scvi.data.fields.MuDataObsmField

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

Attributes table

adata_field	class"~scvi.data.fields.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)	Get summary stats.
preregister(mdata)	Function that is called prior to registering fields.
register_field(mdata)	Register the field.
transfer_field(state_registry, mdata_target, ...)	Transfer the field.
validate_field(mdata)	Validate the field.
view_state_registry(state_registry)	View the state registry.

Attributes

adata_field

MuDataObsmField.adata_field

class”~scvi.data.fields.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:

Optional[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:

Optional[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:

Union[ndarray, DataFrame]

get_modality

MuDataObsmField.get_modality(mdata)

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

Return type:

Union[AnnData, MuData]

get_summary_stats

MuDataObsmField.get_summary_stats(state_registry)

Get summary stats.

Return type:

dict

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)

Register the field.

Return type:

dict

transfer_field

MuDataObsmField.transfer_field(state_registry, mdata_target, **kwargs)

Transfer the field.

Return type:

dict

validate_field

MuDataObsmField.validate_field(mdata)

Validate the field.

Return type:

None

view_state_registry

MuDataObsmField.view_state_registry(state_registry)

View the state registry.

Return type:

Optional[Table]