diff --git a/scvi/model/_multivi.py b/scvi/model/_multivi.py index 4b3053be26..83ca4eede0 100644 --- a/scvi/model/_multivi.py +++ b/scvi/model/_multivi.py @@ -613,6 +613,8 @@ def get_normalized_expression( AnnData object used to initialize the model. indices Indices of cells in adata to use. If `None`, all cells are used. + n_samples_overall + Number of observations to sample from ``indices`` if ``indices`` is provided. transform_batch Batch to condition on. If transform_batch is: @@ -623,10 +625,6 @@ def get_normalized_expression( Return frequencies of expression for a subset of genes. This can save memory when working with large datasets and few genes are of interest. - library_size - Scale the expression frequencies to a common library size. - This allows gene expression levels to be interpreted on a common scale of relevant - magnitude. If set to `"latent"`, use the latent library size. use_z_mean If True, use the mean of the latent distribution, otherwise sample from it n_samples @@ -635,6 +633,8 @@ def get_normalized_expression( Minibatch size for data loading into model. Defaults to `scvi.settings.batch_size`. return_mean Whether to return the mean of the samples. + return_numpy + Return a numpy array instead of a pandas DataFrame. Returns -------