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
For more information on spatialData objects, see the spatialData package, https://spatialdata.scverse.org/en/stable/index.html.