scvi.external.TOTALANVI
=======================

.. currentmodule:: scvi.external

.. add toctree option to make autodoc generate the pages

.. autoclass:: TOTALANVI



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

.. autosummary::

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





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

.. autosummary::

    ~TOTALANVI.convert_legacy_save
    ~TOTALANVI.data_registry
    ~TOTALANVI.deregister_manager
    ~TOTALANVI.differential_abundance
    ~TOTALANVI.differential_expression
    ~TOTALANVI.from_totalvi_model
    ~TOTALANVI.get_aggregated_posterior
    ~TOTALANVI.get_anndata_manager
    ~TOTALANVI.get_elbo
    ~TOTALANVI.get_feature_correlation_matrix
    ~TOTALANVI.get_from_registry
    ~TOTALANVI.get_importance_weights
    ~TOTALANVI.get_latent_library_size
    ~TOTALANVI.get_latent_representation
    ~TOTALANVI.get_likelihood_parameters
    ~TOTALANVI.get_marginal_ll
    ~TOTALANVI.get_normalized_expression
    ~TOTALANVI.get_protein_background_mean
    ~TOTALANVI.get_protein_foreground_probability
    ~TOTALANVI.get_ranked_features
    ~TOTALANVI.get_reconstruction_error
    ~TOTALANVI.get_setup_arg
    ~TOTALANVI.get_state_registry
    ~TOTALANVI.get_var_names
    ~TOTALANVI.load
    ~TOTALANVI.load_query_data
    ~TOTALANVI.load_registry
    ~TOTALANVI.minify_adata
    ~TOTALANVI.minify_mudata
    ~TOTALANVI.posterior_predictive_sample
    ~TOTALANVI.predict
    ~TOTALANVI.prepare_query_anndata
    ~TOTALANVI.prepare_query_mudata
    ~TOTALANVI.register_manager
    ~TOTALANVI.save
    ~TOTALANVI.setup_annbatch
    ~TOTALANVI.setup_anndata
    ~TOTALANVI.setup_mudata
    ~TOTALANVI.shap_adata_predict
    ~TOTALANVI.shap_predict
    ~TOTALANVI.to_device
    ~TOTALANVI.train
    ~TOTALANVI.transfer_fields
    ~TOTALANVI.update_setup_method_args
    ~TOTALANVI.view_anndata_setup
    ~TOTALANVI.view_registry
    ~TOTALANVI.view_setup_args
    ~TOTALANVI.view_setup_method_args





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



.. autoattribute:: TOTALANVI.adata

.. autoattribute:: TOTALANVI.adata_manager

.. autoattribute:: TOTALANVI.device

.. autoattribute:: TOTALANVI.get_normalized_function_name

.. autoattribute:: TOTALANVI.history

.. autoattribute:: TOTALANVI.is_trained

.. autoattribute:: TOTALANVI.minified_data_type

.. autoattribute:: TOTALANVI.registry

.. autoattribute:: TOTALANVI.run_id

.. autoattribute:: TOTALANVI.run_name

.. autoattribute:: TOTALANVI.summary_string

.. autoattribute:: TOTALANVI.test_indices

.. autoattribute:: TOTALANVI.train_indices

.. autoattribute:: TOTALANVI.validation_indices






Methods
~~~~~~~



.. automethod:: TOTALANVI.convert_legacy_save

.. automethod:: TOTALANVI.data_registry

.. automethod:: TOTALANVI.deregister_manager

.. automethod:: TOTALANVI.differential_abundance

.. automethod:: TOTALANVI.differential_expression

.. automethod:: TOTALANVI.from_totalvi_model

.. automethod:: TOTALANVI.get_aggregated_posterior

.. automethod:: TOTALANVI.get_anndata_manager

.. automethod:: TOTALANVI.get_elbo

.. automethod:: TOTALANVI.get_feature_correlation_matrix

.. automethod:: TOTALANVI.get_from_registry

.. automethod:: TOTALANVI.get_importance_weights

.. automethod:: TOTALANVI.get_latent_library_size

.. automethod:: TOTALANVI.get_latent_representation

.. automethod:: TOTALANVI.get_likelihood_parameters

.. automethod:: TOTALANVI.get_marginal_ll

.. automethod:: TOTALANVI.get_normalized_expression

.. automethod:: TOTALANVI.get_protein_background_mean

.. automethod:: TOTALANVI.get_protein_foreground_probability

.. automethod:: TOTALANVI.get_ranked_features

.. automethod:: TOTALANVI.get_reconstruction_error

.. automethod:: TOTALANVI.get_setup_arg

.. automethod:: TOTALANVI.get_state_registry

.. automethod:: TOTALANVI.get_var_names

.. automethod:: TOTALANVI.load

.. automethod:: TOTALANVI.load_query_data

.. automethod:: TOTALANVI.load_registry

.. automethod:: TOTALANVI.minify_adata

.. automethod:: TOTALANVI.minify_mudata

.. automethod:: TOTALANVI.posterior_predictive_sample

.. automethod:: TOTALANVI.predict

.. automethod:: TOTALANVI.prepare_query_anndata

.. automethod:: TOTALANVI.prepare_query_mudata

.. automethod:: TOTALANVI.register_manager

.. automethod:: TOTALANVI.save

.. automethod:: TOTALANVI.setup_annbatch

.. automethod:: TOTALANVI.setup_anndata

.. automethod:: TOTALANVI.setup_mudata

.. automethod:: TOTALANVI.shap_adata_predict

.. automethod:: TOTALANVI.shap_predict

.. automethod:: TOTALANVI.to_device

.. automethod:: TOTALANVI.train

.. automethod:: TOTALANVI.transfer_fields

.. automethod:: TOTALANVI.update_setup_method_args

.. automethod:: TOTALANVI.view_anndata_setup

.. automethod:: TOTALANVI.view_registry

.. automethod:: TOTALANVI.view_setup_args

.. automethod:: TOTALANVI.view_setup_method_args