def plot(drama, caption=True):
plot = ig.Plot(outputfolder + drama.get("title") + ".png",
bbox=(600, 600),
background="white")
try:
graph = ig.VertexClustering(drama.get("graph")).giant()
visual_style = {}
visual_style["layout"] = graph.layout_fruchterman_reingold()
visual_style["vertex_color"] = "#0000ff"
visual_style["vertex_shape"] = "rectangle"
visual_style["vertex_size"] = 8
visual_style["vertex_label"] = graph.vs["name"]
visual_style["vertex_label_size"] = 15
visual_style["vertex_label_dist"] = 1.5
visual_style["edge_color"] = "#6495ed"
visual_style["edge_width"] = graph.es["weight"]
visual_style["bbox"] = (600, 600)
visual_style["margin"] = 50
plot.add(graph, **visual_style)
except:
pass
if caption:
# Make the plot draw itself on the Cairo surface.
plot.redraw()
# Grab the surface, construct a drawing context and a TextDrawer.
ctx = cairo.Context(plot.surface)
ctx.set_font_size(15)
drawer = TextDrawer(ctx, drama.get("title"), halign=TextDrawer.CENTER)
drawer.draw_at(0, 597, width=600)
plot.save()
def _draw_title(title, surface, width, height):
ctx = cairo.Context(surface)
ctx.set_font_size(TITLE_FONT_SIZE)
drawer = TextDrawer(ctx,
title,
halign=TextDrawer.CENTER,
valign=TextDrawer.TOP)
drawer.draw_at(0, PLOT_MARGIN[2] / 3, width=width)
def plot(graph, source_path, index, result_path=None, compute_closeness=True, print_label_size_min=None,
add_legend=True, size_factor=None, bbox_size=None):
graph_object = deepcopy(graph)
l = read_cache(source_path)
if not l:
l = graph_object.layout(PLOT_LAYOUT)
save_cache(source_path, l)
logging.info('complete layout')
if not result_path:
result_path = source_path
png_opt = dict(bbox=(1500, 1500), vertex_size=7, edge_arrow_size=0.2, edge_arrow_width=0.9, edge_width=0.3,
vertex_frame_width=0.4) if index not in PLOT_OPTIONS_PNG else PLOT_OPTIONS_PNG[index]
if bbox_size:
png_opt['bbox'] = (bbox_size, bbox_size)
if print_label_size_min is None:
graph_object.vs['label'] = ['']
else:
for i in graph_object.vs:
try:
if i['size'] < print_label_size_min:
i['label'] = ''
except IndexError:
pass
if size_factor:
m = max(graph_object.vs['size'])
for i in graph_object.vs:
try:
i['size'] = i['size'] / m * size_factor
except IndexError:
pass
p = igraph.plot(graph_object, plot_name(result_path, 'png'), layout=l, **png_opt)
logging.info('plot graph')
if add_legend:
legend = '%s: %d x %d\nclustering coef. %.4f\n' % (index, graph_object.vcount(), graph_object.ecount(),
graph_object.transitivity_undirected(mode="zero"))
if compute_closeness:
legend += 'closeness %.4f' % (sum(graph_object.closeness()) / graph_object.vcount())
logging.info('compute legend %s' % legend)
p.redraw()
ctx = cairocffi.Context(p.surface)
ctx.set_font_size(40)
# todo Use ctx.scale() for big image
drawer = TextDrawer(ctx, legend, halign=TextDrawer.LEFT)
drawer.draw_at(150, 50, width=500)
p.save()
logging.info('save png')
def plot_polar_graph(graph,
legend,
fill,
vertex_coords,
vertex_frame_color,
main_title,
subtitle,
filename=None):
bbox = igraph.BoundingBox(800, 800)
plot = igraph.Plot(filename, bbox=bbox, background="white")
bbox = bbox.contract(50)
plot.add(graph,
bbox=(50, 110, 750, 690),
layout=vertex_coords,
edge_arrow_size=1.5,
vertex_shape='circle',
vertex_frame_color=vertex_frame_color,
vertex_frame_width=1,
vertex_size=30)
plot.redraw()
ctx = cairo.Context(plot.surface)
ctx.set_font_size(36)
drawer = TextDrawer(ctx, main_title, halign=TextDrawer.CENTER)
drawer.draw_at(0, 40, width=800)
ctx.set_font_size(20)
drawer = TextDrawer(ctx, subtitle, halign=TextDrawer.CENTER)
drawer.draw_at(0, 750, width=800)
plot.save()
def make_graph( node_id_map, nodes, edges, edges_predicate, output_fn, tag ):
g = Graph()
g.add_vertices( len(nodes))
graph_edges = list( [node_id_map[e.image_A_id], node_id_map[e.image_B_id]] \
for e in edges if edges_predicate(e))
g.add_edges( graph_edges)
