singlecellexperiment package

Subpackages

• singlecellexperiment.io package
  • Submodules
  • singlecellexperiment.io.h5ad module
    • read_h5ad()
  • singlecellexperiment.io.tenx module
    • read_tenx_h5()
    • read_tenx_mtx()
  • Module contents

Submodules

singlecellexperiment.SingleCellExperiment module

class singlecellexperiment.SingleCellExperiment.SingleCellExperiment(assays: Dict[str, Any] | None = None, row_ranges: GenomicRanges | GenomicRangesList | None = None, row_data: BiocFrame | None = None, column_data: BiocFrame | None = None, row_names: List[str] | None = None, column_names: List[str] | None = None, metadata: dict | None = None, reduced_dims: Dict[str, Any] | None = None, main_experiment_name: str | None = None, alternative_experiments: Dict[str, Any] | None = None, row_pairs: Any | None = None, column_pairs: Any | None = None, validate: bool = True)

Bases: RangedSummarizedExperiment

Container class for single-cell experiments, extending RangedSummarizedExperiment to provide slots for embeddings and alternative experiments that share the same cells.

In contrast to R, ndarray or scipy matrices are unnamed and do not contain rownames and colnames. Hence, these matrices cannot be directly used as values in assays or alternative experiments. We strictly enforce type checks in these cases.

To relax these restrictions for alternative experiments, set type_check_alternative_experiments to False.

If you are using the alternative experiment slot, the number of cells must match the parent experiment. Otherwise, these cells do not share the same sample or annotations and cannot be set in alternative experiments!

Note: Validation checks do not apply to row_pairs or col_pairs.

__copy__()

Returns:

A shallow copy of the current SingleCellExperiment.

__deepcopy__(memo=None, _nil=[])

Returns:

A deep copy of the current SingleCellExperiment.

__repr__() → str

Returns:

A string representation.

alternative_experiment(name: str | int) → Any

Access alternative experiment by name.

Parameters:

name – Name or index position of the alternative experiment.

Raises:

• AttributeError – If the dimension name does not exist.

• IndexError – If index is greater than the number of reduced dimensions.

Returns:

The alternative experiment.

property alternative_experiment_names: List[str]

Alias for get_alternative_experiment_names().

property alternative_experiments: Dict[str, Any]

Alias for get_alternative_experiments().

property column_pair_names: List[str]

Alias for get_column_pair_names().

property column_pairs: Dict[str, Any]

Alias for get_column_pairs().

copy()

Alias for __copy__().

classmethod from_anndata(input: anndata.AnnData) → SingleCellExperiment

Create a SingleCellExperiment from AnnData.

Args:

input:

Input data.

Returns:

A SingleCellExperiment object. If the input contains any data in the uns attribute, the metadata slot of the SingleCellExperiment will contain a key uns.

get_alternative_experiment_names() → List[str]

Access alternative experiment names.

Returns:

List of alternative experiment names.

get_alternative_experiments() → Dict[str, Any]

Access alternative experiments.

Returns:

A dictionary with names of the experiments as keys and value the experiment.

get_column_pair_names() → List[str]

Access column pair names.

Returns:

List of column pair names.

get_column_pairs() → Dict[str, Any]

Access column pairings/relationships between cells.

Returns:

Access column pairs.

get_main_experiment_name() → str | None

Access main experiment name.

Returns:

Name if available, otherwise None.

get_reduced_dim_names() → List[str]

Access reduced dimension names.

Returns:

List of reduced dimensionality names.

get_reduced_dims() → Dict[str, Any]

Access dimensionality embeddings.

Returns:

A dictionary with keys as names of embedding method and value the embedding.

get_row_pair_names() → List[str]

Access row pair names.

Returns:

List of row pair names.

get_row_pairs() → Dict[str, Any]

Access row pairings/relationships between features.

Returns:

Access row pairs.

get_slice(rows: str | int | bool | Sequence | None, columns: str | int | bool | Sequence | None) → SingleCellExperiment

Alias for __getitem__, for back-compatibility.

property main_experiment_name: str | None

Alias for get_main_experiment_name().

reduced_dim(dimension: str | int) → Any

Access an embedding by name.

Parameters:

dimension – Name or index position of the reduced dimension.

Raises:

• AttributeError – If the dimension name does not exist.

• IndexError – If index is greater than the number of reduced dimensions.

Returns:

The embedding.

property reduced_dim_names: List[str]

Alias for get_reduced_dim_names().

property reduced_dims: Dict[str, Any]

Alias for get_reduced_dims().

property row_pair_names: List[str]

Alias for get_row_pair_names().

property row_pairs: Dict[str, Any]

Alias for get_row_pairs().

set_alternative_experiment_names(names: List[str], in_place: bool = False) → SingleCellExperiment

Replace alternative_experiment’s names.

Parameters:

• names – New alternative experiment names.

• in_place – Whether to modify the SingleCellExperiment in place.

Returns:

A modified SingleCellExperiment object, either as a copy of the original or as a reference to the (in-place-modified) original.

set_alternative_experiments(alternative_experiments: Dict[str, Any], in_place: bool = False) → SingleCellExperiment

Set new alternative experiments.

