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.
Attributes table#
The key of the data field within the relevant AnnData attribute. |
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The name of the AnnData attribute where the data is stored. |
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Returns True if the field is empty as a function of its kwargs. |
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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. |
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Returns the requested data as determined by the field for a given AnnData object. |
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Returns a dictionary comprising of summary statistics relevant to the field. |
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Sets up the AnnData object and creates a mapping for scvi-tools models to use. |
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Takes an existing scvi-tools setup dictionary and transfers the same setup to the target AnnData. |
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Validates whether an AnnData object is compatible with this field definition. |
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Returns a |
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#
attr_name#
is_empty#
registry_key#
Methods#
get_data_registry#
- LabelsWithUnlabeledObsField.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#
- LabelsWithUnlabeledObsField.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.
- 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#
- LabelsWithUnlabeledObsField.transfer_field(state_registry, adata_target, allow_missing_labels=False, **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#
- LabelsWithUnlabeledObsField.view_state_registry(state_registry)#
Returns a
rich.table.Table
summarizing a state registry produced by this field.- Parameters
- state_registry :
dict
Dictionary returned by
register_field()
. Printed summary should always be a function of information stored in this dictionary.
- state_registry :
- Return type
- Returns
state_registry_summary Optional
rich.table.Table
summarizing thestate_registry
.