layout = g.layout_circle()
# adding text to plot courtesy http://stackoverflow.com/questions/18250684/add-title-and-legend-to-igraph-plots
plot = Plot(output_fn, bbox=[2000,2000])
plot.add( g, layout=layout, bbox=[50,50,1950,1950])
ctx = cairo.Context( plot.surface )
ctx.set_font_size(36)
drawer = TextDrawer( ctx, "Label: '%s'\n%s\n%d nodes, %d edges" % \
(LABEL, tag, len(nodes), len(graph_edges)), halign=TextDrawer.RIGHT)
drawer.draw_at(10,1900,width=1900)
plot.save()
sys.stderr.write("Info: wrote %s\n" % output_fn)
def graph_plot(graph, visual_style, texts=None):
"""
@param graph:
@param visual_style:
@param texts: a dictionary storing the text to be printed with text[key]: [x,y, fontsize]
e.g texts["M1"] = [0, 180, 30]
@return igplot: an igraph.drawing.Plot object
"""
# an igraph.drawing.Plot object
igplot = ig.plot(graph, **visual_style)
# plot text
if texts is not None:
igplot.redraw()
# Context object
ctx = cairo.Context(igplot.surface)
# draw each text in ig.plot
for text in texts:
val = texts[text]
# fontsize
try:
fontsize = val[2]
except IndexError:
fontsize = 20
# set the font size
ctx.set_font_size(fontsize)
# TextDrawer Object
drawer = TextDrawer(ctx, text, halign=TextDrawer.CENTER)
# draw the text at the coordinates coord
drawer.draw_at(x=val[0], y=val[1], width=300)
return igplot
def plot_network(self, title='Network', membership=None,
outfile=None, width=900, height=600):
if self.edgelist is None:
self.edgelist = self.get_edgelist()
if self.g is None:
self.g = ig.Graph(self.edgelist)
if membership is None:
membership = self.get_membership()
pal_size = max(1, len(self.cluster))
else:
temp = set()
for item in membership:
temp.add(item)
pal_size = max(1, len(temp))
pal = ig.ClusterColoringPalette(pal_size)
visual_style = {}
visual_style['vertex_color'] = [pal.get(id) \
for id in membership]
if self.size <= 100:
visual_style['vertex_size'] = 20
visual_style['vertex_label'] = [str(id+1) \
for id in xrange(self.size)]
else:
visual_style['vertex_size'] = 8
if not self.layout:
if self.size <= 200:
self.layout = self.g.layout('kk')
else:
self.layout = self.g.layout('lgl')
visual_style['margin'] = (20,50,20,20)
visual_style['layout'] = self.layout
visual_style['bbox'] = (width, height)
figure = ig.plot(self.g, **visual_style)
figure.redraw()
ctx = cairo.Context(figure.surface)
ctx.set_font_size(20)
drawer = TextDrawer(ctx, title, halign=TextDrawer.CENTER)
drawer.draw_at(3,30, width=width)
if outfile:
figure.save(outfile)
figure.show()
def plot_four(g1, g2, g3, g4, title):
""" Plots four graphs on a single plot.
"""
# Construct plot
plot = igraph.Plot(title, bbox=(1200, 940), background="white")
plot.add(g1, bbox=(20, 60, 580, 470))
plot.add(g2, bbox=(620, 60, 1180, 470))
plot.add(g3, bbox=(20, 510, 580, 920))
plot.add(g4, bbox=(620, 510, 1180, 920))
plot.redraw()
# Add title
ctx = cairo.Context(plot.surface)
ctx.set_font_size(24)
drawer = TextDrawer(ctx,
'crime count: {}, zip code count: {}'.format(
sum([int(i) for i in g1.vs['description']]),
g1.vcount()),
halign=TextDrawer.CENTER)
drawer.draw_at(0, 40, width=1200)
plot.save()
def plot_polar_graph(
graph,
legend,
fill,
vertex_coords,
vertex_frame_color,
main_title,
subtitle,
filename=None):
bbox = igraph.BoundingBox(800,800)
plot = igraph.Plot(filename, bbox=bbox, background="white")
bbox = bbox.contract(50)
plot.add(graph,bbox=(50,110,750,690),
layout=vertex_coords,
edge_arrow_size=1.5,
vertex_shape='circle',
vertex_frame_color=vertex_frame_color,
vertex_frame_width=1,
vertex_size=30)
plot.redraw()
ctx = cairo.Context(plot.surface)
ctx.set_font_size(36)
drawer = TextDrawer(ctx, main_title, halign=TextDrawer.CENTER)
drawer.draw_at(0, 40, width=800)
ctx.set_font_size(20)
drawer = TextDrawer(ctx, subtitle, halign=TextDrawer.CENTER)
drawer.draw_at(0, 750, width=800)
plot.save()
def DrawGraph(self, fn, title=None):
