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=[5, 95], min_r2=0.01, min_likelihood=0.001, r2_adjusted=None, copy=False, **kwargs)¶
Estimates velocities in a gene-specific manner.
The steady-state model determines velocities by quantifying how observations deviate from a presumed steady-state equilibrium ratio of unspliced to spliced mRNA levels. This steady-state ratio is obtained by performing a linear regression restricting the input data to the extreme quantiles. By including second-order moments, the stochastic model exploits not only the balance of of unspliced to spliced mRNA levels but also their covariation. By contrast, the likelihood-based dynamical model solves the full splicing kinetics and generalizes RNA velocity estimation to transient systems. It is also capable of capturing non-observed steady states.
- data :
Annotated data matrix.
- vkey : str (default: ‘velocity’)
Name under which to refer to the computed velocities for velocity_graph and velocity_embedding.
- mode : ‘steady_state’, ‘deterministic’, ‘stochastic’ or ‘dynamical’ (default: ‘stochastic’)
Whether to run the estimation using the deterministic or stochastic model of transcriptional dynamics. The ‘steady_state’ model is default and refers to the deterministic model. The dynamical model requires to run tl.recover_dynamics first; it is yet under development.
- 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 steady-state fitting shall be restricted.
- constrain_ratio : float or tuple of type float or None: (default: None)
Bounds for the steady-state ratio gamma’.
- 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 when using dynamical mode.
- perc : float (default: None)
Percentile, e.g. 98, upon for extreme quantile fit (to better capture steady states for velocity estimation).
- 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)
- copy : bool (default: False)
Return a copy instead of writing to adata.
- Returns or updates adata with the attributes
- velocity (.layers) – velocity vectors for each individual cell
- variance_velocity (.layers) – velocity vectors for the cell variances
- velocity_offset, velocity_beta, velocity_gamma, velocity_r2 (.var) – parameters
- data :