scvi.external.SCVIVA
====================

.. currentmodule:: scvi.external

.. add toctree option to make autodoc generate the pages

.. autoclass:: SCVIVA



Attributes table
~~~~~~~~~~~~~~~~~~

.. autosummary::

    ~SCVIVA.adata
    ~SCVIVA.adata_manager
    ~SCVIVA.device
    ~SCVIVA.get_normalized_function_name
    ~SCVIVA.history
    ~SCVIVA.is_trained
    ~SCVIVA.minified_data_type
    ~SCVIVA.registry
    ~SCVIVA.run_id
    ~SCVIVA.run_name
    ~SCVIVA.summary_string
    ~SCVIVA.test_indices
    ~SCVIVA.train_indices
    ~SCVIVA.validation_indices





Methods table
~~~~~~~~~~~~~

.. autosummary::

    ~SCVIVA.convert_legacy_save
    ~SCVIVA.data_registry
    ~SCVIVA.deregister_manager
    ~SCVIVA.differential_abundance
    ~SCVIVA.differential_expression
    ~SCVIVA.get_aggregated_posterior
    ~SCVIVA.get_anndata_manager
    ~SCVIVA.get_batch_representation
    ~SCVIVA.get_composition_error
    ~SCVIVA.get_elbo
    ~SCVIVA.get_feature_correlation_matrix
    ~SCVIVA.get_from_registry
    ~SCVIVA.get_importance_weights
    ~SCVIVA.get_latent_library_size
    ~SCVIVA.get_latent_representation
    ~SCVIVA.get_likelihood_parameters
    ~SCVIVA.get_marginal_ll
    ~SCVIVA.get_niche_error
    ~SCVIVA.get_normalized_expression
    ~SCVIVA.get_reconstruction_error
    ~SCVIVA.get_setup_arg
    ~SCVIVA.get_state_registry
    ~SCVIVA.get_var_names
    ~SCVIVA.load
    ~SCVIVA.load_query_data
    ~SCVIVA.load_registry
    ~SCVIVA.minify_adata
    ~SCVIVA.posterior_predictive_sample
    ~SCVIVA.predict_neighborhood
    ~SCVIVA.predict_niche_activation
    ~SCVIVA.prepare_query_anndata
    ~SCVIVA.prepare_query_mudata
    ~SCVIVA.preprocessing_anndata
    ~SCVIVA.preprocessing_query_anndata
    ~SCVIVA.register_manager
    ~SCVIVA.save
    ~SCVIVA.setup_annbatch
    ~SCVIVA.setup_anndata
    ~SCVIVA.to_device
    ~SCVIVA.train
    ~SCVIVA.transfer_fields
    ~SCVIVA.update_setup_method_args
    ~SCVIVA.view_anndata_setup
    ~SCVIVA.view_registry
    ~SCVIVA.view_setup_args
    ~SCVIVA.view_setup_method_args





Attributes
~~~~~~~~~~~



.. autoattribute:: SCVIVA.adata

.. autoattribute:: SCVIVA.adata_manager

.. autoattribute:: SCVIVA.device

.. autoattribute:: SCVIVA.get_normalized_function_name

.. autoattribute:: SCVIVA.history

.. autoattribute:: SCVIVA.is_trained

.. autoattribute:: SCVIVA.minified_data_type

.. autoattribute:: SCVIVA.registry

.. autoattribute:: SCVIVA.run_id

.. autoattribute:: SCVIVA.run_name

.. autoattribute:: SCVIVA.summary_string

.. autoattribute:: SCVIVA.test_indices

.. autoattribute:: SCVIVA.train_indices

.. autoattribute:: SCVIVA.validation_indices






Methods
~~~~~~~



.. automethod:: SCVIVA.convert_legacy_save

.. automethod:: SCVIVA.data_registry

.. automethod:: SCVIVA.deregister_manager

.. automethod:: SCVIVA.differential_abundance

.. automethod:: SCVIVA.differential_expression

.. automethod:: SCVIVA.get_aggregated_posterior

.. automethod:: SCVIVA.get_anndata_manager

.. automethod:: SCVIVA.get_batch_representation

.. automethod:: SCVIVA.get_composition_error

.. automethod:: SCVIVA.get_elbo

.. automethod:: SCVIVA.get_feature_correlation_matrix

.. automethod:: SCVIVA.get_from_registry

.. automethod:: SCVIVA.get_importance_weights

.. automethod:: SCVIVA.get_latent_library_size

.. automethod:: SCVIVA.get_latent_representation

.. automethod:: SCVIVA.get_likelihood_parameters

.. automethod:: SCVIVA.get_marginal_ll

.. automethod:: SCVIVA.get_niche_error

.. automethod:: SCVIVA.get_normalized_expression

.. automethod:: SCVIVA.get_reconstruction_error

.. automethod:: SCVIVA.get_setup_arg

.. automethod:: SCVIVA.get_state_registry

.. automethod:: SCVIVA.get_var_names

.. automethod:: SCVIVA.load

.. automethod:: SCVIVA.load_query_data

.. automethod:: SCVIVA.load_registry

.. automethod:: SCVIVA.minify_adata

.. automethod:: SCVIVA.posterior_predictive_sample

.. automethod:: SCVIVA.predict_neighborhood

.. automethod:: SCVIVA.predict_niche_activation

.. automethod:: SCVIVA.prepare_query_anndata

.. automethod:: SCVIVA.prepare_query_mudata

.. automethod:: SCVIVA.preprocessing_anndata

.. automethod:: SCVIVA.preprocessing_query_anndata

.. automethod:: SCVIVA.register_manager

.. automethod:: SCVIVA.save

.. automethod:: SCVIVA.setup_annbatch

.. automethod:: SCVIVA.setup_anndata

.. automethod:: SCVIVA.to_device

.. automethod:: SCVIVA.train

.. automethod:: SCVIVA.transfer_fields

.. automethod:: SCVIVA.update_setup_method_args

.. automethod:: SCVIVA.view_anndata_setup

.. automethod:: SCVIVA.view_registry

.. automethod:: SCVIVA.view_setup_args

.. automethod:: SCVIVA.view_setup_method_args