scvi.data.AnnDataManager#
- class scvi.data.AnnDataManager(fields=None, setup_method_args=None, validation_checks=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 (
Optional
[List
[Type
[BaseAnnDataField
]]] (default:None
)) – List of AnnDataFields to intialize with.setup_method_args (
Optional
[dict
] (default:None
)) – Dictionary describing the model and arguments passed in by the user to setup this AnnDataManager.validation_checks (
Optional
[AnnDataManagerValidationCheck
] (default:None
)) – DataClass specifying which global validation checks to run on the data object.
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. |
|
Register new fields to a manager instance. |
|
Transfers an existing setup to each field associated with this instance with the target AnnData object. |
|
Update setup method args. |
|
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
- AnnDataManager.adata_uuid[source]#
Returns the UUID for the AnnData object registered with this instance.
data_registry
- AnnDataManager.data_registry[source]#
Returns the data registry for the AnnData object registered with this instance.
registry
- AnnDataManager.registry[source]#
Returns the top-level registry dictionary for the AnnData object registered with this instance as an attrdict.
summary_stats
Methods#
get_from_registry
- AnnDataManager.get_from_registry(registry_key)[source]#
Returns the object in AnnData associated with the key in the data registry.
get_state_registry
- AnnDataManager.get_state_registry(registry_key)[source]#
Returns the state registry for the AnnDataField registered with this instance.
- Return type:
register_fields
- AnnDataManager.register_fields(adata, source_registry=None, **transfer_kwargs)[source]#
Registers each field associated with this instance with the AnnData object.
Either registers or transfers the setup from source_setup_dict if passed in. Sets
self.adata
.- Parameters:
adata (
Union
[AnnData
,MuData
]) – AnnData object to be registered.source_registry (
Optional
[dict
] (default:None
)) – Registry created after registering an AnnData using anAnnDataManager
object.transfer_kwargs – Additional keywords which modify transfer behavior. Only applicable if
source_registry
is set.
register_new_fields
- AnnDataManager.register_new_fields(fields)[source]#
Register new fields to a manager instance.
This is useful to augment the functionality of an existing manager.
- Parameters:
fields (
List
[Type
[BaseAnnDataField
]]) – List of AnnDataFields to register
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:
- Return type:
update_setup_method_args
- AnnDataManager.update_setup_method_args(setup_method_args)[source]#
Update setup method args.
- Parameters:
setup_method_args (
dict
) – This is a bit of a misnomer, this is a dict representing kwargs of the setup method that will be used to update the existing values in the registry of this instance.
validate
- AnnDataManager.validate()[source]#
Checks if AnnData was last setup with this AnnDataManager instance and reregisters it if not.
- Return type:
view_registry
view_setup_method_args