update PCA

scverse · Nov 26, 2024 · 3e24c96 · 3e24c96
1 parent 9df9037
commit 3e24c96
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/src/rapids_singlecell/preprocessing/_scrublet/pipeline.py b/src/rapids_singlecell/preprocessing/_scrublet/pipeline.py
@@ -4,10 +4,9 @@
 
 import cupy as cp
 import numpy as np
-from cupyx import cusparse
 from cupyx.scipy import sparse
 
-from rapids_singlecell.preprocessing._utils import _get_mean_var
+from rapids_singlecell.preprocessing._utils import _get_mean_var, _sparse_to_dense
 
 from .sparse_utils import sparse_multiply, sparse_zscore
 
@@ -60,10 +59,10 @@ def truncated_svd(
 
     self._counts_obs_norm = self._counts_obs_norm.astype(cp.float32)
     self._counts_sim_norm = self._counts_sim_norm.astype(cp.float32)
-    X_obs = cusparse.sparseToDense(self._counts_obs_norm)
+    X_obs = _sparse_to_dense(self._counts_obs_norm)
     svd = TruncatedSVD(n_components=n_prin_comps, random_state=random_state).fit(X_obs)
     X_obs = svd.transform(X_obs)
-    X_sim = svd.transform(cusparse.sparseToDense(self._counts_sim_norm))
+    X_sim = svd.transform(_sparse_to_dense(self._counts_sim_norm))
     self.set_manifold(X_obs, X_sim)
 
 
@@ -80,10 +79,11 @@ def pca(
 
     self._counts_obs_norm = self._counts_obs_norm.astype(cp.float32)
     self._counts_sim_norm = self._counts_sim_norm.astype(cp.float32)
-    X_obs = cusparse.sparseToDense(self._counts_obs_norm)
-    pca = PCA(n_components=n_prin_comps, random_state=random_state).fit(X_obs)
-    X_obs = pca.transform(X_obs)
-    X_sim = pca.transform(cusparse.sparseToDense(self._counts_sim_norm))
+    pca = PCA(n_components=n_prin_comps, random_state=random_state).fit(
+        self._counts_obs_norm
+    )
+    X_obs = pca.transform(self._counts_obs_norm)
+    X_sim = pca.transform(self._counts_sim_norm)
     self.set_manifold(X_obs, X_sim)