SingleCellExperiment 0.6.0__tar.gz → 0.6.2__tar.gz

{singlecellexperiment-0.6.0 → singlecellexperiment-0.6.2}/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
 

{singlecellexperiment-0.6.0 → singlecellexperiment-0.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SingleCellExperiment
-Version: 0.6.0
+Version: 0.6.2
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche

{singlecellexperiment-0.6.0 → singlecellexperiment-0.6.2}/docs/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
 

{singlecellexperiment-0.6.0 → singlecellexperiment-0.6.2}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SingleCellExperiment
-Version: 0.6.0
+Version: 0.6.2
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche

{singlecellexperiment-0.6.0 → singlecellexperiment-0.6.2}/src/singlecellexperiment/SingleCellExperiment.py

@@ -6,6 +6,7 @@ from warnings import warn
 
 import biocframe
 import biocutils as ut
+from summarizedexperiment import SummarizedExperiment
 from summarizedexperiment._combineutils import (
     check_assays_are_equal,
     merge_assays,
@@ -280,7 +281,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             row_names=_row_names_copy,
             column_names=_col_names_copy,
             metadata=_metadata_copy,
-            reduced_dims=_red_dim_copy,
+            reduced_dimensions=_red_dim_copy,
             main_experiment_name=_main_expt_name_copy,
             alternative_experiments=_alt_expt_copy,
             row_pairs=_row_pair_copy,
@@ -302,7 +303,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             row_names=self._row_names,
             column_names=self._column_names,
             metadata=self._metadata,
-            reduced_dims=self._reduced_dims,
+            reduced_dimensions=self._reduced_dims,
             main_experiment_name=self._main_experiment_name,
             alternative_experiments=self._alternative_experiments,
             row_pairs=self._row_pairs,
@@ -342,7 +343,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             output += ", alternative_experiments=" + ut.print_truncated_list(self.alternative_experiment_names)
 
         if self._reduced_dims is not None:
-            output += ", reduced_dims=" + ut.print_truncated_list(self.reduced_dim_names)
+            output += ", reduced_dimensions=" + ut.print_truncated_list(self.reduced_dim_names)
 
         if self._main_experiment_name is not None:
             output += ", main_experiment_name=" + self._main_experiment_name
@@ -381,7 +382,9 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         output += f"column_names({0 if self._column_names is None else len(self._column_names)}): {' ' if self._column_names is None else ut.print_truncated_list(self._column_names)}\n"
 
         output += f"main_experiment_name: {' ' if self._main_experiment_name is None else self._main_experiment_name}\n"
-        output += f"reduced_dims({len(self.reduced_dim_names)}): {ut.print_truncated_list(self.reduced_dim_names)}\n"
+        output += (
+            f"reduced_dimensions({len(self.reduced_dim_names)}): {ut.print_truncated_list(self.reduced_dim_names)}\n"
+        )
         output += f"alternative_experiments({len(self.alternative_experiment_names)}): {ut.print_truncated_list(self.alternative_experiment_names)}\n"
         output += f"row_pairs({len(self.row_pair_names)}): {ut.print_truncated_list(self.row_pair_names)}\n"
         output += f"column_pairs({len(self.column_pair_names)}): {ut.print_truncated_list(self.column_pair_names)}\n"
@@ -407,11 +410,13 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """Alias for :py:meth:`~get_reduced_dimensions`, for back-compatibility."""
         return self.get_reduced_dimensions()
 
-    def set_reduced_dimensions(self, reduced_dims: Dict[str, Any], in_place: bool = False) -> SingleCellExperiment:
+    def set_reduced_dimensions(
+        self, reduced_dimensions: Dict[str, Any], in_place: bool = False
+    ) -> SingleCellExperiment:
         """Set new reduced dimensions.
 
         Args:
-            reduced_dims:
+            reduced_dimensions:
                 New embeddings.
 
             in_place:
@@ -421,15 +426,15 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             A modified ``SingleCellExperiment`` object, either as a copy of the original
             or as a reference to the (in-place-modified) original.
         """
-        _validate_reduced_dims(reduced_dims, self.shape)
+        _validate_reduced_dims(reduced_dimensions, self.shape)
 
         output = self._define_output(in_place)
-        output._reduced_dims = reduced_dims
+        output._reduced_dims = reduced_dimensions
         return output
 
-    def set_reduced_dims(self, reduced_dims: Dict[str, Any], in_place: bool = False) -> SingleCellExperiment:
+    def set_reduced_dims(self, reduced_dimensions: Dict[str, Any], in_place: bool = False) -> SingleCellExperiment:
         """Alias for :py:meth:`~set_reduced_dimensions`, for back-compatibility."""
-        return self.set_reduced_dimensions(reduced_dims=reduced_dims, in_place=in_place)
+        return self.set_reduced_dimensions(reduced_dimensions=reduced_dimensions, in_place=in_place)
 
     @property
     def reduced_dims(self) -> Dict[str, Any]:
@@ -437,13 +442,13 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         return self.get_reduced_dimensions()
 
     @reduced_dims.setter
-    def reduced_dims(self, reduced_dims: Dict[str, Any]):
+    def reduced_dims(self, reduced_dimensions: Dict[str, Any]):
         """Alias for :py:meth:`~set_reduced_dimensions`."""
         warn(
             "Setting property 'reduced_dims' is an in-place operation, use 'set_reduced_dimensions' instead",
             UserWarning,
         )
-        self.set_reduced_dimensions(reduced_dims, in_place=True)
+        self.set_reduced_dimensions(reduced_dimensions, in_place=True)
 
     @property
     def reduced_dimensions(self) -> Dict[str, Any]:
@@ -451,13 +456,13 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         return self.get_reduced_dimensions()
 
     @reduced_dimensions.setter
-    def reduced_dimensions(self, reduced_dims: Dict[str, Any]):
+    def reduced_dimensions(self, reduced_dimensions: Dict[str, Any]):
         """Alias for :py:meth:`~set_reduced_dimensions`."""
         warn(
             "Setting property 'reduced_dimensions' is an in-place operation, use 'set_reduced_dimensions' instead",
             UserWarning,
         )
-        self.set_reduced_dimensions(reduced_dims, in_place=True)
+        self.set_reduced_dimensions(reduced_dimensions, in_place=True)
 
     ####################################
     ######>> reduced_dims_names <<######
@@ -1119,7 +1124,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             column_names=slicer.column_names,
             metadata=self._metadata,
             main_experiment_name=self._main_experiment_name,
-            reduced_dims=new_reduced_dims,
+            reduced_dimensions=new_reduced_dims,
             alternative_experiments=new_alt_expts,
             row_pairs=new_row_pairs,
             column_pairs=new_col_pairs,
@@ -1217,7 +1222,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             row_data=biocframe.BiocFrame.from_pandas(input.var),
             column_data=biocframe.BiocFrame.from_pandas(input.obs),
             metadata=_metadata,
-            reduced_dims=obsm,
+            reduced_dimensions=obsm,
             row_pairs=varp,
             column_pairs=obsp,
         )
@@ -1273,6 +1278,86 @@ class SingleCellExperiment(RangedSummarizedExperiment):
         """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 <<#####

{singlecellexperiment-0.6.0 → singlecellexperiment-0.6.2}/tests/test_sce_methods.py

@@ -5,7 +5,7 @@ from biocframe import BiocFrame
 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