implement fixed bandwidth mnn

KrishnaswamyLab · Sep 18, 2018 · 5f2bd79 · 5f2bd79
1 parent 40d41da
commit 5f2bd79
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/graphtools/graphs.py b/graphtools/graphs.py
@@ -904,6 +904,7 @@ def __init__(self, data, sample_idx,
                  knn=5, beta=1, n_pca=None,
                  adaptive_k='sqrt',
                  decay=None,
+                 bandwidth=None,
                  distance='euclidean',
                  thresh=1e-4,
                  n_jobs=1,
@@ -916,6 +917,7 @@ def __init__(self, data, sample_idx,
         self.knn = knn
         self.decay = decay
         self.distance = distance
+        self.bandwidth = bandwidth
         self.thresh = thresh
         self.n_jobs = n_jobs
         self.weighted_knn = self._weight_knn()
@@ -1043,7 +1045,7 @@ def set_params(self, **params):
                 "Cannot update adaptive_k. Please create a new graph")
 
         # knn arguments
-        knn_kernel_args = ['knn', 'decay', 'distance', 'thresh']
+        knn_kernel_args = ['knn', 'decay', 'distance', 'thresh', 'bandwidth']
         knn_other_args = ['n_jobs', 'random_state', 'verbose']
         for arg in knn_kernel_args:
             if arg in params and params[arg] != getattr(self, arg):
@@ -1085,6 +1087,7 @@ def build_kernel(self):
             graph = Graph(data, n_pca=None,
                           knn=self.weighted_knn[i],
                           decay=self.decay,
+                          bandwidth=self.bandwidth,
                           distance=self.distance,
                           thresh=self.thresh,
                           verbose=self.verbose,

diff --git a/test/test_mnn.py b/test/test_mnn.py
@@ -239,6 +239,7 @@ def test_set_params():
         'adaptive_k': 'sqrt',
         'knn': 3,
         'decay': 10,
+        'bandwidth': None,
         'distance': 'euclidean',
         'thresh': 1e-4,
         'n_jobs': 1