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.
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.
latent_time (.obs) – latent time from learned dynamics for each cell