evolocity.tl.terminal_states¶
-
evolocity.tl.
terminal_states
(data, vkey='velocity', groupby=None, groups=None, self_transitions=False, eps=0.001, random_state=0, exp_scale=50, copy=False, **kwargs)¶ Computes terminal states (root and end points).
The end points and root nodes are obtained as stationary states of the velocity-inferred transition matrix and its transposed, respectively, which is given by left eigenvectors corresponding to an eigenvalue of 1, i.e.
\[μ^{\textrm{end}}=μ^{\textrm{end}} \pi, \quad μ^{\textrm{root}}=μ^{\textrm{root}} \pi^{\small \textrm{T}}.\]evo.tl.terminal_states(adata) evo.pl.scatter(adata, color=['root_nodes', 'end_points'])
- Parameters
- data :
AnnData
Annotated data matrix.
- vkey : str (default: ‘velocity’)
Name of velocity estimates to be used.
- groupby : str, list or np.ndarray (default: None)
Key of observations grouping to consider. Only to be set, if each group is assumed to have a distinct lineage with an independent root and end point.
- groups : str, list or np.ndarray (default: None)
Groups selected to find terminal states on. Must be an element of .obs[groupby]. To be specified only for very distinct/disconnected clusters.
- self_transitions : bool (default: False)
Allow transitions from one node to itself.
- eps : float (default: 1e-3)
Tolerance for eigenvalue selection.
- random_state : int or None (default: 0)
Seed used by the random number generator. If None, use the RandomState instance by np.random.
- copy : bool (default: False)
Return a copy instead of writing to data.
- **kwargs
Passed to evolocity.tl.transition_matrix(), e.g. basis, weight_diffusion.
- data :
- Returns
Returns or updates data with the attributes
root_nodes (.obs) – sparse matrix with transition probabilities.
end_points (.obs) – sparse matrix with transition probabilities.