Python networkx.draw_networkx_edges函数代码示例

def draw_graph(G):
	# an example using Graph as a weighted network.
	# __author__ = """Aric Hagberg ([email protected])"""
	try:
	    import matplotlib.pyplot as plt
	except:
	    raise

	elarge = [(u,v) for (u,v,d) in G.edges(data = True) if d['weight'] > 0.5]
	esmall = [(u,v) for (u,v,d) in G.edges(data = True) if d['weight'] <= 0.5]

	pos = nx.spring_layout(G) # positions for all nodes

	# nodes
	nx.draw_networkx_nodes(G, pos, node_size = 200)

	# edges
	nx.draw_networkx_edges(G, pos, edgelist = elarge, width = 0.4)
	nx.draw_networkx_edges(G, pos, edgelist = esmall, width = 0.4, alpha = 0.6, style = 'dashed')

	# labels
	nx.draw_networkx_labels(G, pos, font_size = 6, font_family = 'sans-serif')

	print 'number of cliques/clusters:', nx.graph_number_of_cliques(G)
	print 'time:', time.time() - start
	plt.show()

    def plot(self):
        """
        Plots an entity relation diagram (ERD) among all nodes that is part
        of the current graph.
        """
        if not self.nodes(): # There is nothing to plot
            logger.warning('Nothing to plot')
            return
        if pygraphviz_layout is None:
            logger.warning('Failed to load Pygraphviz - plotting not supported at this time')
            return

        pos = pygraphviz_layout(self, prog='dot')
        fig = plt.figure(figsize=[10, 7])
        ax = fig.add_subplot(111)
        nx.draw_networkx_nodes(self, pos, node_size=200, node_color='g')
        text_dict = nx.draw_networkx_labels(self, pos, self.node_labels)
        trans = ax.transData + \
            transforms.ScaledTranslation(12/72, 0, fig.dpi_scale_trans)
        for text in text_dict.values():
            text.set_horizontalalignment('left')
            text.set_transform(trans)
        # draw primary key relations
        nx.draw_networkx_edges(self, pos, self.pk_edges, arrows=False)
        # draw non-primary key relations
        nx.draw_networkx_edges(self, pos, self.non_pk_edges, style='dashed', arrows=False)
        apos = np.array(list(pos.values()))
        xmax = apos[:, 0].max() + 200  # TODO: use something more sensible than hard fixed number
        xmin = apos[:, 0].min() - 100
        ax.set_xlim(xmin, xmax)
        ax.axis('off')  # hide axis

 def plot(self):
     if self.pos == None:
         self.pos = nx.graphviz_layout(self)
     NODE_SIZE = 500
     plt.clf()
     nx.draw_networkx_nodes(self, pos=self.pos,
                            nodelist=self.normal,
                            node_color=NORMAL_COLOR,
                            node_size=NODE_SIZE)
     nx.draw_networkx_nodes(self, pos=self.pos,
                            nodelist=self.contam,
                            node_color=CONTAM_COLOR,
                            node_size=NODE_SIZE)
     nx.draw_networkx_nodes(self, pos=self.pos,
                            nodelist=self.immune,
                            node_color=IMMUNE_COLOR,
                            node_size=NODE_SIZE)
     nx.draw_networkx_nodes(self, pos=self.pos,
                            nodelist=self.dead,
                            node_color=DEAD_COLOR,
                            node_size=NODE_SIZE)
     nx.draw_networkx_edges(self, pos=self.pos,
                            edgelist=self.nondead_edges(),
                            width=2,
                            edge_color='0.2')
     nx.draw_networkx_labels(self, pos=self.pos,
                             font_color='0.95', font_size=11)
     plt.gca().get_xaxis().set_visible(False)
     plt.gca().get_yaxis().set_visible(False)
     plt.draw()

def calcMetrics():
    print('\nTrips:')
    for trip in trips:
        trip.display()
    print('\nPairs:')
    for a, b in itertools.combinations(trips, 2):
        # if isTimeTestFail(): continue
        bestDist = getBestDist(a, b)
        sumDist = a.dist + b.dist
        if bestDist > sumDist: continue
        minDist = min(a.dist, b.dist)
        maxDist = max(a.dist, b.dist)
        delta = sumDist - bestDist
        coPathCoeff = maxDist / bestDist
        effect = delta / bestDist
        weight = effect * coPathCoeff
        G.add_edge(a, b, weight=weight)
        print('edge is added', weight)

