silence warning on traditionalgraph

KrishnaswamyLab · Jun 19, 2018 · d52327f · d52327f
1 parent 2f312c9
commit d52327f
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/graphtools/base.py b/graphtools/base.py
@@ -151,10 +151,6 @@ def _reduce_data(self):
             data = self.data
             if sparse.issparse(data):
                 data = data.toarray()
-            if data.shape[1] > 500:
-                warnings.warn("Building a graph on data of shape {} is "
-                              "expensive. Consider setting n_pca.".format(
-                                  data.shape), UserWarning)
             return data
 
     def get_params(self):

diff --git a/graphtools/graphs.py b/graphtools/graphs.py
@@ -59,7 +59,7 @@ class kNNGraph(DataGraph):
 
     def __init__(self, data, knn=5, decay=None,
                  distance='euclidean',
-                 thresh=1e-4, **kwargs):
+                 thresh=1e-4, n_pca=None, **kwargs):
         self.knn = knn
         self.decay = decay
         self.distance = distance
@@ -72,8 +72,12 @@ def __init__(self, data, knn=5, decay=None,
             warnings.warn("Cannot set knn ({k}) to be greater than "
                           "data.shape[0] ({n}). Setting knn={n}".format(
                               k=knn, n=data.shape[0]))
+        if n_pca is None and data.shape[1] > 500:
+            warnings.warn("Building a kNNGraph on data of shape {} is "
+                          "expensive. Consider setting n_pca.".format(
+                              data.shape), UserWarning)
 
-        super().__init__(data, **kwargs)
+        super().__init__(data, n_pca=n_pca, **kwargs)
 
     def get_params(self):
         """Get parameters from this object