multivelovae.velocity

multivelovae.velocity(adata, adata_atac, key, batch_key=None, ref_batch=None, batch_hvg_key=None, batch_correction=False, use_original=False, rna_only=False, likelihood_thred=None, use_only_ref=True, sigma=None, approx=False)

Compute multi-omic velocity for VAE.

Args:

adata (anndata.AnnData):

RNA AnnData object.

adata_atac (anndata.AnnData):

ATAC AnnData object.

key (str):

Key of VAE variables.

batch_key (str, optional):

Field in adata.obs to find batch labels. Defaults to None.

ref_batch (int, optional):

Index to use as the reference batch. Defaults to None.

batch_hvg_key (str, optional):

Prefix of key for batch highly-variable genes in adata.var. Defaults to None.

batch_correction (bool, optional):

Whether the output was generated with batch correction. Defaults to False.

use_original (bool, optional):

whether to use the (noisy) input count to compute the velocity. Defaults to False.

rna_only (bool, optional):

Whether the model was trained with RNA only. Defaults to False.

likelihood_thred (float, optional):

Threshold to set high likelihood velocity genes. Defaults to None.

use_only_ref (bool, optional):

Select velocity genes only from highly variable gene list of the reference batch. Defaults to True.

sigma (float, optional):

Parameter used in Gaussian filtering of velocity values. Defaults to None.

approx (bool, optional):

Whether to use linear approximation to compute velocity. Defaults to False.