coerce SCE to/from RSE/SE (#75)

Author: jkanche

CHANGELOG.md

@@ -1,9 +1,11 @@
 # Changelog
 
-## Version 0.6.0
+## Version 0.6.0 - 0.6.2
 
 - Changed related to SummarizedExperiment and implementation of `CompressedGenomicRangesList` in the genomic ranges package.
 - Update versions of relevant dependency packages.
+- Rename `reduced_dims` to `reduced_dimensions`.
+- Implement coercions to/from RSE/SE.
 
 ## Version 0.5.8 - 0.5.9
 

src/singlecellexperiment/SingleCellExperiment.py

@@ -6,6 +6,7 @@
 
 import biocframe
 import biocutils as ut
+from summarizedexperiment import SummarizedExperiment
 from summarizedexperiment._combineutils import (
     check_assays_are_equal,
     merge_assays,
@@ -1277,6 +1278,86 @@ def combine_columns(self, *other) -> SingleCellExperiment:
         """Wrapper around :py:func:`~combine_columns`."""
         return combine_columns(self, *other)
 
+    #######################
+    ######>> to rse <<#####
+    #######################
+
+    def to_rangedsummarizedexperiment(self) -> RangedSummarizedExperiment:
+        """Coerce to :py:class:`~summarizedexperiment.RangedSummarizedExperiment.RangedSummarizedExperiment`.
+
+        Returns:
+            A ``RangedSummarizedExperiment`` object.
+        """
+        return RangedSummarizedExperiment(
+            assays=self._assays,
+            row_ranges=self._row_ranges,
+            row_data=self._rows,
+            column_data=self._cols,
+            row_names=self._row_names,
+            column_names=self._column_names,
+            metadata=self._metadata,
+            _validate=False,
+        )
+
+    def to_rse(self) -> RangedSummarizedExperiment:
+        """Alias for :py:meth:`~to_rangedsummarizedexperiment`."""
+        return self.to_rangedsummarizedexperiment()
+
+    @classmethod
+    def from_rangedsummarizedexperiment(cls, rse: RangedSummarizedExperiment) -> SingleCellExperiment:
+        """Coerce from :py:class:`~summarizedexperiment.RangedSummarizedExperiment.RangedSummarizedExperiment`.
+
+        Args:
+            rse:
+                A ``RangedSummarizedExperiment`` object.
+
+        Returns:
+            A ``SingleCellExperiment`` object.
+        """
+        return cls(
+            assays=rse.assays,
+            row_ranges=rse.row_ranges,
+            row_data=rse.row_data,
+            column_data=rse.col_data,
+            row_names=rse.row_names,
+            column_names=rse.column_names,
+            metadata=rse.metadata,
+        )
+
+    @classmethod
+    def from_rse(cls, rse: RangedSummarizedExperiment) -> SingleCellExperiment:
+        """Alias for :py:meth:`~from_rangedsummarizedexperiment`."""
+        return cls.from_rangedsummarizedexperiment(rse)
+
+    ########################
+    ######>> from se <<#####
+    ########################
+
+    @classmethod
+    def from_summarizedexperiment(cls, se: SummarizedExperiment) -> SingleCellExperiment:
+        """Coerce from :py:class:`~summarizedexperiment.SummarizedExperiment.SummarizedExperiment`.
+
+        Args:
+            se:
+                A ``SummarizedExperiment`` object.
+
+        Returns:
+            A ``SingleCellExperiment`` object.
+        """
+        return cls(
+            assays=se.assays,
+            row_data=se.row_data,
+            column_data=se.col_data,
+            row_names=se.row_names,
+            column_names=se.column_names,
+            metadata=se.metadata,
+        )
+
+    @classmethod
+    def from_se(cls, se: SummarizedExperiment) -> SingleCellExperiment:
+        """Alias for :py:meth:`~from_summarizedexperiment`."""
+        return cls.from_summarizedexperiment(se)
+
 
 ############################
 ######>> combine ops <<#####

tests/test_sce_methods.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pandas as pd
 import pytest
-from summarizedexperiment import SummarizedExperiment
+from summarizedexperiment import SummarizedExperiment, RangedSummarizedExperiment
 
 from singlecellexperiment import SingleCellExperiment
 from singlecellexperiment.SingleCellExperiment import SingleCellExperiment as sce
@@ -90,3 +90,45 @@ def test_SCE_props():
 
     assert tse.reduced_dim_names is not None
     assert len(tse.reduced_dim_names) == 1
+
+def test_SCE_to_RSE():
+    tse = SingleCellExperiment(
+        assays={"counts": counts}, row_data=row_data, column_data=col_data, row_ranges=gr
+    )
+
+    rse = tse.to_rangedsummarizedexperiment()
+    assert isinstance(rse, RangedSummarizedExperiment)
+    assert not isinstance(rse, SingleCellExperiment)
+    assert rse.shape == tse.shape
+    assert rse.row_ranges is not None
+
+def test_RSE_to_SCE():
+    rse = RangedSummarizedExperiment(
+        assays={"counts": counts}, row_data=row_data, column_data=col_data, row_ranges=gr
+    )
+
+    tse = SingleCellExperiment.from_rangedsummarizedexperiment(rse)
+    assert isinstance(tse, SingleCellExperiment)
+    assert tse.shape == rse.shape
+    assert tse.row_ranges is not None
+
+def test_SCE_to_SE():
+    tse = SingleCellExperiment(
+        assays={"counts": counts}, row_data=row_data, column_data=col_data, row_ranges=gr
+    )
+
+    se = tse.to_summarizedexperiment()
+    assert isinstance(se, SummarizedExperiment)
+    assert not isinstance(se, SingleCellExperiment)
+    assert se.shape == tse.shape
+    assert se.row_data is not None
+    assert "seqnames" in se.row_data.column_names
+
+def test_SE_to_SCE():
+    se = SummarizedExperiment(
+        assays={"counts": counts}, row_data=row_data, column_data=col_data
+    )
+
+    tse = SingleCellExperiment.from_summarizedexperiment(se)
+    assert isinstance(tse, SingleCellExperiment)
+    assert tse.shape == se.shape