Plot

The strengths.plot module provides a few convenient plotting functions for visualization. Those functions internally rely on the Matplotlib package, which thus needs to be installed.

strengths.plot.plot_trajectory(output, species, position=None, *, ax=None)

Plots the time trajectory of one or more species. It relies on the Matplotlib package.

Parameters:

  • output (RDOutput) – simulation output

  • species (str or array of str.) – labels of the species for which the trajectories should be plotted. if given a label, only one trajectory is plotted. if given an array, trajectories of all the labels are plotted.

  • position (None, number, tuple or Coord like) – position of the cell from which we want the trajectory. if None, the global trajectory for the whole system is plotted instead.

  • ax – (optional keyword argument) Matplotlib axis to be used (default = None).

strengths.plot.plot_sample_state_2D(output, species, sample, axis='auto', axis_position=0, environments=None, xmin=None, xmax=None, units_system=None, *, ax=None)

Plots the distribution for the quantity of a species on a plan of the system space. It relies on the Matplotlib package.

Parameters:

  • output (RDOutput) – simulation output

  • spacies – label of the species of which the state should be plotted

  • sample (int) – index of the sample at chich the state should be taken

  • axis (str) –

    axis along which the state slice should be taken. accepted values are :

    • ”auto” : the axis that seems the most appropriate is used

    • ”x” : the x axis is taken

    • ”y” : the y axis used

    • ”z” : the z axis is used

  • axis_position (int) – position of the slice along the slice axis

  • ax – (optional keyword argument) Matplotlib axis to be used (default = None).

strengths.plot.plot_state_2D(system, species, axis='auto', axis_position=0, *, ax=None)

Plots the distribution for the quantity of a species on a plan of the system space. It relies on the Matplotlib package.

strengths.plot.plot_environments_2D(system, axis='auto', axis_position=0, env_color_dict=None, *, ax=None)

Plots the distribution of the reaction diffusion environments on a plan of the system space. env_color_dict allow to define which color should be used to represent each environment. If it is ignored, a gray scale will be used. It relies on the Matplotlib package.

strengths.plot.plot_chemostats_2D(system, species, axis='auto', axis_position=0, color_no='white', color_yes='black', *, ax=None)

Plots the distribution of the chemostats for a given species on a plan of the system space. color_no and color_yes are colors to be used to indicate the absence or prence of chemostats. defaults are “white” and “black”. It relies on the Matplotlib package.