pygot.tools.traj.simulate_trajectory

pygot.tools.traj.simulate_trajectory(adata, odefunc, embedding_key, start, end, n_points=100)

Simulate trajecotry using trained NeuralODE model.

Arguments:

adata: AnnData

Annotated data matrix.

odefunc: class:~ODEwrapper or class:~ODEwrapperNoTime

trained NeuralODE model by function fit_velocity_model

embedding_key: `str’

Name of latent space to fit, in adata.obsm

start: int

Start time of simulation

end: int

End time of simulation

n_points: int

Number of points in one trajectory (e.g. 100 points from day0 -> day7)

returns:

trajectory – Trajectory array, (n_points, n_cells, latent_dim)

rtype:

:class`~np.ndarray`