Merge pull request #22 from kevin931/fix_issue_18

[BUG] Fix the issue of not updating lineage channel indices

PyCytoData/data.py

@@ -417,6 +417,8 @@ def subset(self, channels: Optional[ArrayLike]=None, sample: Optional[ArrayLike]
         self.channels = self.channels[channel_filter_condition]
         if self.lineage_channels is not None:
             self.lineage_channels = self.lineage_channels[np.isin(self.lineage_channels, self.channels)]
+        else:
+            self._lineage_channels_indices = np.arange(self.n_channels)
         self.sample_index = self.sample_index[filter_condition]
         self.cell_types = self.cell_types[filter_condition]
 
@@ -786,6 +788,7 @@ def lineage_channels(self, lineage_channels: ArrayLike):
         if not np.all(np.isin(lineage_channels, self._channels)):
             raise ValueError("Some lineage channels are not listed in channel names.")
         self._lineage_channels: Optional[np.ndarray] = lineage_channels if lineage_channels is None else np.array(lineage_channels).flatten()
+        self._lineage_channels_indices = np.where(np.isin(self.lineage_channels, self.channels))
 
 
     @property

tests/test_data.py

@@ -359,7 +359,21 @@ def test_subset_channels(self):
         assert exprs.n_channels == 2
         assert exprs.lineage_channels is not None
         assert exprs.lineage_channels.shape[0] == 2
+        assert np.all(np.equal(exprs._lineage_channels_indices, np.array([0, 1])))
         assert not np.isin("Channel0", exprs.lineage_channels)
+
+
+    def test_subset_channels_lineage_indices(self):
+        exprs_matrix: np.ndarray = np.random.rand(100, 10)
+        channels: np.ndarray = np.arange(10).astype(str)
+        exprs = PyCytoData(exprs_matrix, channels=channels)
+        exprs.subset(channels=["1", "2"])
+        assert exprs.n_cells == 100
+        assert exprs.n_channels == 2
+        assert exprs.lineage_channels is None
+        assert exprs._lineage_channels_indices.shape[0] == 2
+        assert np.all(np.equal(exprs._lineage_channels_indices, np.array([0, 1])))
+        assert not np.isin("0", exprs.lineage_channels)
 
 
     def test_subset_cell_types(self):