# Draw graph and save to file.
plot = igraph.Plot(fn, bbox = (900, 780), background="white")
if self.style['layout'] == None:
self.style['layout'] = self.g.layout("kk")
low = min( map(lambda(agent) : agent.initialOpinion, self.g.vs['agency']) )
high = max( map(lambda(agent) : agent.initialOpinion, self.g.vs['agency']) )
for (u, agent) in self.IterAgents():
u['color'] = ScaleColor(UNSHIFT(agent.opinion) / UNSHIFT(high))
u['label'] = agent.GetLabel()
u['label_dist'] = 2
u['label_size'] = 10
plot.add(self.g, **self.style)
plot.redraw()
ctx = cairo.Context(plot.surface)
ctx.set_font_size(22)
if title:
drawer = TextDrawer(ctx, title, halign=TextDrawer.CENTER)
drawer.draw_at(0, 40, width=900)
ctx.set_font_size(18)
drawer = TextDrawer(ctx, 'Round No. %d' % self.round_no, halign=TextDrawer.RIGHT)
drawer.draw_at(860, 770, width=9)
plot.save()
from igraph import Graph, Plot
from igraph.drawing.text import TextDrawer
import cairo
# Construct the plot
plot = Plot("plot.png", bbox=(600, 650), background="white")
# Create the graph and add it to the plot
g = Graph.GRG(100, 0.2)
plot.add(g, bbox=(20, 70, 580, 630))
# Make the plot draw itself on the Cairo surface
plot.redraw()
# Grab the surface, construct a drawing context and a TextDrawer
ctx = cairo.Context(plot.surface)
ctx.set_font_size(36)
drawer = TextDrawer(ctx, "Test title", halign=TextDrawer.CENTER)
drawer.draw_at(0, 40, width=600)
# Save the plot
plot.save()
def plotgraph(filename, characters, title, community=True):
m = len(characters)
g = Graph()
g.add_vertices(m)
for i in range(m):
if type(characters[i]) is list:
g.vs[i]['label'] = characters[i][0]
else:
g.vs[i]['label'] = characters[i]
for i in range(m):
for j in range(i, m):
g.add_edge(i, j)
g.es[g.get_eid(i, j)]['weight'] = 0
with open(filename + '.pdf', 'rb') as f:
pdf = pdftotext.PDF(f)
for pg in pdf:
tmp = [0] * m
for i in range(m):
if type(characters[i]) is list:
for charname in characters[i]:
if pg.find(charname) != -1:
tmp[i] = 1
else:
if pg.find(characters[i]) != -1:
tmp[i] = 1
for i in range(m):
if not tmp[i]:
continue
for j in range(m):
if tmp[j] and i != j:
g.es[g.get_eid(i, j)]['weight'] += 1
maxweight = 0
for e in g.es:
if maxweight < e['weight']:
maxweight = e['weight']
g1 = g.copy()
edges_to_delete = []
for e in g1.es:
if e['weight'] < maxweight / 30:
edges_to_delete.append(e)
g1.delete_edges(edges_to_delete)
if community:
cl = g1.community_fastgreedy(weights=g1.es['weight'])
membership = cl.as_clustering().membership
edges_to_delete = []
for e in g1.es():
if membership[e.tuple[0]] != membership[e.tuple[1]]:
edges_to_delete.append(e)
g1.delete_edges(edges_to_delete)
edges_to_delete = []
for e in g.es:
if e['weight'] < maxweight / 50:
edges_to_delete.append(e)
g.delete_edges(edges_to_delete)
vertices_to_delete = []
for v in g.vs:
if v.degree() < 1:
vertices_to_delete.append(v)
g.delete_vertices(vertices_to_delete)
g1.delete_vertices(vertices_to_delete)
coords = g1.layout_kamada_kawai()
for e in g.es:
e['width'] = e['weight'] * 4 / maxweight
visual_style = {
'vertex_size': 5,
'vertex_label_size': 18,
'vertex_label_dist': 3,
'bbox': (1000, 1000),
'margin': 120,
'edge_curved': True
}
plot = Plot(target=filename + '.png',
bbox=(1000, 1000),
background="white")
plot.add(g, layout=coords, **visual_style)
plot.redraw()
ctx = cairo.Context(plot.surface)
ctx.set_font_size(24)
drawer = TextDrawer(ctx, title, halign=TextDrawer.CENTER)
drawer.draw_at(0, 40, width=1000)
plot.save()
def buildGraphAcctBal(networkGraph2):
fileName = "NetworkWikiAcctBalanceWD2018.png"
color_dict = {"G20": "blue", "NotG20": "yellow", "No Data": "gray"}
