scHopfield.plotting.plot_reference_flow

scHopfield.plotting.plot_reference_flow(adata: AnnData, basis: str = 'umap', velocity_key: str | None = None, ax: Axes | None = None, scale: float = 1.0, color: str = 'black', alpha: float = 0.8, show_background: bool = True, background_color: str = 'lightgray', s: float = 10, figsize: Tuple[float, float] = (8, 8), title: str = 'Reference Velocity', **quiver_kwargs) → Axes[source]

Plot reference velocity flow (e.g., from scVelo).

Parameters:

  • adata (AnnData) – Annotated data with velocity

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

  • velocity_key (str, optional) – Key for velocity in obsm

  • ax (plt.Axes, optional) – Axes to plot on

  • scale (float, optional (default: 1.0)) – Scale factor for arrows

  • color (str, optional (default: 'black')) – Arrow color

  • alpha (float, optional (default: 0.8)) – Arrow transparency

  • show_background (bool, optional (default: True)) – Show background scatter

  • background_color (str, optional (default: 'lightgray')) – Background scatter color

  • s (float, optional (default: 10)) – Scatter point size

  • figsize (tuple, optional) – Figure size

  • title (str, optional) – Plot title

  • **quiver_kwargs – Additional arguments for quiver plot

Return type:

plt.Axes