scvelo.tl.velocity¶

scvelo.tl.
velocity
(data, vkey='velocity', mode='stochastic', fit_offset=False, fit_offset2=False, filter_genes=False, groups=None, groupby=None, groups_for_fit=None, constrain_ratio=None, use_raw=False, use_latent_time=None, perc=None, min_r2=0.01, min_likelihood=0.001, r2_adjusted=None, use_highly_variable=True, diff_kinetics=None, copy=False, **kwargs)¶ Estimates velocities in a genespecific manner.
The steadystate model [Manno et al., 2018] determines velocities by quantifying how observations deviate from a presumed steadystate equilibrium ratio of unspliced to spliced mRNA levels. This steadystate ratio is obtained by performing a linear regression restricting the input data to the extreme quantiles. By including secondorder moments, the stochastic model [Bergen et al., 2020] exploits not only the balance of unspliced to spliced mRNA levels but also their covariation. By contrast, the likelihoodbased dynamical model [Bergen et al., 2020] solves the full splicing kinetics and generalizes RNA velocity estimation to transient systems. It is also capable of capturing nonobserved steady states.
 data:
AnnData
Annotated data matrix.
 vkey: str (default: ‘velocity’)
Name under which to refer to the computed velocities for velocity_graph and velocity_embedding.
 mode: ‘deterministic’, ‘stochastic’ or ‘dynamical’ (default: ‘stochastic’)
Whether to run the estimation using the steadystate/deterministic, stochastic or dynamical model of transcriptional dynamics. The dynamical model requires to run tl.recover_dynamics first.
 fit_offset: bool (default: False)
Whether to fit with offset for first order moment dynamics.
 fit_offset2: bool, (default: False)
Whether to fit with offset for second order moment dynamics.
 filter_genes: bool (default: True)
Whether to remove genes that are not used for further velocity analysis.
 groups: str, list (default: None)
Subset of groups, e.g. [‘g1’, ‘g2’, ‘g3’], to which velocity analysis shall be restricted.
 groupby: str, list or np.ndarray (default: None)
Key of observations grouping to consider.
 groups_for_fit: str, list or np.ndarray (default: None)
Subset of groups, e.g. [‘g1’, ‘g2’, ‘g3’], to which steadystate fitting shall be restricted.
 constrain_ratio: float or tuple of type float or None: (default: None)
Bounds for the steadystate ratio.
 use_raw: bool (default: False)
Whether to use raw data for estimation.
 use_latent_time: bool`or `None (default: None)
Whether to use latent time as a regularization for velocity estimation.
 perc: float (default: [5, 95])
Percentile, e.g. 98, for extreme quantile fit.
 min_r2: float (default: 0.01)
Minimum threshold for coefficient of determination
 min_likelihood: float (default: None)
Minimal likelihood for velocity genes to fit the model on.
 r2_adjusted: bool (default: None)
Whether to compute coefficient of determination on full data fit (adjusted) or extreme quantile fit (None)
 use_highly_variable: bool (default: True)
Whether to use highly variable genes only, stored in .var[‘highly_variable’].
 copy: bool (default: False)
Return a copy instead of writing to adata.
 Returns
velocity (.layers) – velocity vectors for each individual cell
velocity_genes, velocity_beta, velocity_gamma, velocity_r2 (.var) – parameters
 data: