Network plot

If PLOT_NETWORK=True, network plots of the start and the optimised transition matrix are created. If SAVE_OUTPUT=True, the plots are saved as pdf files with names NETWORK_PLOT_FILE_NAME_start and NETWORK_PLOT_FILE_NAME_final.

The edges are coloured with the colours provided in GRAPH_COLOURS, where the first and second colour represent the colour of the edges that cannot and can be adjusted, respectively. The nodes are coloured by the colour map specified in COLOUR_MAP according to their stationary distribution values. The edge weights are multiplied by EDGE_FACTOR to determine the edge width of the network plot.