ -239,6 +239,23 @@ def test_use_raw_None():
     sc.tl.score_genes(adata, adata_raw.var_names[:3], use_raw=None)
 
 
+def test_layer():
+    adata = _create_adata(100, 1000, p_zero=0, p_nan=0)
+
+    sc.pp.normalize_per_cell(adata, counts_per_cell_after=1e4)
+    sc.pp.log1p(adata)
+
+    # score X
+    gene_set = adata.var_names[:10]
+    sc.tl.score_genes(adata, gene_set, score_name="X_score")
+    # score layer (`del` makes sure it actually uses the layer)
+    adata.layers["test"] = adata.X.copy()
+    del adata.X
+    sc.tl.score_genes(adata, gene_set, score_name="test_score", layer="test")
+
+    np.testing.assert_array_equal(adata.obs["X_score"], adata.obs["test_score"])
+
+
 @pytest.mark.parametrize("gene_pool", [[], ["foo", "bar"]])
 def test_invalid_gene_pool(gene_pool):
     adata = _create_adata(100, 1000, p_zero=0, p_nan=0)

scanpy/tools/_score_genes.py

@@ -66,6 +66,7 @@ def score_genes(
     random_state: AnyRandom = 0,
     copy: bool = False,
     use_raw: bool | None = None,
+    layer: str | None = None,
 ) -> AnnData | None:
     """\
     Score a set of genes :cite:p:`Satija2015`.
@@ -101,6 +102,8 @@ def score_genes(
 
         .. versionchanged:: 1.4.5
            Default value changed from `False` to `None`.
+    layer
+        Key from `adata.layers` whose value will be used to perform tests on.
 
     Returns
     -------
@@ -145,7 +148,7 @@ def score_genes(
     # interval of expression.
 
     def get_subset(genes: pd.Index[str]):
-        x = _get_obs_rep(adata, use_raw=use_raw)
+        x = _get_obs_rep(adata, use_raw=use_raw, layer=layer)
         if len(genes) == len(var_names):
             return x
         idx = var_names.get_indexer(genes)