    pos = nx.random_layout(G)
    nx.draw_networkx_nodes(G, pos)
    nx.draw_networkx_edges(G, pos, width=weight,)
    plt.axis('off')
    plt.savefig("weighted_graph.png")  # save as png
    plt.show()  # display

def display_retweet_network(network, outfile=None, show=False):
    """
    Take a DiGraph (retweet network?) and display+/save it to file.
    Nodes must have a 'color' property, represented literally and indicating their type
    Edges must have a 'weight' property, represented as edge width
    """
    import networkx as nx
    import matplotlib.pyplot as plt

    # Create a color list corresponding to nodes.
    node_colors = [ n[1]["color"] for n in network.nodes(data=True) ]

    # Get edge weights from graph
    edge_weights = [ e[2]["weight"] for e in network.edges(data=True) ]

    # Build up graph figure
    #pos = nx.random_layout(network)
    pos = nx.spring_layout(network)
    nx.draw_networkx_edges(network, pos, alpha=0.3 , width=edge_weights, edge_color='m')
    nx.draw_networkx_nodes(network, pos, node_size=400, node_color=node_colors, alpha=0.4)
    nx.draw_networkx_labels(network, pos, fontsize=6)

    plt.title("Retweet Network", { 'fontsize': 12 })
    plt.axis('off')

    if outfile:
        print "Saving network to file: {0}".format(outfile)
        plt.savefig(outfile)

    if show:
        print "Displaying graph. Close graph window to resume python execution"
        plt.show()

def plot_networkx_topology_graph(topology):
    import matplotlib.pyplot as plt
    import networkx as nx

    G = nx.Graph()
    top_graph = topology.get_graph()
    labels = {}
    types = {}
    n_types = 0
    colors = []
    for v in top_graph.get_vertices():
        G.add_node(v.particle_index)
        labels[v.particle_index] = v.label
        if not v.particle_type() in types:
            types[v.particle_type()] = n_types
            n_types += 1
        colors.append(types[v.particle_type()])
    for v in top_graph.get_vertices():
        for vv in v:
            G.add_edge(v.particle_index, vv.get().particle_index)

    pos = nx.spring_layout(G)  # positions for all nodes

    nx.draw_networkx_nodes(G, pos, node_size=700, node_color=colors, cmap=plt.cm.summer)
    nx.draw_networkx_edges(G, pos, width=3)
    nx.draw_networkx_labels(G, pos, font_size=20, labels=labels, font_family='sans-serif')
    plt.show()

 def _graph_intelligence_nx(bot, file_path):
     # TODO: Make BehaviorGraph track the launch node and mark it in the graph output
     print("Saving Champion Intelligence Graph...")
     behavior_nodes = bot.behavior.behavior_nodes
     network = nx.DiGraph()
     network.add_nodes_from(behavior_nodes)
     # Add the behavior nodes to the network and link them together
     for node in behavior_nodes:
         if node.node_type == NodeRegister.statement:
             network.add_edge(node, node.next_node, label='')
         elif node.node_type == NodeRegister.conditional:
             network.add_edge(node, node.true_node, label='1')
             network.add_edge(node, node.false_node, label='0')
     # Draw the network
     layout = nx.shell_layout(network, scale=3)
     plt.figure(figsize=(10, 10))
     plt.axis('equal')
     plt.title("%s: Born:%s, Age:%s, Peak Energy:%s, Children:%s" %
               (str(bot), str(bot.birthday), str(bot.age), str(bot.peak_energy), str(bot.number_children)))
     nx.draw_networkx_edges(network, layout, width=0.5, alpha=0.75, edge_color='black', arrows=True)
     statement_color = '#D7E7F7'
     conditional_color = '#F7D7DA'
     colors = [statement_color if node.node_type == NodeRegister.statement else conditional_color
               for node in network.nodes()]
     nx.draw_networkx_nodes(network, layout, node_size=1800, node_color=colors, alpha=1)
     # Reformat node names to make them easier to read
     names = [(node, str(node.function.__name__).replace('_', '\n')) for node in behavior_nodes]
     labels = {key: value for (key, value) in names}
     nx.draw_networkx_labels(network, layout, labels, font_size=10, font_family='sans-serif')
     edge_names = nx.get_edge_attributes(network, 'label')
     nx.draw_networkx_edge_labels(network, layout, edge_labels=edge_names, label_pos=0.7)
     plt.axis('off')
     plt.savefig(file_path + '.png', dpi=80, pad_inches=0.0, bbox_inches='tight')

