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 : str | NoneOptional[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)	Returns a dictionary comprising of summary statistics relevant to the field.
register_field(adata)	Sets up the AnnData/MuData 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/MuData 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

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

Return type:

str | NoneOptional[str]

attr_name

LayerField.attr_name

Return type:

str

is_empty

LayerField.is_empty

Return type:

bool

mod_key

LayerField.mod_key

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

Return type:

str | NoneOptional[str]

registry_key

LayerField.registry_key

Return type:

str

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:

ndarray | DataFrameUnion[ndarray, DataFrame]

get_summary_stats

LayerField.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

LayerField.register_field(adata)

Sets up the AnnData/MuData 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/MuData object.

transfer_field

LayerField.transfer_field(state_registry, adata_target, **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/MuData 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

LayerField.validate_field(adata)

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

Return type:

None

view_state_registry

LayerField.view_state_registry(_state_registry)

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

Parameters:

state_registry

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.