Parameters:

• alternative_experiments – New alternative experiments.

• in_place – Whether to modify the SingleCellExperiment in place.

Returns:

A modified SingleCellExperiment object, either as a copy of the original or as a reference to the (in-place-modified) original.

set_column_pair_names(names: List[str], in_place: bool = False) → SingleCellExperiment

Replace column_pair’s names.

Parameters:

• names – New names.

• in_place – Whether to modify the SingleCellExperiment in place.

Returns:

A modified SingleCellExperiment object, either as a copy of the original or as a reference to the (in-place-modified) original.

set_column_pairs(pairs: Dict[str, Any], in_place: bool = False) → SingleCellExperiment

Replace column_pairs’s names.

Parameters:

• names – New column pairs.

• in_place – Whether to modify the SingleCellExperiment in place.

Returns:

A modified SingleCellExperiment object, either as a copy of the original or as a reference to the (in-place-modified) original.

set_main_experiment_name(name: str | None, in_place: bool = False) → SingleCellExperiment

Set new experiment data (assays).

Parameters:

• name – New main experiment name.

• in_place – Whether to modify the SingleCellExperiment in place.

Returns:

A modified SingleCellExperiment object, either as a copy of the original or as a reference to the (in-place-modified) original.

set_reduced_dim_names(names: List[str], in_place: bool = False) → SingleCellExperiment

Replace reduced_dims’s names.

Parameters:

• names – New dimensionality names.

• in_place – Whether to modify the SingleCellExperiment in place.

Returns:

A modified SingleCellExperiment object, either as a copy of the original or as a reference to the (in-place-modified) original.

set_reduced_dims(reduced_dims: Dict[str, Any], in_place: bool = False) → SingleCellExperiment

Set new reduced dimensions.

Parameters:

• reduced_dims – New embeddings.

• in_place – Whether to modify the SingleCellExperiment in place.

Returns:

A modified SingleCellExperiment object, either as a copy of the original or as a reference to the (in-place-modified) original.

set_row_pair_names(names: List[str], in_place: bool = False) → SingleCellExperiment

Replace row_pair’s names.

Parameters:

• names – New names.

• in_place – Whether to modify the SingleCellExperiment in place.

Returns:

A modified SingleCellExperiment object, either as a copy of the original or as a reference to the (in-place-modified) original.

set_row_pairs(pairs: Dict[str, Any], in_place: bool = False) → SingleCellExperiment

Replace row_pairs’s names.

Parameters:

• names – New row pairs.

• in_place – Whether to modify the SingleCellExperiment in place.

Returns:

A modified SingleCellExperiment object, either as a copy of the original or as a reference to the (in-place-modified) original.

to_anndata(include_alternative_experiments: bool = False)

Transform SingleCellExperiment-like into a AnnData representation.

Parameters:

include_alternative_experiments – Whether to transform alternative experiments.

Returns:

A tuple with AnnData main experiment and a list of alternative experiments.

to_mudata()

Transform SingleCellExperiment object into MuData representation.

If main_experiment_name is None, this experiment is called Unknown Modality in the MuData object.

Returns:

A MuData object.

singlecellexperiment.SingleCellExperiment.combine_columns(*x: SingleCellExperiment) → SingleCellExperiment

Combine multiple SingleCellExperiment objects by column.

All assays must contain the same assay names. If you need a flexible combine operation, checkout relaxed_combine_columns().

Returns:

A combined SingleCellExperiment.

singlecellexperiment.SingleCellExperiment.combine_rows(*x: SingleCellExperiment) → SingleCellExperiment

Combine multiple SingleCellExperiment objects by row.

All assays must contain the same assay names. If you need a flexible combine operation, checkout relaxed_combine_rows().

Returns:

A combined SingleCellExperiment.

singlecellexperiment.SingleCellExperiment.relaxed_combine_columns(*x: SingleCellExperiment) → SingleCellExperiment

A relaxed version of the combine_columns() method for SingleCellExperiment objects. Whereas combine_columns expects that all objects have the same rows, relaxed_combine_columns allows for different rows. Absent columns in any object are filled in with appropriate placeholder values before combining.

Parameters:

x – One or more SingleCellExperiment objects, possibly with differences in the number and identity of their rows.

Returns:

A SingleCellExperiment that combines all experiments along their columns and contains the union of all rows. Rows absent in any x are filled in with placeholders consisting of Nones or masked NumPy values.

singlecellexperiment.SingleCellExperiment.relaxed_combine_rows(*x: SingleCellExperiment) → SingleCellExperiment

A relaxed version of the combine_rows() method for SingleCellExperiment objects. Whereas combine_rows expects that all objects have the same columns, relaxed_combine_rows allows for different columns. Absent columns in any object are filled in with appropriate placeholder values before combining.

Parameters:

x – One or more SingleCellExperiment objects, possibly with differences in the number and identity of their columns.

Returns:

A SingleCellExperiment that combines all experiments along their rows and contains the union of all columns. Columns absent in any x are filled in with placeholders consisting of Nones or masked NumPy values.

Module contents