color_dict_edge = {"G20": "#5bbbfb", "NotG20": "#95afc0"}
visual_style = {}
visual_style["vertex_label_size"] = 15
visual_style["vertex_label_color"] = "#130f40"
visual_style["edge_color"] = "#95afc0"
visual_style["vertex_size"] = 0
total = 0
tc = 0
counter = 0
for acctBal in networkGraph2.vs["account-balance"]:
if acctBal == 0:
networkGraph2.vs[counter]["status"] = "No Data"
counter += 1
else:
counter += 1
tc += 1
total += acctBal
total = total / tc
visual_style["vertex_size"] = [10 + (balance - total) for balance in \
networkGraph2.vs["account-balance"]]
visual_style["vertex_color"] = [color_dict[status] for status in \
networkGraph2.vs["status"]]
ce = 0
for edge in networkGraph2.es:
v1 = "NotG20"
v2 = "NotG20"
if networkGraph2.vs[edge.target]["name"] in G20_NAMES:
v1 = "G20"
if networkGraph2.vs[edge.source]["name"] in G20_NAMES:
v2 = "G20"
if v1 == "G20" and v2 == "G20":
networkGraph2.es[ce]["connection_type"] = "G20"
else:
networkGraph2.es[ce]["connection_type"] = "NotG20"
ce += 1
visual_style["edge_color"] = [color_dict_edge[conntype] for conntype in \
networkGraph2.es["connection_type"]]
networkGraph2.vs["label"] = networkGraph2.vs["name"]
layout = networkGraph2.layout("rt_circular")
plot2 = Plot(fileName, bbox=(1100, 1100), background="#dff9fb")
plot2.add(networkGraph2, bbox= (55, 55, 900, 900), layout = layout, \
**visual_style)
plot2.redraw()
ctx = cairo.Context(plot2.surface)
ctx.set_font_size(20)
drawer = TextDrawer(ctx, "Wikipedia G20 Network Analysis viz. AcctBalance",\
halign=TextDrawer.CENTER)
drawer.draw_at(0, 40, width=1000)
plot2.save()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('file')
parser.add_argument('--key-label', default='AstChild', type=str)
parser.add_argument('--layout',
default='rt',
help='for big graphs, try rt_circular')
parser.add_argument('--node-color', default='viridis')
parser.add_argument('--edge-color', default='viridis')
args = parser.parse_args()
with open(args.file) as f:
json_f = json.load(f)
nodes = json_f['nodes']
edges = json_f['edges']
G = Graph()
dG = Graph(directed=True)
for n in nodes:
G.add_vertex(str(n['id']))
dG.add_vertex(str(n['id']))
if all('token' in n for n in nodes):
dG.vs["label"] = [n['token'] for n in nodes]
dG.vs['color'] = colorize([n['ast_type'] for n in nodes], args.node_color)
for c in dG.vs['color']:
c[-1] = 0.4
def proc_edges(es):
return [(str(e['src']), str(e['dst'])) for e in es]
def edge_of_label(lab):
return list(e for e in edges if e['edge_type'] == lab)
key_label = args.key_label
rest_labels = list(set(e['edge_type'] for e in edges) - {key_label})
cidxmap = {key_label: 0}
cs = [key_label] * len(edge_of_label(key_label))
for rl in rest_labels:
cidxmap[rl] = len(cs)
cs += [rl] * len(edge_of_label(rl))
dG.add_edges(proc_edges(edge_of_label(key_label)))
for rl in rest_labels:
dG.add_edges(proc_edges(edge_of_label(rl)))
print('{:.2f} {:.2f} {}'.format(
np.mean(dG.degree()),
dG.average_path_length(),
dG.diameter(),
))
return
G.add_edges(proc_edges(edge_of_label(key_label)))
lay = G.layout(args.layout)
dG.es['color'] = colorize(cs, args.edge_color)
plot = Plot("plot.png", bbox=(800, 670), background="white")
plot.add(dG, layout=lay, vertex_size=40, bbox=(40, 70, 580, 630))
plot.redraw()
# Grab the surface, construct a drawing context and a TextDrawer
ctx = cairo.Context(plot.surface)
ctx.set_font_size(20)
drawer = TextDrawer(ctx, "Legend", halign=TextDrawer.CENTER)
drawer.draw_at(680, 40, width=40)
ctx.rectangle(620, 20, 160, 125)
ctx.rectangle(620, 48, 160, 1)
ctx.stroke()
ctx.set_source_rgb(0., 0., 0.)
