Plotting#

plot_cells(ax, df_cells, intra_low, intra_high)#
plot_cells_at_all_iterations(intra_min: float, intra_max: float, output_path: Path | None = None, save_path: Path | None = None, overwrite: bool = False, transparent: bool = True) list#
plot_cells_at_iter(iteration: int, intra_low: float, intra_high: float, output_path: Path | None = None, save_path: Path | None = None, overwrite: bool = False, transparent: bool = False)#

Plot all cells for a given iteration

Parameters:
  • iteration (int) – Iteration to store. Can be obtained via get_all_iterations.

  • intra_low (float) – Lower boundary for colorscale of intracellular plotting.

  • intra_high (float) – Upper boundary for colorscale of intracellular plotting.

  • output_path (Path | None = None) – Path where simulation run is stored. If not specified will be given with get_last_output_path.

  • save_path (Path | None = None) – Where to store the generated image. By default, chooses Path(output_path / "images").

  • overwrite (bool) – Overwrite a filename which is already present with identical name.

  • transparent (bool) – Sets the background to transparent if True.

Raises:

ValueError: – See get_last_output_path.