New plots for the network example

[riberaborrell]

re-write

• plot_density() method
• plot_effective_current() method
  To do:
• In the ergodic case: remove edge 1-2 from visualization since the transition probability between 1 and 2 is zero.
• Similarly, remove edges from the periodic and finite-time case when zero transition probability.
• Color bar in the right
• The normalized reactive density is not defined for times n=0 and n=N-1 for the finite-time case.
• similar for the current
• similar for the rate
• for plotting the rates: use plt.ylim(np.nanmin(rate_p)-0.005, np.nanmax(rate_p)+0.005) to change the y limits of the rate plot and use plt.legend(ncol=2) to show the two (or three) legend items next to another
• different colorscheme such that the numbers on the nodes (e.g. A, B,2,...) can be read well (also Niklas was confused that the color of the reactive density in the network example is purple in A and B, maybe its more intuitive/better to have a color scheme that gives color white to the value 0)
• increase the image quality

[riberaborrell]

Luzie's suggestion:

[riberaborrell]

networkx allows to have multiple edges but does not plot them as we wish:
https://stackoverflow.com/questions/22785849/drawing-multiple-edges-between-two-nodes-with-networkx

[LuzieH]

There is some problem with the plots of the small network.

[LuzieH]