ctx.set_font_size(18)
y = 40 + 30
for lab in [key_label] + rest_labels:
ctx.set_source_rgb(*dG.es['color'][cidxmap[lab]][:3])
ctx.rectangle(640, y - 8, 20, 1)
ctx.stroke()
ctx.set_source_rgb(0., 0., 0.)
drawer = TextDrawer(ctx, str(lab), halign=TextDrawer.CENTER)
drawer.draw_at(700, y, width=40)
y += 15
# Save the plot
plot.save()
# degree for vertex_size
strength = g.strength(weights='weight')
visual_style['vertex_size'] = np.array(strength) / max(
strength) * max_size
# plot graph grouped by communities
plot = ig.Plot('./figures/time/graph-%s.png' % str(i),
bbox=(1000, 1000),
background="white")
plot.add(g, **visual_style)
# Make the plot draw itself on the Cairo surface
plot.redraw()
# Grab the surface, construct a drawing context and a TextDrawer
ctx = cairo.Context(plot.surface)
ctx.set_font_size(28)
drawer = TextDrawer(ctx, time_range, halign=TextDrawer.CENTER)
drawer.draw_at(0, 80, width=1000)
# Save the plot
plot.save()
print('graph saved')
# current date + 1 month
current = current + relativedelta(months=1)
# increase counter
i += 1
########################################################################
# TIME ANALYSIS / DYNAMICS
# detect changes
elif v.degree() > 7:
v['color'] = 'green'
v['size'] = 30
elif v.degree() > 6:
v['color'] = 'pink'
v['size'] = 20
# Construimos el plot
plot = Plot("smallworld.png", bbox=(600, 400), background="white")
plot.add(g1, bbox=(20, 80, 500, 300))
# Añadimos el grafo al plot
plot.redraw()
# Preparamos el canvas donde escribiremos el grafo
ctx = cairo.Context(plot.surface)
ctx.set_font_size(14)
## Dibujamos la leyenda
drawer = TextDrawer(ctx, "Cyan : Degree(v)>9", halign=TextDrawer.RIGHT)
drawer.draw_at(0, 20, width=580)
drawer = TextDrawer(ctx, "Amarillo : Degree(v)>8", halign=TextDrawer.RIGHT)
drawer.draw_at(0, 40, width=580)
drawer = TextDrawer(ctx, "Verde : Degree(v)>7", halign=TextDrawer.RIGHT)
drawer.draw_at(0, 60, width=580)
drawer = TextDrawer(ctx, "Rosa : Degree(v)>6", halign=TextDrawer.RIGHT)
drawer.draw_at(0, 80, width=580)
drawer = TextDrawer(ctx, "Rojo : Degree(v)<=5", halign=TextDrawer.RIGHT)
drawer.draw_at(0, 100, width=580)
# Save the plot
plot.save()
plot.show()
lay_kk = gg.layout('kk')
pp_kk = ig.plot(gg, layout=lay_kk)
lay_lgl = gg.layout('lgl')
pp_lgl = ig.plot(gg, layout=lay_lgl)
pp_lgl.show()
g.vs['size'] = 20
g.vs['color'] = [color_list[id] for id in cd.membership]
lay_kk = g.layout('kk')
pp_kk = ig.plot(g, target='haha.pdf',margin=(20,50,20,20), layout=lay_kk)
pp_kk.redraw()
ctx = cairo.Context(pp_kk.surface)
ctx.set_font_size(20)
drawer = TextDrawer(ctx, "Test title", halign=TextDrawer.CENTER)
drawer.draw_at(3, 30, width=600)
pp_kk.show()
pp_kk.show()
pp_lgl.show()
#generate graph from stochastic block model
gg = ig.Graph.SBM(n=120, pref_matrix=list(prob1),
block_sizes=list(size1))
#gg = ig.Graph.Erdos_Renyi(100, 0.1)
cc = gg.community_leading_eigenvector()
adjlist = gg.get_adjlist()
def plot(self, t):
visual_style = {}
visual_style["vertex_size"] = 20
visual_style["layout"] = self.g.layout("grid")
visual_style["vertex_label"] = range(self.g.vcount())
## Presence Graph
self.g.vs["color"] = "yellow"
self.g.vs[self.target.position]["color"] = "red"
# for idx in self.searchers.positions:
# self.g.vs[idx]["color"] = "green"
for idx in range(self.N):
if self.capture[idx, t].X[0]:
self.g.vs[idx]["color"] = "green"
if idx == self.target.position:
self.g.vs[idx]["color"] = "#fc03db"
## Belief Graph
self.belief_g.vs["color"] = '#4287f5'
capture_belief = self.beliefs[0, t].X[0]
capture_belief = round(capture_belief, 2) # Round to 2 decimals
