scHopfield.plotting.visualize_perturbation_flow

scHopfield.plotting.visualize_perturbation_flow(adata: AnnData, basis: str = 'umap', velocity_key: str | None = None, cluster_key: str = 'cell_type', colors: Dict[str, str] | None = None, scale_reference: float = 1.0, scale_perturbation: float = 1.0, figsize: Tuple[float, float] = (20, 10), vm: float = 1.0) → Figure[source]

Create comprehensive visualization of perturbation flow analysis.

Creates a 2x3 figure with: - Row 0: Clusters, Reference velocity, Perturbation flow - Row 1: Inner product on embedding, Inner product + flow, Inner product by cluster

Parameters:

  • adata (AnnData) – Annotated data with perturbation simulation results

  • basis (str, optional (default: 'umap')) – Embedding basis

  • velocity_key (str, optional) – Key for reference velocity

  • cluster_key (str, optional (default: 'cell_type')) – Key for cluster labels

  • colors (dict, optional) – Colors for clusters

  • scale_reference (float, optional (default: 1.0)) – Scale for reference flow arrows

  • scale_perturbation (float, optional (default: 1.0)) – Scale for perturbation flow arrows

  • figsize (tuple, optional) – Figure size

  • vm (float, optional (default: 1.0)) – Max value for inner product colorscale

Return type:

plt.Figure