scgen.SCGEN.get_latent_representation¶
- SCGEN.get_latent_representation(adata=None, indices=None, give_mean=True, mc_samples=5000, batch_size=None, return_dist=False)¶
Return the latent representation for each cell.
This is typically denoted as \(z_n\).
- Parameters
- adata
AnnData|NoneOptional[AnnData] (default:None) AnnData object with equivalent structure to initial AnnData. If None, defaults to the AnnData object used to initialize the model.
- indices
Sequence[int] |NoneOptional[Sequence[int]] (default:None) Indices of cells in adata to use. If None, all cells are used.
- give_mean
bool(default:True) Give mean of distribution or sample from it.
- mc_samples
int(default:5000) For distributions with no closed-form mean (e.g., logistic normal), how many Monte Carlo samples to take for computing mean.
- batch_size
int|NoneOptional[int] (default:None) Minibatch size for data loading into model. Defaults to scvi.settings.batch_size.
- return_dist
bool(default:False) Return (mean, variance) of distributions instead of just the mean. If True, ignores give_mean and mc_samples. In the case of the latter, mc_samples is used to compute the mean of a transformed distribution. If return_dist is true the untransformed mean and variance are returned.
- adata
- Return type
ndarray|Tuple[ndarray,ndarray]Union[ndarray,Tuple[ndarray,ndarray]]- Returns
Low-dimensional representation for each cell or a tuple containing its mean and variance.