scvi.data.fields.MuDataObsmField

class scvi.data.fields.MuDataObsmField(*args, mod_key=None, mod_required=False, **kwargs)

Attributes table

adata_field	AnnDataField instance that this class instance wraps.
attr_key	The key of the data field within the relevant AnnData/MuData attribute.
attr_name	The name of the AnnData/MuData 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_modality(mdata)	Fetches the appropriate modality from the MuData object using self.mod_key.
get_summary_stats(state_registry)	Returns a dictionary comprising of summary statistics relevant to the field.
preregister(mdata)	Function that is called prior to registering fields.
register_field(mdata)	Sets up the AnnData/MuData object and creates a mapping for scvi-tools models to use.
transfer_field(state_registry, mdata_target, ...)	Takes an existing scvi-tools setup dictionary and transfers the same setup to the target AnnData.
validate_field(mdata)	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

adata_field

MuDataObsmField.adata_field

AnnDataField instance that this class instance wraps.

Return type:

Type[BaseAnnDataField]

attr_key

MuDataObsmField.attr_key

The key of the data field within the relevant AnnData/MuData attribute.

Return type:

str | NoneOptional[str]

attr_name

MuDataObsmField.attr_name

The name of the AnnData/MuData attribute where the data is stored.

Return type:

str

is_empty

MuDataObsmField.is_empty

Return type:

bool

mod_key

MuDataObsmField.mod_key

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

Return type:

str | NoneOptional[str]

registry_key

MuDataObsmField.registry_key

The key that is referenced by models via a data loader.

Return type:

str

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:

dict

get_field_data

MuDataObsmField.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_modality

MuDataObsmField.get_modality(mdata)

Fetches the appropriate modality from the MuData object using self.mod_key.

Return type:

AnnData | MuDataUnion[AnnData, MuData]

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.

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.

preregister

MuDataObsmField.preregister(mdata)

Function that is called prior to registering fields.

Function that is be called at the beginning of register_field() and transfer_field(). Used when data manipulation is necessary across modalities.

Return type:

None

register_field

MuDataObsmField.register_field(mdata)

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

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.

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

MuDataObsmField.validate_field(mdata)

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

Return type:

None

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.

Return type:

Table | NoneOptional[Table]

Returns:

state_registry_summary Optional rich.table.Table summarizing the state_registry.