spatialdata_to_domain#

spatialdata_to_domain(spatialdata, name_of_domain='spatialData domain', include_elements=None, annData_tables_and_vars={'table': ['__all__']}, import_shapes_as_points=True, number_of_points_in_cirlces=30, print_summary=True)#

Import a SpatialData object as a MuSpAn domain.

Parameters:
spatialdatasd.SpatialData

The spatialdata object to be converted.

name_of_domainstr, optional

The name of the resulting MuSpAn domain, by default ‘spatialData domain’.

include_elementslist or tuple, optional

A list or tuple of element labels to include from the spatialdata object, by default None.

annData_tables_and_varsdict, optional

A dictionary specifying which annData tables and variables of the tables to add, by default {}. The keys are the names of the tables in the spatialdata object, and the values are lists of the variables to add. If a value is [‘__all__’], all variables in the annData table are added. For example, {‘table1’:[‘var1’,’var2’],’table2’:[‘__all__’]}.

import_shapes_as_pointsbool, optional

If True, import shapes as points, by default True. Set to True if there is a large number of shapes in the spatialdata object for memory efficiency.

number_of_points_in_cirlcesint, optional

Number of points to use when creating circles, by default 30. Circles are created when shape cicrles are imported as points.

print_summarybool, optional

If True, print a summary of the resulting domain, by default True.

Returns:
ms.domain

The resulting MuSpAn domain.

Raises:
TypeError

If the input is not a spatialdata object.

ValueError

If include_elements is not a list or tuple, or if it contains invalid keys. If no elements are included in the domain. If an unrecognized shape type is encountered in the spatialdata object. If a specified table is not in the spatialdata object.

Notes

Important

We assume the structure and file name conventions of spatialData objects as provided in the spatialData reference datasets.

An Example SpatialData object (with points, shapes and a table):
├── Images (optional - not used in this importer)
|
├── Points
│     └── 'some set of points': DataFrame with shape: (<Delayed>, 3) (2D points)
├── Shapes
│     ├── 'some shapes 1': GeoDataFrame shape: (n, m) (2D shapes)
│     └── 'some shapes 2': GeoDataFrame shape: (k, d) (2D shapes)
└── Tables
    └── 'table': AnnData (k, b) (table data associated with spatial objects - obs must have 'region' column indicating the spatial object collection they relate to, e.g. 'some shapes 2' here)

For more information on spatialData objects, see the spatialData package. SpatialData object

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