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 (Optional[str]) – Key to access the field in the AnnData obs mapping. If None, defaults to registry_key.

• unlabeled_category (Union[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.
mod_key	The modality key of the data field within the MuData (if applicable).
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 data field.
get_field_data(adata)	Returns the requested data as determined by the field for a given AnnData/MuData object.
get_summary_stats(state_registry)	Get summary stats.
register_field(adata)	Register the field.
transfer_field(state_registry, adata_target)	Transfer the field.
validate_field(adata)	Validate field.
view_state_registry(state_registry)	View state registry.

Attributes

LabelsWithUnlabeledObsField.CATEGORICAL_MAPPING_KEY = 'categorical_mapping'

LabelsWithUnlabeledObsField.ORIGINAL_ATTR_KEY = 'original_key'

LabelsWithUnlabeledObsField.UNLABELED_CATEGORY = 'unlabeled_category'

LabelsWithUnlabeledObsField.attr_key

LabelsWithUnlabeledObsField.attr_name

LabelsWithUnlabeledObsField.is_empty

LabelsWithUnlabeledObsField.mod_key

The modality key of the data field within the MuData (if applicable).

LabelsWithUnlabeledObsField.registry_key

Methods

LabelsWithUnlabeledObsField.get_data_registry()

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

The dictionary is of the form {“mod_key”: mod_key, “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

LabelsWithUnlabeledObsField.get_field_data(adata)

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

Return type

Union[ndarray, DataFrame]

LabelsWithUnlabeledObsField.get_summary_stats(state_registry)

Get summary stats.

Return type

dict

LabelsWithUnlabeledObsField.register_field(adata)

Register the field.

Return type

dict

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

Transfer the field.

Return type

dict

LabelsWithUnlabeledObsField.validate_field(adata)

Validate field.

Return type

None

LabelsWithUnlabeledObsField.view_state_registry(state_registry)

View state registry.

Return type

Optional[Table]