capture_belief = abs(capture_belief) # To get rid of "-0.00"
belief_array = np.array(
[round(b.X[0], 2) for b in self.beliefs[1:, t]])
max_belief = np.max(belief_array)
for idx in range(self.N):
if belief_array[idx] > 0:
alpha = int(255 * belief_array[idx] / max_belief)
# Alpha value defines opacity of color
# We use it to denote how confident we think the
# target is situated in that vertex
self.belief_g.vs[idx]["color"] = f'#ff0000{alpha:0>2x}'
# Construct the plot
WIDTH = 700
GRAPH_WIDTH = 560
L = 70
H = 100
plot = ig.Plot(os.path.join(sys.path[0], f'../results/path_t={t}.png'),
bbox=(2 * WIDTH, WIDTH),
background="white")
# Add the graphs to the plot
plot.add(self.g,
bbox=(L, H, L + GRAPH_WIDTH, H + GRAPH_WIDTH),
**visual_style)
plot.add(self.belief_g,
bbox=(WIDTH + L, H, WIDTH + L + GRAPH_WIDTH, H + GRAPH_WIDTH),
**visual_style)
# Make the plot draw itself on the Cairo surface
plot.redraw()
# Grab the surface, construct a drawing context and a TextDrawer
ctx = cairo.Context(plot.surface)
ctx.set_font_size(24)
title = f"[Positions and Beliefs at t={t}]\n"
title += f"Max occupancy belief: {max_belief}, "
title += f"Capture belief: {capture_belief}"
drawer = TextDrawer(ctx, title, halign=TextDrawer.CENTER)
drawer.draw_at(0, 40, width=2 * WIDTH)
# Save the plot
plot.save()
def render_igraph(mol_net,
save_name=None,
layout='auto',
title=None,
positions=None,
cluster=False,
node_size=50,
bbox=None,
margin=None,
inline=False):
"""
Parameters
----------
mol_net : networkx.DiGraph
networkx graph
save_name : str
Save name
layout : str
title : str, optional
positions : list, optional
bbox : list
cluster : bool
margin : list
node_size : int
Returns
-------
"""
try:
import cairo
except ImportError:
print("Please install pycairo to use igraph plotting")
return
try:
import igraph
from igraph.drawing.text import TextDrawer
from igraph.drawing.colors import color_name_to_rgba
except ImportError:
print("No igraph, cannot use plotting function")
return
g = nx_to_igraph(mol_net)
if not isinstance(g, igraph.Graph):
print("Error converting to Igraph")
return
if bbox is None:
bbox = [2400, 2400]
if margin is None:
margin = [50, 50, 50, 50]
_valid_layouts = {
"kk", "drl", "lgl", "tree", "graphopt", "mds", "sugiyama", "auto"
}
assert layout in _valid_layouts, \
'layout {} not in {}'.format(layout, _valid_layouts)
mark_groups = None
membership = None
if cluster and 'termName' in g.vs.attributes():
cl = igraph.VertexClustering(g).FromAttribute(g, attribute='termName')
membership = cl.membership
if membership is not None:
gcopy = g.copy()
# edges = []
# for edge in g.es():
# if membership[edge.tuple[0]] != membership[edge.tuple[1]]:
# edges.append(edge)
# gcopy.delete_edges(edges)
if positions is None:
positions = gcopy.layout(layout)
n_clusters = len(set(membership))
rgb_colors = sns.color_palette("tab20", n_clusters)
colors = rgb_colors.as_hex()
mark_groups = dict()
for n, color in enumerate(colors):
mem = tuple(i for i, j in enumerate(membership) if j == n)
mark_groups[mem] = color
if positions is None:
positions = g.layout(layout)
visual_style = dict()
visual_style["vertex_label_dist"] = 0
visual_style["vertex_shape"] = "circle"
visual_style["vertex_size"] = node_size
visual_style["layout"] = positions
visual_style["margin"] = margin
# visual_style["edge_curved"] = True
if 'color' in g.es.attributes():
visual_style["edge_color"] = g.es["color"]
if save_name is not None:
if not save_name.endswith('.png'):
save_name += '.png'
if cluster:
# add some white space to add labels
bbox_plus_margin = [bbox[0] + bbox[0] * .45, bbox[1] + bbox[0] * .1]
margin[2] += bbox[0] * .25
