diff --git a/docs/user_guide/models/multivi.rst b/docs/user_guide/models/multivi.rst index cfced254d0..473e95f4cb 100644 --- a/docs/user_guide/models/multivi.rst +++ b/docs/user_guide/models/multivi.rst @@ -96,7 +96,7 @@ The latent variables, along with their description are summarized in the followi - Low-dimensional representation capturing the state of a cell. - N/A * - :math:`\rho_n \in \Delta^{G-1}` - - Denoised/normalized gene expression. This is a vector that sums to 1 within a cell, unless `size_factor_key is not None` in :class:`~scvi.model.MULTVI.setup_anndata`, in which case this is only force to be non-negative via softplus. + - Denoised/normalized gene expression. This is a vector that sums to 1 within a cell, unless `size_factor_key is not None` in :class:`~scvi.model.MULTVI.setup_anndata`, in which case this is only forced to be non-negative via softplus. - ``px_scale`` * - :math:`\ell_n \in (0, \infty)` - Library size for RNA. diff --git a/docs/user_guide/models/scvi.rst b/docs/user_guide/models/scvi.rst index 55b31c9388..c75db06b0d 100644 --- a/docs/user_guide/models/scvi.rst +++ b/docs/user_guide/models/scvi.rst @@ -90,7 +90,7 @@ The latent variables, along with their description are summarized in the followi - Low-dimensional representation capturing the state of a cell. - N/A * - :math:`\rho_n \in \Delta^{G-1}` - - Denoised/normalized gene expression. This is a vector that sums to 1 within a cell, unless `size_factor_key is not None` in :class:`~scvi.model.SCVI.setup_anndata`, in which case this is only force to be non-negative via softplus. + - Denoised/normalized gene expression. This is a vector that sums to 1 within a cell, unless `size_factor_key is not None` in :class:`~scvi.model.SCVI.setup_anndata`, in which case this is only forced to be non-negative via softplus. - ``px_scale`` * - :math:`\ell_n \in (0, \infty)` - Library size for RNA. Here it is modeled as a latent variable, but the recent default for scVI is to treat library size as observed, equal to the total RNA UMI count of a cell. This can be controlled by passing ``use_observed_lib_size=False`` to :class:`~scvi.model.SCVI`. The library size can also be set manually using `size_factor_key` in :class:`~scvi.model.SCVI.setup_anndata`. diff --git a/docs/user_guide/models/totalvi.rst b/docs/user_guide/models/totalvi.rst index 291ba2a672..7ba828d17b 100644 --- a/docs/user_guide/models/totalvi.rst +++ b/docs/user_guide/models/totalvi.rst @@ -115,7 +115,7 @@ The latent variables, along with their description are summarized in the followi - Low-dimensional representation capturing joint state of a cell - N/A * - :math:`\rho_n \in \Delta^{G-1}` - - Denoised/normalized gene expression. This is a vector that sums to 1 within a cell, unless `size_factor_key is not None` in :class:`~scvi.model.TOTALVI.setup_anndata`, in which case this is only force to be non-negative via softplus. + - Denoised/normalized gene expression. This is a vector that sums to 1 within a cell, unless `size_factor_key is not None` in :class:`~scvi.model.TOTALVI.setup_anndata`, in which case this is only forced to be non-negative via softplus. - ``px_["scale"]`` * - :math:`\alpha_n \in [1, \infty)^T` - Foreground scaling factor for proteins, identifies the mixture distribution (see below)