    def plot(self, show_labels=False):
        nodes = nx.draw_networkx_nodes(self,
                                       self.pos,
                                       node_size=NODE_SIZE_NORMAL,
                                       node_color=NODE_COLOR_NORMAL,
                                       linewidths=NODE_LINEWIDTH_NORMAL,
                                       alpha=NODE_ALPHA_NORMAL)
        if nodes != None:
            nodes.set_edgecolor(NODE_BORDER_COLOR_NORMAL)
        ws = nx.get_node_attributes(self, 'w')
        sizes = [NODE_SIZE_PHOTO_MIN + ws[v]*NODE_SIZE_PHOTO_SCALE
                 for v in self.photo_nodes()]
        nodes = nx.draw_networkx_nodes(self,
                                       self.pos,
                                       nodelist=self.photo_nodes(),
                                       node_shape=NODE_SHAPE_PHOTO,
                                       node_size=sizes,
                                       node_color=NODE_COLOR_PHOTO)

        if nodes != None:
            nodes.set_edgecolor(NODE_BORDER_COLOR_PHOTO)
        if show_labels:
            nx.draw_networkx_labels(self,
                                    self.pos,
                                    font_color=LABEL_COLOR_NORMAL,
                                    font_size=LABEL_FONT_SIZE_NORMAL)
        nx.draw_networkx_edges(self,
                               self.pos,
                               width=EDGE_WIDTH_NORMAL,
                               edge_color=EDGE_COLOR_NORMAL,
                               alpha=EDGE_ALPHA_NORMAL)

 def plot_path(self, path):
     if path == None:
         edgelist = []
     else:
         edgelist = zip(path[:-1], path[1:])
     if edgelist == []:
         return
     nodes = nx.draw_networkx_nodes(self,
                                    self.pos,
                                    nodelist=path,
                                    node_size=NODE_SIZE_PATH,
                                    node_color=NODE_COLOR_PATH)
     if nodes != None:
         nodes.set_edgecolor(NODE_BORDER_COLOR_PATH)
     ws = nx.get_node_attributes(self, 'w')
     photo_path_nodes = self.photo_nodes(path)
     if photo_path_nodes != []:
         sizes = [NODE_SIZE_PHOTO_MIN + ws[v]*NODE_SIZE_PHOTO_SCALE
                  for v in photo_path_nodes]
         nodes = nx.draw_networkx_nodes(self,
                                        self.pos,
                                        nodelist=photo_path_nodes,
                                        node_shape=NODE_SHAPE_PHOTO,
                                        node_size=sizes,
                                        node_color=NODE_COLOR_PHOTO_PATH)
     if nodes != None:
         nodes.set_edgecolor(NODE_BORDER_COLOR_PATH)
     nx.draw_networkx_edges(self,
                            self.pos,
                            edgelist=edgelist,
                            width=EDGE_WIDTH_PATH,
                            edge_color=EDGE_COLOR_PATH)

