diff --git a/src/singlecellexperiment/SingleCellExperiment.py b/src/singlecellexperiment/SingleCellExperiment.py index 40f7391..7beac65 100644 --- a/src/singlecellexperiment/SingleCellExperiment.py +++ b/src/singlecellexperiment/SingleCellExperiment.py @@ -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, @@ -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, @@ -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 @@ -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" @@ -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: @@ -421,15 +425,15 @@ 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]: @@ -437,13 +441,13 @@ def reduced_dims(self) -> Dict[str, Any]: 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 +455,13 @@ def reduced_dimensions(self) -> Dict[str, Any]: 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 +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, @@ -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, )