scvi.data.fields.LayerField

class scvi.data.fields.LayerField(registry_key, layer, is_count_data=True, correct_data_format=True)

An AnnDataField for layer or X attributes in the AnnData data structure.

Parameters:

• registry_key (str) – Key to register field under in data registry.

• layer (Optional[str]) – Key to access the field in the AnnData layers mapping. If None, uses the data in .X.

• is_count_data (bool (default: True)) – If True, checks if the data are counts during validation.

• correct_data_format (bool (default: True)) – If True, checks and corrects that the AnnData field is C_CONTIGUOUS and csr if it is dense numpy or sparse respectively.

• save_column_names – If True, saves var names to the associated state registry as column_names.

Attributes table

COLUMN_NAMES_KEY
N_CELLS_KEY
N_OBS_KEY
N_VARS_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).
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

COLUMN_NAMES_KEY

LayerField.COLUMN_NAMES_KEY = 'column_names'

N_CELLS_KEY

LayerField.N_CELLS_KEY = 'n_cells'

N_OBS_KEY

LayerField.N_OBS_KEY = 'n_obs'

N_VARS_KEY

LayerField.N_VARS_KEY = 'n_vars'

attr_key

LayerField.attr_key

attr_name

LayerField.attr_name

is_empty

LayerField.is_empty

mod_key

LayerField.mod_key

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

registry_key

LayerField.registry_key

Methods

get_data_registry

LayerField.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

get_field_data

LayerField.get_field_data(adata)

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

Return type:

Union[ndarray, DataFrame]

get_summary_stats

LayerField.get_summary_stats(state_registry)

Get summary stats.

Return type:

dict

register_field

LayerField.register_field(adata)

Register the field.

Return type:

dict

transfer_field

LayerField.transfer_field(state_registry, adata_target, **kwargs)

Transfer the field.

Return type:

dict

validate_field

LayerField.validate_field(adata)

Validate the field.

Return type:

None

view_state_registry

LayerField.view_state_registry(_state_registry)

View the state registry.

Return type:

Optional[Table]