def addGraphPretty(model, ax, \
positions = None, \
cmap = cm.tab20, **kwargs):
from matplotlib.patches import FancyArrowPatch, Circle, ConnectionStyle, Wedge
r = .115 # radius for circle
graph = model.graph
if positions is None:
positions = nx.circular_layout(graph)
# colors = cm.tab20(arange(model.nNodes))
# colors = cm.get_cmap('tab20')(arange(model.nNodes))
if graph.number_of_nodes() > 20:
cmap = cm.get_cmap('gist_rainbow')
colors = cmap(arange(model.nNodes))
# DEFAULTS
circlekwargs = dict(\
radius = r, \
alpha = 1, \
edgecolor = 'black', \
linewidth = 1, \
linestyle = 'solid',\
zorder = 2)
for k, v in kwargs.get('circle', {}).items():
circlekwargs[k] = v
annotatekwargs = dict(\
horizontalalignment = 'center', \
verticalalignment = 'center', \
transform = ax.transAxes, \
fontsize = 12,\
)
for k, v in kwargs.get('annotate', {}).items():
annotatekwargs[k] = v
for n in graph:
# make circle
c = Circle(positions[n], facecolor = colors[model.mapping[n]],\
**circlekwargs)
# add label
# print(c.center[:2], pos[n])
# ax.text(*c.center, n, horizontalalignment = 'center', \
# verticalalignment = 'center', transform = ax.transAxes)
annotatekwargs['fontsize'] = .95 * circlekwargs['radius']
ax.annotate(n, c.center, **annotatekwargs)
# add to ax
ax.add_patch(c)
# TODO : remove tis for member assignment
# bookkeep for adding edge
graph.node[n]['patch'] = c
seen = {} # bookkeeping
from copy import copy
# arrow style for drawing
arrowsprops = dict(\
arrowstyle = '-|>' if graph.is_directed() else '<|-|>' ,\
mutation_scale = 15.0,\
lw = 2,\
alpha = 1,\
)
edgesScaling = {(u, v): graph[u][v]['weight'] for u, v in graph.edges()}
minWeight, maxWeight = min(edgesScaling.values()), max(
edgesScaling.values())
for u, v in graph.edges():
n1 = graph.node[u]['patch']
n2 = graph.node[v]['patch']
d = graph[u][v]['weight']
rad = 0.1
if (u, v) in seen:
rad = seen.get((u, v))
rad = (rad + np.sign(rad) * 0.1) * -1
# set properties of the edge
alphaEdge = clip(abs(d), .2, 1)
arrowsprops['color'] = 'green' if d > 0 else 'red'
# arrowsprops['alpha'] = alphaEdge
arrowsprops['lw'] = ((d - minWeight) / (maxWeight - minWeight)) * 5
# self-edge is a special case
if u == v:
n2 = copy(n1)
n1 = copy(n1)
theta = random.uniform(0, 2 * pi)
rotation = pi
corner1 = array([sin(theta), cos(theta)]) * r
corner2 = array([sin(theta + rotation), cos(theta + rotation)]) *\
r + .12 * sign(random.randn()) * r
n1.center = array(n1.center) + corner1
n2.center = array(n2.center) + corner2
# n1.center = (n1.center[0] + r, n1.center[1] )
# n2.center = (n2.center[0] - r, n2.center[1])
rad = radians(135) # trial and error
# add edge
e = FancyArrowPatch(n2.center, n1.center, **arrowsprops)
e.set_arrowstyle(head_length=head_length)
else:
e = FancyArrowPatch(n1.center,n2.center, patchA = n1, patchB = n2,\
connectionstyle = f'arc3,rad={rad}',
**arrowsprops)
seen[(u, v)] = rad
ax.add_patch(e)
ax.autoscale()
ax.set_aspect('equal')
return ax
def showGraph(graph, attr='weight'):
'''
Shows the adjacency matrix and the 'graphical layout'
'''
# TODO: add curved arreas
# TODO: plot add zeros
# ugly af
# style.use('seaborn-white')
fig, axes = subplots(1, 2)
u = unique(list(nx.get_edge_attributes(graph, attr).values()))
cmap = cm.get_cmap('viridis')
# cmap = cm.get_cmap('viridis')(linspace(-1, 1, 20))
# cmap[0,:] = 0
# cmap.set_over('DarkViolet')
# adjacency plot
adj = nx.adjacency_matrix(graph, weight='weight').todense()
# adj = (adj - adj.min()) / (adj.max() - adj.min())
# adj[adj == 0] = nan
cmap.set_bad('gray', .2)
h = axes[0].imshow(\
adj, aspect = 'auto',\
cmap = cmap,\
)
cbar = colorbar(h, ax=axes[0], pad=.01)
text(1.15, .5 , 'weight', rotation = 90,\
horizontalalignment='center', \
fontsize = 20,\
transform = axes[0].transAxes)
cbar.set_ticks([round(min(u), 2), round(max(u), 2)])
x = arange(len(graph.nodes()))
axes[0].set_xticks(x)
axes[0].set_xticklabels(graph.nodes(), ha='center', va='top', minor=False)
axes[0].set_yticks(x)
axes[0].set_yticklabels(graph.nodes(), ha='center', minor=False)
axes[0].tick_params(axis='y', which='major', pad=35)
# cbar.set_ticklabels([])
setp(axes[0], **dict(xlabel='node', ylabel='node'))
