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reduced dim changes #74

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Merged
jkanche merged 1 commit into from
Jan 4, 2026
Merged

reduced dim changes #74

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36 changes: 20 additions & 16 deletions src/singlecellexperiment/SingleCellExperiment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -280,7 +280,7 @@ def __deepcopy__(self, memo=None, _nil=[]):
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,
Expand All @@ -302,7 +302,7 @@ def __copy__(self):
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,
Expand Down Expand Up @@ -342,7 +342,7 @@ def __repr__(self) -> str:
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
Expand Down Expand Up @@ -381,7 +381,9 @@ def __str__(self) -> str:
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"
Expand All @@ -407,11 +409,13 @@ def get_reduced_dims(self) -> Dict[str, Any]:
"""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:
Expand All @@ -421,43 +425,43 @@ def set_reduced_dimensions(self, reduced_dims: Dict[str, Any], in_place: bool =
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]:
"""Alias for :py:meth:`~get_reduced_dimensions`."""
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]:
"""Alias for :py:meth:`~get_reduced_dimensions`."""
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 <<######
Expand Down Expand Up @@ -1119,7 +1123,7 @@ def get_slice(
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,
Expand Down Expand Up @@ -1217,7 +1221,7 @@ def from_anndata(cls, input: "anndata.AnnData") -> SingleCellExperiment:
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,
)
Expand Down