scvelo.tl.latent_time

scvelo.tl.latent_time(data, vkey='velocity', min_likelihood=0.1, min_confidence=0.75, min_corr_diffusion=None, weight_diffusion=None, root_key=None, end_key=None, t_max=None, copy=False)

Computes a gene-shared latent time.

Gene-specific latent timepoints obtained from the dynamical model are coupled to a universal gene-shared latent time, which represents the cell’s internal clock and is based only on its transcriptional dynamics.

Parameters:

• data (AnnData) – Annotated data matrix

• vkey (str (default: ‘velocity’)) – Name of velocity estimates to be used.

• min_likelihood (float between 0 and 1 or None (default: .1)) – Minimal likelihood fitness for genes to be included to the weighting.

• min_confidence (float between 0 and 1 (default: .75)) – Parameter for local coherence selection.

• min_corr_diffusion (float between 0 and 1 or None (default: None)) – Only select genes that correlate with velocity pseudotime obtained from diffusion random walk on velocity graph.

• weight_diffusion (float or None (default: None)) – Weight applied to couple latent time with diffusion-based velocity pseudotime.

• root_key (str or None (default: ‘root_cells’)) – Key (.uns, .obs) of root cell to be used. If not set, it obtains root cells from velocity-inferred transition matrix.

• end_key (str or None (default: None)) – Key (.obs) of end points to be used.

• t_max (float or None (default: None)) – Overall duration of differentiation process. If not set, a overall transcriptional timescale of 20 hours is used as prior.

• copy (bool (default: False)) – Return a copy instead of writing to adata.

Returns:

latent_time – latent time from learned dynamics for each cell

Return type:

.obs