scvi.data.AnnDataManager#
- class scvi.data.AnnDataManager(fields=None, setup_method_args=None)[source]#
Provides an interface to validate and process an AnnData object for use in scvi-tools.
A class which wraps a collection of AnnDataField instances and provides an interface to validate and process an AnnData object with respect to the fields.
- Parameters
- fields :
Sequence
[Type
[BaseAnnDataField
]] |None
Optional
[Sequence
[Type
[BaseAnnDataField
]]] (default:None
) List of AnnDataFields to intialize with.
- setup_method_args :
dict
|None
Optional
[dict
] (default:None
) Dictionary describing the model and arguments passed in by the user to setup this AnnDataManager.
- fields :
Examples
>>> fields = [LayerField("counts", "raw_counts")] >>> adata_manager = AnnDataManager(fields=fields) >>> adata_manager.register_fields(adata)
Notes
This class is not initialized with a specific AnnData object, but later sets
self.adata
viaregister_fields()
. This decouples the generalized definition of the scvi-tools interface with the registration of an instance of data.
Attributes table#
Returns the UUID for the AnnData object registered with this instance. |
|
Returns the data registry for the AnnData object registered with this instance. |
|
Returns the top-level registry dictionary for the AnnData object registered with this instance as an attrdict. |
|
Returns the summary stats for the AnnData object registered with this instance. |
Methods table#
|
Returns the object in AnnData associated with the key in the data registry. |
|
Returns the state registry for the AnnDataField registered with this instance. |
|
Registers each field associated with this instance with the AnnData object. |
|
Transfers an existing setup to each field associated with this instance with the target AnnData object. |
|
Checks if AnnData was last setup with this AnnDataManager instance and reregisters it if not. |
|
Prints summary of the registry. |
|
Prints setup kwargs used to produce a given registry. |
Attributes#
adata_uuid#
data_registry#
registry#
summary_stats#
Methods#
get_from_registry#
get_state_registry#
register_fields#
transfer_fields#
- AnnDataManager.transfer_fields(adata_target, **kwargs)[source]#
Transfers an existing setup to each field associated with this instance with the target AnnData object.
Creates a new
AnnDataManager
instance with the same set of fields. Then, registers the fields with a target AnnData object, incorporating details of the source registry where necessary (e.g. for validation or modified data setup).- Parameters
- adata_target :
AnnData
AnnData object to be registered.
- kwargs
Additional keywords which modify transfer behavior.
- adata_target :
- Return type