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]] | NoneOptional[Sequence[Type[BaseAnnDataField]]] (default: None): List of AnnDataFields to intialize with.
setup_method_args : dict | NoneOptional[dict] (default: None): Dictionary describing the model and arguments passed in by the user to setup this AnnDataManager.

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 via register_fields(). This decouples the generalized definition of the scvi-tools interface with the registration of an instance of data.

Attributes table#

`adata_uuid`	Returns the UUID for the AnnData object registered with this instance.
`data_registry`	Returns the data registry for the AnnData object registered with this instance.
`registry`	Returns the top-level registry dictionary for the AnnData object registered with this instance as an attrdict.
`summary_stats`	Returns the summary stats for the AnnData object registered with this instance.

Methods table#

`get_from_registry`(registry_key)	Returns the object in AnnData associated with the key in the data registry.
`get_state_registry`(registry_key)	Returns the state registry for the AnnDataField registered with this instance.
`register_fields`(adata[, source_registry])	Registers each field associated with this instance with the AnnData object.
`transfer_fields`(adata_target, **kwargs)	Transfers an existing setup to each field associated with this instance with the target AnnData object.
`validate`()	Checks if AnnData was last setup with this AnnDataManager instance and reregisters it if not.
`view_registry`([hide_state_registries])	Prints summary of the registry.
`view_setup_method_args`(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.

Return type:: str

data_registry#

AnnDataManager.data_registry[source]#

Returns the data registry for the AnnData object registered with this instance.

Return type:: attrdict

registry#

AnnDataManager.registry[source]#

Returns the top-level registry dictionary for the AnnData object registered with this instance as an attrdict.

Return type:: dict

summary_stats#

AnnDataManager.summary_stats[source]#

Returns the summary stats for the AnnData object registered with this instance.

Return type:: attrdict

Methods#

get_from_registry#

AnnDataManager.get_from_registry(registry_key)[source]#

Returns the object in AnnData associated with the key in the data registry.

Parameters:

registry_key : str: key of object to get from self.data_registry

Return type:

ndarray | DataFrameUnion[ndarray, DataFrame]

Returns:

The requested data.

get_state_registry#

AnnDataManager.get_state_registry(registry_key)[source]#

Returns the state registry for the AnnDataField registered with this instance.

Return type:: attrdict

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 : AnnData | MuDataUnion[AnnData, MuData]: AnnData object to be registered.
source_registry : dict | NoneOptional[dict] (default: None): Registry created after registering an AnnData using an AnnDataManager object.
transfer_kwargs: Additional keywords which modify transfer behavior. Only applicable if source_registry is set.

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 | MuDataUnion[AnnData, MuData]: AnnData object to be registered.
kwargs: Additional keywords which modify transfer behavior.

Return type:

AnnDataManager

validate#

AnnDataManager.validate()[source]#

Checks if AnnData was last setup with this AnnDataManager instance and reregisters it if not.

Return type:: None

view_registry#

AnnDataManager.view_registry(hide_state_registries=False)[source]#

Prints summary of the registry.

Parameters:

hide_state_registries : bool (default: False): If True, prints a shortened summary without details of each state registry.

Return type:

None

view_setup_method_args#

static AnnDataManager.view_setup_method_args(registry)[source]#

Prints setup kwargs used to produce a given registry.

Parameters:

registry : dict: Registry produced by an AnnDataManager.

Return type:

None