simulate

scdiffeq.tools._simulation.simulate(adata: AnnData, diffeq: LightningModule, idx: Index | None = None, use_key: str = 'X_pca', time_key: str = 'Time point', N: int | None = 1, t: Tensor | None = None, dt: float | None = 0.1, device: device | None = device(type='cpu'), *args, **kwargs) → AnnData

Simulate trajectories by sampling from an scDiffEq model.

Parameters:

• adata (AnnData) – Input AnnData object.

• idx (pd.Index) – Cell indices (corresponding to adata) from which the model should initiate sampled trajectories.

• diffeq (lightning.LightningModule) – The differential equation model.

• use_key (str, optional) – adata accession key for the input data. Default is “X_pca”.

• N (int, optional) – Number of trajectories to sample from the model. Default is 2000.

• device (device, optional) – Device to run the simulation on. Default is True.

Returns:

AnnData object encapsulating scDiffEq model simulation.

Return type:

AnnData

Controlling class

• Simulation
  • Simulation
    • Simulation.__init__()
    • Simulation.idx
    • Simulation.Z0
    • Simulation.t
    • Simulation.forward()
    • Simulation._to_adata_sim()
    • Simulation.__call__()
    • Simulation.__parse__()
    • Simulation.__update__()