diff --git a/Orange/widgets/visualize/owheatmap.py b/Orange/widgets/visualize/owheatmap.py
index 23036903474..6a28b7c9fdb 100644
--- a/Orange/widgets/visualize/owheatmap.py
+++ b/Orange/widgets/visualize/owheatmap.py
@@ -617,9 +617,15 @@ def _make_parts(self, data, group_var=None):
             _col_data = table_column_data(data, group_var)
             row_indices = [np.flatnonzero(_col_data == i)
                            for i in range(len(group_var.values))]
+
             row_groups = [RowPart(title=name, indices=ind,
                                   cluster=None, cluster_ordered=None)
                           for name, ind in zip(group_var.values, row_indices)]
+            if np.any(_col_data.mask):
+                row_groups.append(RowPart(
+                    title="N/A", indices=np.flatnonzero(_col_data.mask),
+                    cluster=None, cluster_ordered=None
+                ))
         else:
             row_groups = [RowPart(title=None, indices=range(0, len(data)),
                                   cluster=None, cluster_ordered=None)]
diff --git a/Orange/widgets/visualize/tests/test_owheatmap.py b/Orange/widgets/visualize/tests/test_owheatmap.py
index 03e1cf6ea9d..7aba80d85fc 100644
--- a/Orange/widgets/visualize/tests/test_owheatmap.py
+++ b/Orange/widgets/visualize/tests/test_owheatmap.py
@@ -33,6 +33,7 @@ def setUpClass(cls):
 
         cls.housing = Table("housing")
         cls.titanic = Table("titanic")
+        cls.brown_selected = Table("brown-selected")
 
         cls.signal_name = "Data"
         cls.signal_data = cls.data
@@ -211,7 +212,7 @@ def test_saved_selection(self):
         self.assertEqual(len(self.get_output(w.Outputs.selected_data)), 21)
 
     def test_set_split_var(self):
-        data = Table("brown-selected")
+        data = self.brown_selected[::3]
         w = self.widget
         self.send_signal(self.widget.Inputs.data, data, widget=w)
         self.assertIs(w.split_by_var, data.domain.class_var)
@@ -221,6 +222,15 @@ def test_set_split_var(self):
         self.assertIs(w.split_by_var, None)
         self.assertEqual(len(w.parts.rows), 1)
 
+    def test_set_split_var_missing(self):
+        data = self.brown_selected[::3].copy()
+        data.Y[::5] = np.nan
+        w = self.widget
+        self.send_signal(self.widget.Inputs.data, data, widget=w)
+        self.assertIs(w.split_by_var, data.domain.class_var)
+        self.assertEqual(len(w.parts.rows),
+                         len(data.domain.class_var.values) + 1)
+
     def test_palette_centering(self):
         data = np.arange(2).reshape(-1, 1)
         table = Table.from_numpy(Domain([ContinuousVariable("y")]), data)
diff --git a/Orange/widgets/visualize/utils/heatmap.py b/Orange/widgets/visualize/utils/heatmap.py
index a616fa1c5d0..c51b0210e1f 100644
--- a/Orange/widgets/visualize/utils/heatmap.py
+++ b/Orange/widgets/visualize/utils/heatmap.py
@@ -368,21 +368,18 @@ def setHeatmaps(self, parts: 'Parts') -> None:
         row_dendrograms: List[Optional[DendrogramWidget]] = [None] * N
         right_side_colors: List[Optional[GraphicsPixmapWidget]] = [None] * N
 
-        ncols = sum(c.size for c in parts.columns)
-        nrows = sum(r.size for r in parts.rows)
         data = parts.data
         if parts.col_names is None:
-            col_names = np.full(ncols, "", dtype=object)
+            col_names = np.full(data.shape[1], "", dtype=object)
         else:
             col_names = np.asarray(parts.col_names, dtype=object)
         if parts.row_names is None:
-            row_names = np.full(nrows, "", dtype=object)
+            row_names = np.full(data.shape[0], "", dtype=object)
         else:
             row_names = np.asarray(parts.row_names, dtype=object)
 
-        assert data.shape == (nrows, ncols)
-        assert len(col_names) == ncols
-        assert len(row_names) == nrows
+        assert len(col_names) == data.shape[1]
+        assert len(row_names) == data.shape[0]
 
         for i, rowitem in enumerate(parts.rows):
             if rowitem.title:
@@ -710,8 +707,6 @@ def set_visible(item: GraphicsPixmapWidget):
             legend_container.setVisible(True)
 
         parts = self.parts.rows
-        nrows = sum(p.size for p in parts)
-        assert len(data) == nrows
         for p, item in zip(parts, items):
             if item is not None:
                 subset = data[p.normalized_indices]