def report_ctg(ctg, filename):
    """
    Reports Clustered Task Graph in the Console and draws CTG in file
    :param ctg: clustered task graph
    :param filename: drawing file name
    :return: None
    """
    print "==========================================="
    print "      REPORTING CLUSTERED TASK GRAPH"
    print "==========================================="
    cluster_task_list_dict = {}
    cluster_weight_dict = {}
    for node in ctg.nodes():
        print ("\tCLUSTER #: "+str(node)+"\tTASKS:"+str(ctg.node[node]['TaskList'])+"\tUTILIZATION: " +
               str(ctg.node[node]['Utilization']))
        cluster_task_list_dict[node] = ctg.node[node]['TaskList']
    for edge in ctg.edges():
        print ("\tEDGE #: "+str(edge)+"\tWEIGHT: "+str(ctg.edge[edge[0]][edge[1]]['Weight']))
        cluster_weight_dict[edge] = ctg.edge[edge[0]][edge[1]]['Weight']
    print ("PREPARING GRAPH DRAWINGS...")
    pos = networkx.shell_layout(ctg)
    networkx.draw_networkx_nodes(ctg, pos, node_size=2200, node_color='#FAA5A5')
    networkx.draw_networkx_edges(ctg, pos)
    networkx.draw_networkx_edge_labels(ctg, pos, edge_labels=cluster_weight_dict)
    networkx.draw_networkx_labels(ctg, pos, labels=cluster_task_list_dict)
    plt.savefig("GraphDrawings/"+filename)
    plt.clf()
    print ("\033[35m* VIZ::\033[0mGRAPH DRAWINGS DONE, CHECK \"GraphDrawings/"+filename+"\"")
    return None

def draw_graph(edges, up_words, down_words, node_size, node_color='blue', node_alpha=0.3,
               node_text_size=12, edge_color='blue', edge_alpha=0.3, edge_tickness=2,
               text_font='sans-serif', file_name="graph"):
    plt.clf()
    g = nx.Graph()

    for edge in edges:
        g.add_edge(edge[0], edge[1])

    graph_pos = nx.shell_layout(g)  # layout for the network

    # up_words = map(lambda x: translate_node(x), up_words)
    # down_words = map(lambda x: x + "(" + translate_node(x) + ")", down_words)  # add translated nodes to graph

    try:
        nx.draw_networkx_nodes(g, graph_pos, nodelist=up_words, node_size=node_size,
                               alpha=node_alpha, node_color='red')
        nx.draw_networkx_nodes(g, graph_pos, nodelist=down_words, node_size=node_size,
                               alpha=node_alpha, node_color=node_color)
        nx.draw_networkx_edges(g, graph_pos, width=edge_tickness,
                               alpha=edge_alpha, edge_color=edge_color)
        nx.draw_networkx_labels(g, graph_pos, font_size=node_text_size,
                                font_family=text_font)
    except:
        print 'draw error'

    plt.savefig(result_path + file_name, format="PNG")

def graph_terms_to_topics(lda, num_terms=num_top):
    #topic names: select appropriate "t" based on number of topics
    #Use line below for num_top = 15.
    t = ['0','1', '2','3','4','5','6','7','8','9','10','11','12','13','14']
    #Use line below for num_top = 25.
    #t = ['0','1', '2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24']
    #Use line below for num_top = 35.
    #t = ['0','1', '2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34']       
    #Use line below for num_top = 45.
    #t = ['0','1', '2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44']       
    
#Create a network graph and size it.
    G = nx.Graph()
    plt.figure(figsize=(16,16))
    # generate the edges
    for i in range(0, lda.num_topics):
        topicLabel = t[i]
        terms = [term for term, val in lda.show_topic(i, num_terms+1)]
        for term in terms:
            G.add_edge(topicLabel, term, edge_color='red')
    
    pos = nx.spring_layout(G) # positions for all nodes
    
    #Plot topic labels and terms labels separately to have different colours
    g = G.subgraph([topic for topic, _ in pos.items() if topic in t])
    nx.draw_networkx_labels(g, pos, font_size=20, font_color='r')
    #If network graph is difficult to read, don't plot ngrams titles.
    #g = G.subgraph([term for term, _ in pos.items() if str(term) not in t])
    #nx.draw_networkx_labels(g, pos, font_size=12, font_color='orange')
    #Plot edges
    nx.draw_networkx_edges(G, pos, edgelist=G.edges(), alpha=0.3)
    #Having trouble saving graph to file automatically; below code not working. Must manually save.
    plt.axis('off')
    plt.show(block=False)
    plt.savefig('/Users/Marcia/OneDrive/UNCC General/DSBA_6880/Misc_Analysis_Files/TopicNetwork'+num+'.png', bbox_inches='tight')

def plot_co_x(cox, start, end, size = (20,20), title = '', weighted=False, weight_threshold=10):

