def plot(self):
"Function to plot a debruijn graph"
e0 = [i[0] for i in self.edges]
e1 = [i[1] for i in self.edges]
self.plot = plot
toyplot.graph(e0, e1, tmarker=">", vlstyle={'font-size': '8px'})
return self.plot
def plot(self):
"""Plots the graph."""
parents, children = zip(*self.edges())
singletons = [
i for i in range(self.num_vertices()) if self.degree(i) == 0
]
parent_names = list(map(self.vertex_label, parents))
child_names = list(map(self.vertex_label, children))
singleton_names = list(map(self.vertex_label, singletons))
canvas, axes, mark = toyplot.graph(parent_names,
child_names,
singleton_names,
ecolor="black",
tmarker=">",
vcolor="white",
vmarker="o",
vsize=80,
vstyle={"stroke": "black"})
# keep vertices from falling outside of the canvas
axes.padding = 50
def plot_vertexes(x, y, n, edges_plot):
coordinates = np.transpose(np.vstack((x, y)))
layout = toyplot.layout.FruchtermanReingold()
vstyle = {"stroke": toyplot.color.black}
vlstyle = {"fill": "white"}
colormap = toyplot.color.LinearMap(toyplot.color.Palette(
["white"])) #, "yellow", "red"]))
canvas, axes, mark = toyplot.graph(
edges_plot, #extra_vertices ,
vcoordinates=coordinates,
layout=layout,
vcolor=colormap,
vsize=30,
vstyle=vstyle,
width=10000)
axes.show = True
axes.aspect = None
axes.y.show = False
axes.x.show = False
toyplot.pdf.render(canvas, "nodes.pdf")
def plot(self):
"This function return a toyplot graph"
e0 = [i[0] for i in self.edges]
e1 = [i[1] for i in self.edges]
toyplot.graph(e0, e1, tmarker=">", vlstyle={'font-size': '8px'});
def plot(self):
e0 = [i[0] for i in self.edges]
e1 = [i[1] for i in self.edges]
toyplot.graph(e0, e1, tmarker=">", vlstyle={'font-size': '8px'})
#
# node_df = pd.DataFrame(node_data)
# edge_df = pd.DataFrame(edge_data)
#
# node_df.to_csv('node.csv', index=False)
# edge_df.to_csv('edge.csv', index=False)
edges = []
for u, v, meta in G.edges(data=True):
if meta['back_edge']:
continue
verbs = list(meta['verbs'])
is_sub = len(verbs) == 1 and verbs[0] == 'subset'
dead_end = G.degree[u] <= 2 and is_sub
if dead_end:
continue
u_head = G.nodes[u]['head']
v_head = G.nodes[v]['head']
edge = [format_text(u_head), format_text(v_head)]
edges.append(edge)
canvas, axes, mark = toyplot.graph(np.array(edges),
vsize=30,
width=5000,
height=5000)
to_pdf.render(canvas, 'figure1.pdf')
tedges = []
for i in range(0, len(offset) - 1):
start = offset[i]
end = offset[i + 1]
if start == end:
extra_nodes.append(i)
while start < end:
l = [i, edges[start]]
tedges.append(l)
start += 1
vcoordinates = np.ma.masked_all((len(offset), 2))
for i in range(0, len(offset)):
vcoordinates[i] = (xy[i][0], xy[i][1])
colormap = toyplot.color.LinearMap(
toyplot.color.Palette(["white", "yellow", "red"]))
vstyle = {"stroke": toyplot.color.black}
tedges = np.array(tedges)
layout = toyplot.layout.FruchtermanReingold()
c, y, z = toyplot.graph(tedges,
extra_nodes,
vcoordinates=vcoordinates,
width=600) #,vcolor=colormap, vsize=5, vstyle=vstyle)
# toyplot.png.render(c, "figure1.png")
toyplot.pdf.render(c, "figure1.pdf")
c1, y1, z1 = toyplot.graph(
tedges, width=600) #,vcolor=colormap, vsize=5, vstyle=vstyle)
toyplot.pdf.render(c1, "figure2.pdf")