scvi.data.fields.MuDataObsmField#

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

Parameters:

mod_key (Optional[str]) –
mod_required (bool) –

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[source]#: class”~scvi.data.fields.AnnDataField instance that this class instance wraps.

attr_key

MuDataObsmField.attr_key[source]#: The key of the data field within the relevant AnnData/MuData attribute.

attr_name

MuDataObsmField.attr_name[source]#: The name of the AnnData/MuData attribute where the data is stored.

is_empty

MuDataObsmField.is_empty[source]#

mod_key

MuDataObsmField.mod_key[source]#: The modality key of the data field within the MuData (if applicable).

registry_key

MuDataObsmField.registry_key[source]#: The key that is referenced by models via a data loader.

Methods#

get_data_registry

MuDataObsmField.get_data_registry()[source]#

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)[source]#

Returns the requested data as determined by the field for a given AnnData/MuData object.

Parameters:: adata (Union[AnnData, MuData]) –
Return type:: Union[ndarray, DataFrame]

get_modality

MuDataObsmField.get_modality(mdata)[source]#

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

Parameters:: mdata (MuData) –
Return type:: Union[AnnData, MuData]

get_summary_stats

MuDataObsmField.get_summary_stats(state_registry)[source]#

Get summary stats.

Parameters:: state_registry (dict) –
Return type:: dict

preregister

MuDataObsmField.preregister(mdata)[source]#

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.

Parameters:: mdata (MuData) –
Return type:: None

register_field

MuDataObsmField.register_field(mdata)[source]#

Parameters:: mdata (MuData) –
Return type:: dict

transfer_field

MuDataObsmField.transfer_field(state_registry, mdata_target, **kwargs)[source]#

Transfer the field.

Parameters:

state_registry (dict) –
mdata_target (MuData) –

Return type:

dict

validate_field

MuDataObsmField.validate_field(mdata)[source]#

Validate the field.

Parameters:: mdata (MuData) –
Return type:: None

view_state_registry

MuDataObsmField.view_state_registry(state_registry)[source]#

View the state registry.

Parameters:: state_registry (dict) –
Return type:: Optional[Table]