fix bug when executing pca on raw counts

src/nichepca/workflows/_nichepca.py

@@ -161,6 +161,9 @@ def nichepca(
                 suffix="",
             )
         elif fn == "pca":
+            # pca requires float dtype
+            if "float" not in str(ad_tmp.X.dtype):
+                ad_tmp.X = ad_tmp.X.astype(np.float32)
             sc.tl.pca(ad_tmp, n_comps=n_comps)
             # run harmony if sample_key is provided and obs key is None
             if sample_key is not None and obs_key is None and allow_harmony:

tests/test_workflows.py

@@ -68,6 +68,22 @@ def test_nichepca_single():
 
     assert np.all(X_npca_0 == X_npca_1)
 
+    # test with pca on raw counts
+    pipeline = ("pca", "agg")
+
+    adata = generate_dummy_adata()
+    npc.wf.nichepca(adata, knn=5, pipeline=pipeline)
+    X_npca_0 = adata.obsm["X_npca"]
+
+    adata = generate_dummy_adata()
+    adata.X = adata.X.astype(np.float32)
+    sc.pp.pca(adata, n_comps=30)
+    npc.gc.knn_graph(adata, knn=5)
+    npc.ne.aggregate(adata, obsm_key="X_pca")
+    X_npca_1 = adata.obsm["X_pca_agg"]
+
+    assert np.all(X_npca_0 == X_npca_1)
+
 
 def test_nichepca_multi_sample():
     adata_1 = generate_dummy_adata()