scvi.data.fields.LayerField#
- class scvi.data.fields.LayerField(registry_key, layer, is_count_data=True, correct_data_format=True)[source]#
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
|None
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.
- registry_key :
Attributes table#
The key of the data field within the relevant AnnData attribute. |
|
The name of the AnnData attribute where the data is stored. |
|
Returns True if the field is empty as a function of its kwargs. |
|
The key that is referenced by models via a data loader. |
Methods table#
Returns a nested dictionary which describes the mapping to the AnnData data field. |
|
|
Returns the requested data as determined by the field for a given AnnData object. |
|
Returns a dictionary comprising of summary statistics relevant to the field. |
|
Sets up the AnnData object and creates a mapping for scvi-tools models to use. |
|
Takes an existing scvi-tools setup dictionary and transfers the same setup to the target AnnData. |
|
Validates whether an AnnData object is compatible with this field definition. |
|
Returns a |
Attributes#
N_CELLS_KEY#
- LayerField.N_CELLS_KEY = 'n_cells'#
N_VARS_KEY#
- LayerField.N_VARS_KEY = 'n_vars'#
attr_key#
attr_name#
is_empty#
registry_key#
Methods#
get_data_registry#
- LayerField.get_data_registry()#
Returns a nested dictionary which describes the mapping to the AnnData data field.
The dictionary is of the form {“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
get_field_data#
get_summary_stats#
- LayerField.get_summary_stats(state_registry)[source]#
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.
- state_registry :
- Return type
- 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#
transfer_field#
- LayerField.transfer_field(state_registry, adata_target, **kwargs)[source]#
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 object that is being registered.
- **kwargs
Keyword arguments to modify transfer behavior.
- state_registry :
- Return type
- Returns
dict A dictionary containing any additional state required for scvi-tools models not stored directly on the AnnData object.
validate_field#
view_state_registry#
- LayerField.view_state_registry(_state_registry)[source]#
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
- Returns
state_registry_summary Optional
rich.table.Table
summarizing thestate_registry
.