spatialfeatureexperiment package

Submodules

spatialfeatureexperiment.SpatialFeatureExperiment module

class spatialfeatureexperiment.SpatialFeatureExperiment.SpatialFeatureExperiment(assays=None, row_ranges=None, row_data=None, column_data=None, row_names=None, column_names=None, metadata=None, reduced_dims=None, main_experiment_name=None, alternative_experiments=None, alternative_experiment_check_dim_names=True, row_pairs=None, column_pairs=None, spatial_coords=None, img_data=None, col_geometries=None, row_geometries=None, annot_geometries=None, spatial_graphs=None, unit='full_res_image_pixel', validate=True, **kwargs)[source]

Bases: SpatialExperiment

Container class for storing data from spatial-omics experiments with feature geometries.

This class extends SpatialExperiment to provide slots for geometries of spots/cells, tissue boundaries, pathologist annotations and other spatial features.

__copy__()[source]
Returns:

A shallow copy of the current SpatialExperiment.

__deepcopy__(memo=None, _nil=[])[source]
Returns:

A deep copy of the current SpatialExperiment.

__init__(assays=None, row_ranges=None, row_data=None, column_data=None, row_names=None, column_names=None, metadata=None, reduced_dims=None, main_experiment_name=None, alternative_experiments=None, alternative_experiment_check_dim_names=True, row_pairs=None, column_pairs=None, spatial_coords=None, img_data=None, col_geometries=None, row_geometries=None, annot_geometries=None, spatial_graphs=None, unit='full_res_image_pixel', validate=True, **kwargs)[source]

Initialize a spatial feature class.

Parameters:

  • assays (Dict[str, Any]) –

    A dictionary containing matrices, with assay names as keys and 2-dimensional matrices represented as either ndarray or spmatrix.

    Alternatively, you may use any 2-dimensional matrix that has the shape property and implements the slice operation using the __getitem__ dunder method.

    All matrices in assays must be 2-dimensional and have the same shape (number of rows, number of columns).

  • row_ranges (Union[GenomicRanges, GenomicRangesList, None]) – Genomic features, must be the same length as the number of rows of the matrices in assays.

  • row_data (Optional[BiocFrame]) –

    Features, must be the same length as the number of rows of the matrices in assays.

    Feature information is coerced to a BiocFrame. Defaults to None.

  • column_data (Optional[BiocFrame]) –

    Sample data, must be the same length as the number of columns of the matrices in assays. For instances of the SpatialExperiment class, the sample data must include a column named sample_id. If any ‘sample_id’ in the sample data is not present in the ‘sample_id’s of ‘img_data’, a warning will be issued.

    If sample_id is not present, a column with this name will be created and filled with the default value sample01.

    Sample information is coerced to a BiocFrame. Defaults to None.

  • row_names (Optional[List[str]]) – A list of strings, same as the number of rows.Defaults to None.

  • column_names (Optional[List[str]]) – A list of strings, same as the number of columns. Defaults to None.

  • metadata (Optional[dict]) – Additional experimental metadata describing the methods. Defaults to None.

  • reduced_dims (Optional[Dict[str, Any]]) –

    Slot for low-dimensionality embeddings.

    Usually a dictionary with the embedding method as keys (e.g., t-SNE, UMAP) and the dimensions as values.

    Embeddings may be represented as a matrix or a data frame, must contain a shape.

  • main_experiment_name (Optional[str]) – A string, specifying the main experiment name.

  • alternative_experiments (Optional[Dict[str, Any]]) –

    Used to manage multi-modal experiments performed on the same sample/cells.

    Alternative experiments must contain the same cells (rows) as the primary experiment. It’s a dictionary with keys as the names of the alternative experiments (e.g., sc-atac, crispr) and values as subclasses of SummarizedExperiment.

  • alternative_experiment_check_dim_names (bool) –

    Whether to check if the column names of the alternative experiment match the column names of the main experiment. This is the equivalent to the withDimnames parameter in the R implementation.

    Defaults to True.

  • row_pairs (Optional[Any]) –

    Row pairings/relationships between features.

    Defaults to None.

  • column_pairs (Optional[Any]) –

    Column pairings/relationships between cells.

    Defaults to None.

  • spatial_coords (Union[BiocFrame, ndarray, None]) –

    Optional ndarray or BiocFrame containing columns of spatial coordinates. Must be the same length as column_data.

    If spatial_coords is a BiocFrame, typical column names might include:

    • [‘x’, ‘y’]: For simple 2D coordinates.

    • [‘pxl_col_in_fullres’, ‘pxl_row_in_fullres’]: For pixel-based

    coordinates in full-resolution images.

    If spatial coordinates is a DataFrame or None, it is coerced to a BiocFrame. Defaults to None.

  • img_data (Optional[BiocFrame]) –

    Optional BiocFrame containing the image data, structured with the following columns:

    • sample_id (str): A string identifier for the sample to which an image corresponds.

