abagen.mouse.get_unionization_from_gene

abagen.mouse.get_unionization_from_gene(id=None, acronym=None, name=None, slicing_direction='sagittal', structures=None, attributes=None, average=True, verbose=False)[source]

Gets unionization data for provided gene(s)

One of id, acronym, or name must be provided.

Parameters:

  • id (int, optional) – Numerical gene ID

  • acronym (str, optional) – Short-form gene acronym (case sensitive)

  • name (str, optional) – Full gene name (case sensitive)

  • slicing_direction ({'sagittal', 'coronal'}, optional) – Slicing direction of brain tissue

  • structures (list, optional) – List of structures (id, acronym, or name) for which to get unionization information associated with provided experiment_id. If not specified uses structures documented in [MI1]. Specifying either the id or name is recommended as acronyms are not unique to structures. Default: None

  • attributes (str or list, optional) – Which attributes / information to obtain for the provided gene. See abagen.mouse.available_gene_info() for list of available attributes to request. If not specified then only ‘expression_density’ will be returned. Specifying ‘all’ will return all information. Default: None

  • average (bool, optional) – Whether to average across experiments if there are multiple experiments corresponding to any provided gene(s). Only experiments probing the same gene will be considered for averaging, and distinct structures will be retained. Default: True

  • verbose (bool, optional) – Whether to print status messages. Default: False

Returns:

unionization – Where columns are unionization attributes and the index corresponds to strucuture and gene ids (if experiments is provided as a list with multiple genes). If average=False, experiments will also be a level in index

Return type:

pandas.DataFrame

Examples

>>> from abagen import mouse
>>> mouse.get_unionization_from_gene(acronym='Pdyn',
...                                  structures=[22, 31])  
                      expression_density
gene_id structure_id
18376   22                      0.024840
        31                      0.017199
>>> mouse.get_unionization_from_gene(acronym=['Ace', 'Cd99'],
...                                  structures=[22, 31])  
                      expression_density
gene_id structure_id
11210   22                      0.001283
        31                      0.001427
163028  22                      0.067537
        31                      0.056442