margin[0] += bbox[0] * .05
else:
bbox_plus_margin = bbox
# create entire surface
plot = igraph.Plot(save_name, bbox=bbox_plus_margin, background='white')
# add plot to surface
plot.add(g, mark_groups=mark_groups, bbox=bbox, **visual_style)
# have to redraw to add the plot
plot.redraw()
if membership is not None:
# Grab the surface, construct a drawing context and a TextDrawer
ctx = cairo.Context(plot.surface)
ctx.set_font_size(36)
if title is not None:
drawer = TextDrawer(ctx, title, halign=TextDrawer.CENTER)
drawer.draw_at(0, 40, width=600)
labels = dict()
for vertex in g.vs():
name = vertex['termName'].replace(',', '\n')
if name in labels:
continue
labels[name] = rgb_colors[membership[vertex.index]]
spacing = bbox[1] / len(labels)
ctx.set_font_size(24)
for n, (label, rgb_c) in enumerate(labels.items()):
text_drawer = TextDrawer(ctx, text=label, halign=TextDrawer.LEFT)
x_coord = bbox[0] + 25
y_coord = 100 + (n * spacing)
text_drawer.draw_at(x=x_coord, y=y_coord, width=300, wrap=True)
ctx.set_source_rgba(*rgb_c)
ctx.arc(x_coord - 1.5 * node_size, y_coord, node_size, 0, 6.28)
ctx.fill()
ctx.set_source_rgba(0, 0, 0, 1)
# Save the plot
if save_name is not None:
plot.save()
if inline:
return plot
return plot, positions
def plot_coefficient(self, i, j):
import cairo
from igraph.drawing.text import TextDrawer
random.seed(1)
g = self.graphList[i].graph
if(g != None and len(g.vs["name"]) < 1000):
#layout = g.layout("kamada_kawai")
layout = g.layout("fr")
g.es["curved"] = False
visual_style = {}
visual_style["vertex_size"] = 20
#visual_style["vertex_color"] = [color_dict[gender] for gender in g.vs["gender"]]
visual_style["vertex_label"] = g.vs["name"]
l = self.graphList[i].centrality[j]
m = max(l)
l1 = [(float(l[i]) / float(m)) * 100 for i in range(len(l))]
col = []
pal = RainbowPalette(n=120)
for n, val in enumerate(l1):
col.append(pseudocolor(val,0,100))
visual_style["vertex_color"] = col
visual_style["edge_width"] = [float(weight) for weight in g.es["weight"]]
visual_style["edge_color"] = ["red" if (w < 0) else "black" for w in g.es["weight"]]
visual_style["edge_color"] = ["red" if (w < 0) else "black" for w in g.oldes]
visual_style["layout"] = layout
#visual_style["bbox"] = (800, 800)
visual_style["margin"] = 20
visual_style["edge-curved"] = False
plot = Plot("plot.png", bbox=(720, 760), background="white")
# # Create the graph and add it to the plot
plot.add(g, bbox=(20, 80, 580, 630), **visual_style)
# save_img = PhotoImage(file="save.gif")
#plot.add(save_img, bbox=(20, 70, 580, 630))
# Make the plot draw itself on the Cairo surface
plot.redraw()
# Grab the surface, construct a drawing context and a TextDrawer
ctx = cairo.Context(plot.surface)
ctx.set_font_size(36)
drawer = TextDrawer(ctx, columnNames[j+1], halign=TextDrawer.CENTER)
drawer.draw_at(0, 40, width=600)
image_surface = cairo.ImageSurface.create_from_png("rainbow.png")
ctx.set_source_surface(image_surface, 55, 680)
ctx.paint()
#ctx.plot(image_surface, target=None, bbox=(0, 0, 600, 600))
#plot.add(image_surface, bbox=(20, 20, 580, 580))
print type(plot)
return plot
def draw_igraph(mol_net, save_name=None, layout='auto', title=None,
positions=None, cluster=False, node_size=50,
bbox=None, margin=None, inline=False, node_font_size=24,
font_size=36):
"""
Parameters
----------
mol_net : networkx.DiGraph
networkx graph
save_name : str
Save name
layout : str
Options = "kk", "fr", "drl", "lgl", "tree", "graphopt", "mds", "sugiyama",
"auto", "grid_fr"
title : str, optional
positions : list, optional
bbox : list
cluster : bool
Add a shape around species that are tagged the same.