    • image_id (str): A unique string identifier for each image within each sample.

    • data (VirtualSpatialImage): The image itself, represented as a VirtualSpatialImage object or one of its subclasses.

    • scale_factor (float): A numerical value that indicates the scaling factor applied to the image.

    All ‘sample_id’s in ‘img_data’ must be present in the ‘sample_id’s of ‘column_data’.

    Image data are coerced to a BiocFrame. Defaults to None.

  • col_geometries (Optional[Dict[str, GeoDataFrame]]) – Dictionary of GeoDataFrames containing geometries for columns (e.g. cells, spots).

  • row_geometries (Optional[Dict[str, GeoDataFrame]]) – Dictionary of GeoDataFrames containing geometries for rows (e.g. genes).

  • annot_geometries (Optional[Dict[str, GeoDataFrame]]) – Dictionary of GeoDataFrames containing annotation geometries (e.g. tissue boundaries).

  • spatial_graphs (Optional[BiocFrame]) – BiocFrame containing spatial neighborhood graphs.

  • unit (str) – Unit for spatial coordinates (‘full_res_image_pixel’ or ‘micron’).

  • validate (bool) – Internal use only.

__repr__()[source]

Get string representation.

Return type:

str

property annot_geometries: Dict[str, GeoDataFrame]

Get annotation geometries.

property col_geometries: Dict[str, GeoDataFrame]

Get column geometries.

copy()[source]

Alias for __copy__().

get_annot_geometries()[source]

Get annotation geometries.

Return type:

Dict[str, GeoDataFrame]

get_col_geometries()[source]

Get column geometries.

Return type:

Dict[str, GeoDataFrame]

get_row_geometries()[source]

Get row geometries.

Return type:

Dict[str, GeoDataFrame]

get_slice(rows=None, columns=None)[source]

Get a slice of the experiment.

Parameters:
Return type:

ProxySpatialFeatureExperiment

Returns:

Sliced ProxySpatialFeatureExperiment.

get_spatial_graphs()[source]

Get spatial neighborhood graphs.

Return type:

Optional[BiocFrame]

get_unit()[source]

Get the coordinate unit.

Return type:

str

property row_geometries: Dict[str, GeoDataFrame]

Get row geometries.

set_annot_geometries(geometries, in_place=False)[source]

Set annotation geometries.

Parameters:

  • geometries (Dict[str, GeoDataFrame]) – New annotation geometries.

  • in_place (bool) – Whether to modify the ProxySpatialFeatureExperiment in place. Defaults to False.

Return type:

ProxySpatialFeatureExperiment

Returns:

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

set_col_geometries(geometries, in_place=False)[source]

Set column geometries.

Parameters:

  • geometries (Dict[str, GeoDataFrame]) – New column geometries.

  • in_place (bool) – Whether to modify the ProxySpatialFeatureExperiment in place. Defaults to False.

Return type:

ProxySpatialFeatureExperiment

Returns:

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

set_column_data(cols, replace_column_names=False, in_place=False)[source]

Override: Set sample data.

Parameters:

  • cols (Optional[BiocFrame]) –

    New sample data. If ‘cols’ contains a column named ‘sample_id’s, a check is performed to ensure that all ‘sample_id’s in the ‘img_data’ are present. If any ‘sample_id’ in the ‘cols’ is not present in the ‘sample_id’s of ‘img_data’, a warning will be issued.

    If ‘sample_id’ is not present or ‘cols’ is None, the original ‘sample_id’s are retained.

  • replace_column_names (bool) – Whether to replace experiment’s column_names with the names from the new object. Defaults to False.

  • in_place (bool) – Whether to modify the ProxySpatialFeatureExperiment in place. Defaults to False.

Return type:

ProxySpatialFeatureExperiment

Returns:

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

set_row_geometries(geometries, in_place=False)[source]

Set row geometries.

Parameters:

  • geometries (Dict[str, GeoDataFrame]) – New row geometries.

  • in_place (bool) – Whether to modify the ProxySpatialFeatureExperiment in place. Defaults to False.

Return type:

ProxySpatialFeatureExperiment

Returns:

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

set_spatial_graphs(graphs, in_place=False)[source]

Set spatial neighborhood graphs.

Parameters:

  • graphs (Optional[BiocFrame]) – New spatial graphs as BiocFrame.

  • in_place (bool) – Whether to modify the ProxySpatialFeatureExperiment in place. Defaults to False.

Return type:

ProxySpatialFeatureExperiment

Returns:

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

set_unit(unit, in_place=False)[source]

Set the coordinate unit.

Parameters:

  • unit (str) – New unit (‘full_res_image_pixel’ or ‘micron’).

  • in_place (bool) – Whether to modify the ProxySpatialFeatureExperiment in place. Defaults to False.

Return type:

ProxySpatialFeatureExperiment

Returns:

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

property spatial_graphs: BiocFrame | None

Get spatial graphs.

property unit: str

Get coordinate unit.

Module contents