squash

q2_emperor/_plot.py

@@ -66,7 +66,8 @@ def plot(output_dir: str, pcoa: skbio.OrdinationResults,
         pcoa.features = None
     if pcoa.features is not None:
         raise ValueError("Arrows cannot be visualized with the 'plot' method, "
-                         "use 'biplot' instead.")
+                         "use 'biplot' instead, or enable "
+                         "`ignore_pcoa_features`.")
 
     generic_plot(output_dir, master=pcoa, metadata=metadata, other_pcoa=None,
                  ignore_missing_samples=ignore_missing_samples,

q2_emperor/plugin_setup.py

@@ -30,7 +30,8 @@
     )
 }
 
-PLOT_PARAMETERS_DESC = {**PARAMETERS_DESC,
+PLOT_PARAMETERS_DESC = {
+    **PARAMETERS_DESC,
     'ignore_pcoa_features': 'Biplot arrows cannot be visualized using this '
                             'method. If you want to visualize biplot arrows '
                             'use the `biplot` method. Enabling this setting '

q2_emperor/tests/test_plot.py

@@ -86,6 +86,21 @@ def test_plot_custom_axes(self):
             self.assertTrue(os.path.exists(index_fp))
             self.assertTrue('src="./emperor.html"' in open(index_fp).read())
 
+    def test_plot_with_pcoa_features(self):
+        # using the biplot test data, since it has features
+        with tempfile.TemporaryDirectory() as output_dir:
+            plot(output_dir, self.biplot, self.metadata,
+                 ignore_pcoa_features=True)
+            self.assertTrue(True)  # checkpoint, everything should be good
+
+    def test_plot_with_pcoa_features_ignored(self):
+        # using the biplot test data, since it has features
+        with tempfile.TemporaryDirectory() as output_dir, \
+                self.assertRaisesRegex(ValueError,
+                                       'Arrows cannot be visualized'):
+            plot(output_dir, self.biplot, self.metadata,
+                 ignore_pcoa_features=False)
+
     def test_plot_procrustes(self):
         with tempfile.TemporaryDirectory() as output_dir:
             procrustes_plot(output_dir, self.pcoa, other_pcoa=self.other,