mypackage.MyModel.get_latent_representation¶
-
MyModel.get_latent_representation(adata=None, indices=None, give_mean=True, mc_samples=5000, batch_size=None)¶ Return the latent representation for each cell.
This is denoted as \(z_n\) in our manuscripts.
- 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 :
boolbool(default:True) Give mean of distribution or sample from it.
- mc_samples :
intint(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.
- adata :
- Return type
- Returns
-latent_representation (
ndarray) Low-dimensional representation for each cell