fig.autofmt_xdate() # slant overlapping labels
# there probably is a wrapper keyword for this....
from matplotlib.patches import FancyArrowPatch, Circle, ConnectionStyle
# graphical layout
edges = nx.get_edge_attributes(graph, 'weight')
negatives = {}
positives = {}
maxWeight = max(list(edges.values()))
for key, value in edges.items():
value = round(value, 3)
edges[key] = value
if value < 0:
negatives[key] = value
else:
positives[key] = value
r = 2
pos = nx.circular_layout(graph, scale=20)
for n in graph:
c=Circle(positions[n], radius=r,alpha=1, facecolor = 'white',\
edgecolor = 'black', linewidth = 1, linestyle = 'solid')
text(*c.center,
n,
horizontalalignment='center',
verticalalignment='center')
axes[1].add_patch(c)
graph.node[n]['patch'] = c
x, y = positions[n]
# pos = nx.circular_layout(graph, scale = .5)
# tmp = nx.get_edge_attributes(graph, 'weight')
# tmp = {key: abs(value) for key, value in tmp.items()}
# nx.set_edge_attributes(graph, tmp, 'absweight')
# pos = nx.kamada_kawai_layout(graph, weight= 'absweight', scale= 100000)
# patches = nx.draw_networkx_nodes(graph, pos = pos, alpha = 1, node_size = 1500, edgecolors = 'black', node_color = 'white')
seen = {}
from copy import copy
for u, v in graph.edges():
n1 = graph.node[u]['patch']
n2 = graph.node[v]['patch']
d = graph[u][v]['weight']
rad = 0.1
if (u, v) in seen:
rad = seen.get((u, v))
rad = (rad + np.sign(rad) * 0.1) * -1
print(u, v)
if u == v:
j = .1
n2 = copy(n1)
n1 = copy(n1)
n1.center = (n1.center[0] + r, n1.center[1])
n2.center = (n2.center[0] - r, n2.center[1])
# n1.center = tuple(i - j for i in n1.center)
# n2.center = tuple(i + j for i in n2.center)
print(n1, n2)
rad = 1.6
print(n1.center, n2.center)
e = FancyArrowPatch(n2.center, n1.center, connectionstyle = f'arc3,rad={rad}',\
arrowstyle = '-|>',\
mutation_scale = 10.0,
lw = 2,
alpha = abs(d),
color = 'red' if d < 0 else 'green')
e.set_arrowstyle(arrowstyle='-|>', head_length=1.5)
else:
connectionstyle = f'arc3,rad={rad}'
e = FancyArrowPatch(n1.center,n2.center, patchA = n1, patchB = n2,\
arrowstyle = '->',
connectionstyle = connectionstyle,
mutation_scale = 10.0,
lw=2,
alpha= abs(d),
color= 'red' if d < 0 else 'green')
# if (u,v) not in seen:
# center = (n1.center + n2.center) / 2 + random.rand()
# text(*center, round(d,2))
seen[(u, v)] = rad
axes[1].add_patch(e)
# nx.draw_networkx_labels(graph, pos = pos,\
# node_labels = graph.nodes())
#
# nx.draw_networkx_edges(graph,
# pos,
# edgelist = negatives,
# width = list(negatives.values()), edge_color = 'red',
# edge_labels = negatives, ax = axes[-1])
# nx.draw_networkx_edges(graph,
# pos,
# edgelist = positives,
# width = list(positives.values()), edge_color = 'green',
# edge_labels = positives, ax = axes[-1]
# )
# nx.draw_networkx_edge_labels(graph, pos, edge_labels = edges, ax = axes[-1], label_pos = .5)
axes[-1].autoscale()
axes[-1].axis('off')
