scvi.data.fields.NumericalJointObsField#

class scvi.data.fields.NumericalJointObsField(registry_key, obs_keys)[source]#

An AnnDataField for a collection of numerical .obs fields in the AnnData data structure.

Creates an .obsm field containing each .obs field to be referenced as a whole a model.

Parameters:

registry_key (str) – Key to register field under in data registry.
obs_keys (Optional[List[str]]) – Sequence of keys to combine to form the obsm field.

Attributes table#

`COLUMNS_KEY`
`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).
`obs_keys`	List of .obs keys that make up this joint field.
`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 the field.
`view_state_registry`(state_registry)	View the state registry.

Attributes#

COLUMNS_KEY

NumericalJointObsField.COLUMNS_KEY = 'columns'#

attr_key

NumericalJointObsField.attr_key[source]#

Return type:: str

attr_name

NumericalJointObsField.attr_name[source]#

Return type:: str

is_empty

NumericalJointObsField.is_empty[source]#

Return type:: bool

mod_key

NumericalJointObsField.mod_key[source]#

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

Return type:: Optional[str]

obs_keys

NumericalJointObsField.obs_keys[source]#

List of .obs keys that make up this joint field.

Return type:: List[str]

registry_key

NumericalJointObsField.registry_key[source]#

Return type:: str

Methods#

get_data_registry

NumericalJointObsField.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

NumericalJointObsField.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

NumericalJointObsField.get_summary_stats(_state_registry)[source]#

Get summary stats.

Return type:: dict

register_field

NumericalJointObsField.register_field(adata)[source]#

Return type:: dict

transfer_field

NumericalJointObsField.transfer_field(state_registry, adata_target, **kwargs)[source]#

Transfer the field.

Return type:: dict

validate_field

NumericalJointObsField.validate_field(adata)[source]#

Validate the field.

Return type:: None

view_state_registry

NumericalJointObsField.view_state_registry(state_registry)[source]#

View the state registry.

Return type:: Optional[Table]