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[FIX] heatmap: Do not crash on all zero column #2916

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Feb 23, 2018
Merged

[FIX] heatmap: Do not crash on all zero column #2916

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2 changes: 2 additions & 0 deletions Orange/widgets/visualize/owheatmap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -822,6 +822,8 @@ def cluster_columns(self, data, parts):
if need_dist:
data = Orange.distance._preprocess(data)
matrix = Orange.distance.PearsonR(data, axis=0)
# nan values break clustering below
matrix = np.nan_to_num(matrix)

if cluster is None:
cluster = hierarchical.dist_matrix_clustering(matrix)
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11 changes: 10 additions & 1 deletion Orange/widgets/visualize/tests/test_owheatmap.py
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Expand Up @@ -19,7 +19,7 @@ def setUpClass(cls):
cls.signal_data = cls.data

def setUp(self):
self.widget = self.create_widget(OWHeatMap)
self.widget = self.create_widget(OWHeatMap) # type: OWHeatMap

def test_input_data(self):
"""Check widget's data with data on the input"""
Expand Down Expand Up @@ -117,3 +117,12 @@ def test_data_column_nans(self):
table = datasets.data_one_column_nans()
self.widget.controls.merge_kmeans.setChecked(True)
self.send_signal(self.widget.Inputs.data, table)

def test_cluster_column_on_all_zero_column(self):
# Pearson distance used for clustering of columns does not
# handle all zero columns well
iris = Table("iris")
iris[:, 0] = 0

self.widget.col_clustering = True
self.widget.set_dataset(iris)