plot dyn system

for_jc.py

"""
sudo apt-get install python-dev graphviz libgraphviz-dev pkg-config
pip install pygraphviz
"""
%matplotlib inline
import numpy as np
import os
import networkx as nx
from networkx.drawing.nx_agraph import to_agraph
from IPython.display import Image

def plot(W, O, labels):
    G = nx.DiGraph(W)
   
    # add graphviz layout options (see https://stackoverflow.com/a/39662097)
    G.graph['edge'] = {'arrowsize': '1.', 'splines': 'curved',
                       'fontsize':10, 'fontcolor':'gray'}
    G.graph['node'] = {'shape': 'circle', 'style': 'filled',
                       'fontcolor':'white', 'fillcolor':'k'}
    G.graph['graph'] = {'scale': '3'}

    # Change node color observable
    for i, (obs, label) in enumerate(zip(O, labels)):
        if not obs:
            G.nodes[i]['fillcolor'] = 'white'
            G.nodes[i]['fontcolor'] = 'k'
        G.nodes[i]['label'] = label
        
        # change arrow for negative weights
        for j, edge in G[i].items():
            edge['xlabel'] = W[i, j]
            if W[i, j] < 0:
                edge['arrowhead'] = 'dot'
                
    
    A = to_agraph(G)
    A.layout('dot')                                                                 
    A.draw('_graph.png')
    return Image(filename='_graph.png')
    
# define the graph as per your question
W = np.zeros((3, 3))
W[0, 1] = 1
W[1, 1] = .99
W[1, 2] = .1
W[2, 2] = .99
W[2, 1] = -.1

# observables
O = np.zeros(3)
O[0] = 1
O[1] = 1

plot(W=W, O=[1, 1, 0], labels=['u', '<x<SUB>1</SUB>>', '<x<SUB>2</SUB>>'])