scvi.data.fields.MuDataObsmField#
- class scvi.data.fields.MuDataObsmField(*args, mod_key=None, mod_required=False, **kwargs)#
Attributes table#
AnnDataField instance that this class instance wraps. |
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The key of the data field within the relevant AnnData/MuData attribute. |
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The name of the AnnData/MuData 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 modality key of the data field within the MuData (if applicable). |
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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 data field. |
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Returns the requested data as determined by the field for a given AnnData/MuData object. |
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Fetches the appropriate modality from the MuData object using |
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Returns a dictionary comprising of summary statistics relevant to the field. |
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Function that is called prior to registering fields. |
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Sets up the AnnData/MuData 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/MuData object is compatible with this field definition. |
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Returns a |
Attributes#
adata_field#
- MuDataObsmField.adata_field#
AnnDataField instance that this class instance wraps.
- Return type:
attr_key#
attr_name#
is_empty#
mod_key#
registry_key#
Methods#
get_data_registry#
- MuDataObsmField.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:
get_field_data#
get_modality#
get_summary_stats#
- MuDataObsmField.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.
preregister#
- MuDataObsmField.preregister(mdata)#
Function that is called prior to registering fields.
Function that is be called at the beginning of
register_field()
andtransfer_field()
. Used when data manipulation is necessary across modalities.- Return type:
register_field#
transfer_field#
- MuDataObsmField.transfer_field(state_registry, mdata_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/MuData 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#
- MuDataObsmField.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
.