g.node[0][term_name]='dna'
g.node[0][term_name]='dna'
This will be grouped together.
margin : list
Margin of white space for boxes. This should be considered for the
labels of the nodes
node_size : int
node_font_size: int
Size of node labels
font_size : int
Title and group name (if clustering) font size
inline : bool
Return plot as svg view ipython
Returns
-------
"""
try:
import cairo
except ImportError:
ImportError("Please install pycairo to use igraph plotting")
try:
import igraph
from igraph.drawing.text import TextDrawer
from igraph.drawing.colors import color_name_to_rgba
except ImportError:
raise ImportError("No igraph, cannot use plotting function")
if isinstance(mol_net, igraph.Graph):
g = mol_net
else:
g = nx_to_igraph(mol_net)
if not isinstance(g, igraph.Graph):
print("Error converting to Igraph")
return
if inline:
if bbox is None:
bbox = [500, 500]
if margin is None:
margin = [50, 50, 50, 50]
if bbox is None:
bbox = [2400, 2400]
if margin is None:
margin = [50, 50, 50, 50]
_valid_layouts = {
"kk", "fr", "drl", "lgl", "tree", "graphopt", "mds", "sugiyama",
"auto", "grid_fr",
}
if layout not in _valid_layouts:
raise Exception('layout {} not in {}'.format(layout, _valid_layouts))
mark_groups = None
membership = None
if cluster and 'termName' in g.vs.attributes():
cl = igraph.VertexClustering(g).FromAttribute(g, attribute='termName')
membership = cl.membership
if membership is not None:
gcopy = g.copy()
# edges = []
# for edge in g.es():
# if membership[edge.tuple[0]] != membership[edge.tuple[1]]:
# edges.append(edge)
# gcopy.delete_edges(edges)
if positions is None:
positions = gcopy.layout(layout)
n_clusters = len(set(membership))
rgb_colors = sns.color_palette("tab20", n_clusters)
colors = rgb_colors.as_hex()
mark_groups = dict()
for n, color in enumerate(colors):
mem = tuple(i for i, j in enumerate(membership) if j == n)
mark_groups[mem] = color
if positions is None:
positions = g.layout(layout)
visual_style = dict()
visual_style["vertex_label_dist"] = 0
visual_style["vertex_shape"] = "circle"
visual_style["vertex_size"] = node_size
visual_style["vertex_label_size"] = node_font_size
visual_style["layout"] = positions
visual_style["margin"] = margin
# visual_style["edge_curved"] = True
if 'color' in g.es.attributes():
visual_style["edge_color"] = g.es["color"]
if save_name is not None:
if not save_name.endswith('.png'):
save_name += '.png'
if cluster:
# add some white space to add labels
bbox_plus_margin = [bbox[0] + bbox[0] * .45, bbox[1] + bbox[0] * .1]
margin[2] += bbox[0] * .25
margin[0] += bbox[0] * .05
else:
bbox_plus_margin = bbox
# create entire surface
plot = igraph.Plot(save_name,
bbox=bbox_plus_margin,
background='white')
# add plot to surface
plot.add(g, mark_groups=mark_groups, bbox=bbox, **visual_style)
# have to redraw to add the plot
plot.redraw()
# Grab the surface, construct a drawing context and a TextDrawer
ctx = cairo.Context(plot.surface)
ctx.set_font_size(font_size)
if title is not None:
drawer = TextDrawer(ctx, title, halign=TextDrawer.CENTER)
drawer.draw_at(0, 40, width=600)
if membership is not None:
labels = dict()
for vertex in g.vs():
name = vertex['termName'].replace(',', '\n')
if name in labels:
continue
labels[name] = rgb_colors[membership[vertex.index]]
spacing = bbox[1] / len(labels)
ctx.set_font_size(24)
for n, (label, rgb_c) in enumerate(labels.items()):
text_drawer = TextDrawer(ctx, text=label, halign=TextDrawer.LEFT)
x_coord = bbox[0] + 25
y_coord = 100 + (n * spacing)
text_drawer.draw_at(x=x_coord, y=y_coord, width=300, wrap=True)
ctx.set_source_rgba(*rgb_c)
ctx.arc(x_coord - 1.5 * node_size, y_coord, node_size, 0, 6.28)
ctx.fill()
ctx.set_source_rgba(0, 0, 0, 1)
# Save the plot
if save_name is not None:
plot.save()
if inline:
return plot
return plot, positions
