scvi.data.fields.LabelsWithUnlabeledObsField

class scvi.data.fields.LabelsWithUnlabeledObsField(registry_key, obs_key, unlabeled_category)

An AnnDataField for labels which include explicitly unlabeled cells.

Remaps the unlabeled category to the final index if present in labels. The unlabeled category is a specific category name specified by the user.

Parameters

registry_key : str

Key to register field under in data registry.

obs_key : str | NoneOptional[str]

Key to access the field in the AnnData obs mapping. If None, defaults to registry_key.

unlabeled_category : str | int | floatUnion[str, int, float]

Value assigned to unlabeled cells.

Attributes table

CATEGORICAL_MAPPING_KEY
ORIGINAL_ATTR_KEY
UNLABELED_CATEGORY
attr_key	The key of the data field within the relevant AnnData attribute.
attr_name	The name of the AnnData attribute where the data is stored.
is_empty	Returns True if the field is empty as a function of its kwargs.
registry_key	The key that is referenced by models via a data loader.

Methods table

get_data_registry()	Returns a nested dictionary which describes the mapping to the AnnData data field.
get_field_data(adata)	Returns the requested data as determined by the field for a given AnnData object.
get_summary_stats(state_registry)	Returns a dictionary comprising of summary statistics relevant to the field.
register_field(adata)	Sets up the AnnData object and creates a mapping for scvi-tools models to use.
transfer_field(state_registry, adata_target)	Takes an existing scvi-tools setup dictionary and transfers the same setup to the target AnnData.
validate_field(adata)	Validates whether an AnnData object is compatible with this field definition.
view_state_registry(state_registry)	Returns a rich.table.Table summarizing a state registry produced by this field.

Attributes

CATEGORICAL_MAPPING_KEY

LabelsWithUnlabeledObsField.CATEGORICAL_MAPPING_KEY = 'categorical_mapping'

ORIGINAL_ATTR_KEY

LabelsWithUnlabeledObsField.ORIGINAL_ATTR_KEY = 'original_key'

UNLABELED_CATEGORY

LabelsWithUnlabeledObsField.UNLABELED_CATEGORY = 'unlabeled_category'

attr_key

LabelsWithUnlabeledObsField.attr_key

Return type

str

attr_name

LabelsWithUnlabeledObsField.attr_name

Return type

str

is_empty

LabelsWithUnlabeledObsField.is_empty

Return type

bool

registry_key

LabelsWithUnlabeledObsField.registry_key

Return type

str

Methods

get_data_registry

LabelsWithUnlabeledObsField.get_data_registry()

Returns a nested dictionary which describes the mapping to the AnnData data field.

The dictionary is of the form {“attr_name”: attr_name, “attr_key”: attr_key}. This mapping is then combined with the mappings of other fields to make up the data registry.

Return type

dict

get_field_data

LabelsWithUnlabeledObsField.get_field_data(adata)

Returns the requested data as determined by the field for a given AnnData object.

Return type

ndarray | DataFrameUnion[ndarray, DataFrame]

get_summary_stats

LabelsWithUnlabeledObsField.get_summary_stats(state_registry)

Returns a dictionary comprising of summary statistics relevant to the field.

Parameters

state_registry : dict

Dictionary returned by register_field(). Summary stats should always be a function of information stored in this dictionary.

Return type

dict

Returns

summary_stats_dict The dictionary is of the form {summary_stat_name: summary_stat_value}. This mapping is then combined with the mappings of other fields to make up the summary stats mapping.

register_field

LabelsWithUnlabeledObsField.register_field(adata)

Sets up the AnnData object and creates a mapping for scvi-tools models to use.

Return type

dict

Returns

dict A dictionary containing any additional state required for scvi-tools models not stored directly on the AnnData object.

transfer_field

LabelsWithUnlabeledObsField.transfer_field(state_registry, adata_target, allow_missing_labels=False, **kwargs)

Takes an existing scvi-tools setup dictionary and transfers the same setup to the target AnnData.

Used when one is running a pretrained model on a new AnnData object, which requires the mapping from the original data to be applied to the new AnnData object.

Parameters

state_registry : dict

state_registry dictionary created after registering an AnnData using an AnnDataManager object.

adata_target : AnnData

AnnData object that is being registered.

**kwargs

Keyword arguments to modify transfer behavior.

Return type

dict

Returns

dict A dictionary containing any additional state required for scvi-tools models not stored directly on the AnnData object.

validate_field

LabelsWithUnlabeledObsField.validate_field(adata)

Validates whether an AnnData object is compatible with this field definition.

Return type

None

view_state_registry

LabelsWithUnlabeledObsField.view_state_registry(state_registry)

Returns a rich.table.Table summarizing a state registry produced by this field.

Parameters

state_registry : dict

Dictionary returned by register_field(). Printed summary should always be a function of information stored in this dictionary.

Return type

Table | NoneOptional[Table]

Returns

state_registry_summary Optional rich.table.Table summarizing the state_registry.