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
.