scvi.data.fields.LabelsWithUnlabeledObsField#

class scvi.data.fields.LabelsWithUnlabeledObsField(registry_key, obs_key, unlabeled_category)[source]#

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#

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[source]#

attr_name

LabelsWithUnlabeledObsField.attr_name[source]#

is_empty

LabelsWithUnlabeledObsField.is_empty[source]#

mod_key

LabelsWithUnlabeledObsField.mod_key[source]#: The modality key of the data field within the MuData (if applicable).

registry_key

LabelsWithUnlabeledObsField.registry_key[source]#

Methods#

get_data_registry

LabelsWithUnlabeledObsField.get_data_registry()[source]#

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

get_field_data

LabelsWithUnlabeledObsField.get_field_data(adata)[source]#

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

Return type:: Union[ndarray, DataFrame]

get_summary_stats

LabelsWithUnlabeledObsField.get_summary_stats(state_registry)[source]#

Get summary stats.

Return type:: dict

register_field

LabelsWithUnlabeledObsField.register_field(adata)[source]#

Return type:: dict

transfer_field

LabelsWithUnlabeledObsField.transfer_field(state_registry, adata_target, allow_missing_labels=False, **kwargs)[source]#

Transfer the field.

Return type:: dict

validate_field

LabelsWithUnlabeledObsField.validate_field(adata)[source]#

Validate field.

Return type:: None

view_state_registry

LabelsWithUnlabeledObsField.view_state_registry(state_registry)[source]#

View state registry.

Return type:: Optional[Table]