do PCA on imputed dimensions even if data was not sparse

KrishnaswamyLab · Jul 5, 2018 · 79f6d93 · 79f6d93
1 parent e5d53aa
commit 79f6d93
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/python/magic/magic.py b/python/magic/magic.py
@@ -490,8 +490,7 @@ def transform(self, X=None, genes=None, t_max=20,
 
         # return selected genes
         if isinstance(genes, str) and genes == "pca_only":
-            if sparse.issparse(self.graph.data):
-                X_magic = PCA().fit_transform(X_magic)
+            X_magic = PCA().fit_transform(X_magic)
             genes = ["PC{}".format(i + 1) for i in range(X_magic.shape[1])]
         else:
             X_magic = graph.inverse_transform(X_magic, columns=genes)