support renaming channels in Sample class (closes #198)

src/flowkit/_models/sample.py

@@ -693,6 +693,33 @@ def get_channel_events(self, channel_index, source='xform', subsample=False):
 
         return events
 
+    def rename_channel(self, current_label, new_label, new_pns_label=None):
+        """
+        Rename a channel label.
+
+        :param current_label: PnN label of a channel
+        :param new_label: new PnN label
+        :param new_pns_label: optional new PnS label
+        :return: None
+        """
+        try:
+            chan_idx = self.pnn_labels.index(current_label)
+        except ValueError:
+            raise ValueError("Label %s was not found in self.pnn_labels")
+
+        self.pnn_labels[chan_idx] = new_label
+
+        # Use same index for PnS label
+        if new_pns_label is not None:
+            self.pns_labels[chan_idx] = new_pns_label
+
+        # Update self.channels
+        self.channels['pnn'] = self.pnn_labels
+        self.channels['pns'] = self.pns_labels
+
+        # Update self._flowjo_pnn_labels
+        self._flowjo_pnn_labels[chan_idx] = new_label.replace('/', '_')
+
     def _transform(self, transform, include_scatter=False):
         if isinstance(transform, _transforms.RatioTransform):
             raise NotImplementedError(

tests/sample_tests.py

@@ -347,6 +347,30 @@ def test_get_events_as_data_frame_new_column_names(self):
 
         self.assertListEqual(list(df.columns), new_cols)
 
+    def test_rename_channel(self):
+        sample = copy.deepcopy(data1_sample)
+        chan_orig = 'FL1-H'
+        chan_new = 'CD4-H'
+        chan_pns_new = 'FITC'
+
+        sample.rename_channel(chan_orig, chan_new, new_pns_label=chan_pns_new)
+
+        chan_num = sample.get_channel_number_by_label(chan_new)
+        self.assertEqual(chan_num, 3)
+
+        chan_idx = sample.get_channel_index(chan_new)
+        self.assertEqual(chan_idx, 2)
+
+        pnn_labels = sample.pnn_labels
+        pns_labels = sample.pns_labels
+
+        self.assertEqual(chan_new, pnn_labels[chan_idx])
+        self.assertEqual(chan_pns_new, pns_labels[chan_idx])
+
+        df_channels = sample.channels
+        self.assertEqual(chan_new, df_channels.loc[chan_idx].pnn)
+        self.assertEqual(chan_pns_new, df_channels.loc[chan_idx].pns)
+
     @staticmethod
     def test_fully_custom_transform():
         sample1 = Sample(fcs_path_or_data=data1_fcs_path)