        """ Plotting function for keyword graphs

        Parameters
        --------------------
        cox: the coword networkx graph; assumes that nodes have attribute 'topic'
        start: start year
        end: end year
        """

        plt.figure(figsize=size)
        plt.title(title +' %s - %s'%(start,end), fontsize=18)
        if weighted:
            elarge=[(u,v) for (u,v,d) in cox.edges(data=True) if d['weight'] >weight_threshold]
            esmall=[(u,v) for (u,v,d) in cox.edges(data=True) if d['weight'] <=weight_threshold]
            pos=nx.graphviz_layout(cox) # positions for all nodes
            nx.draw_networkx_nodes(cox,pos,
                node_color= [s*4500 for s in nx.eigenvector_centrality(cox).values()],
                node_size = [s*6+20  for s in nx.degree(cox).values()],
                alpha=0.7)
            # edges
            nx.draw_networkx_edges(cox,pos,edgelist=elarge,
                                width=1, alpha=0.5, edge_color='black') #, edge_cmap=plt.cm.Blues
            nx.draw_networkx_edges(cox,pos,edgelist=esmall,
                                width=0.3,alpha=0.5,edge_color='yellow',style='dotted')
            # labels
            nx.draw_networkx_labels(cox,pos,font_size=10,font_family='sans-serif')
            plt.axis('off')
        else:
            nx.draw_graphviz(cox, with_labels=True,
                         alpha = 0.8, width=0.1,
                         fontsize=9,
                         node_color = [s*4 for s in nx.eigenvector_centrality(cox).values()],
                         node_size = [s*6+20 for s in nx.degree(cox).values()])

def draw_fault_scenario(title, fault_edge, pp, dp, fwp):
    nx.draw(G, pos, node_size=300, font_size=10, node_color='w', alpha=1, with_labels=True)

    if title is not None:
        plt.text(0.5, 0.5, title, fontsize=12)

    if pp is not None:
        draw_edge_node(pp, 0.8, 'b')
        # Source
        nx.draw_networkx_nodes(G, pos,
                               nodelist=[pp[0]],
                               node_color='black',
                               node_size=500,
                               label='S',
                               font_size=10,
                               node_shape='s',
                               alpha=0.5)
    # Detour path
    if dp is not None:
        draw_edge_node(dp, 0.8, 'g')

    # Fault edge
    if fault_edge is not None:
        nx.draw_networkx_edges(G, pos,
                               edgelist=[fault_edge],
                               width=4, alpha=0.8,
                               edge_color='r')
    # FW Back path
    if fwp is not None:
        draw_edge_node(fwp, 0.8, 'y', 'dashed')

def draw_graph(username, password, filename='graph.txt', label_flag=True, remove_isolated=True, different_size=True, iso_level=10, node_size=40):
    """Reading data from file and draw the graph.If not exists, create the file and re-scratch data from net"""
    print "Generating graph..."
    try:
        with open(filename, 'r') as f:
            G = p.load(f)
    except:
        G = getgraph(username, password)
        with open(filename, 'w') as f:
            p.dump(G, f)
    #nx.draw(G)
    # Judge whether remove the isolated point from graph
    if remove_isolated is True:
        H = nx.empty_graph()
        for SG in nx.connected_component_subgraphs(G):
            if SG.number_of_nodes() > iso_level:
                H = nx.union(SG, H)
        G = H
    # Ajust graph for better presentation
    if different_size is True:
        L = nx.degree(G)
        G.dot_size = {}
        for k, v in L.items():
            G.dot_size[k] = v
        node_size = [G.dot_size[v] * 10 for v in G]
    pos = nx.spring_layout(G, iterations=50)
    nx.draw_networkx_edges(G, pos, alpha=0.2)
    nx.draw_networkx_nodes(G, pos, node_size=node_size, node_color='r', alpha=0.3)
    # Judge whether shows label
    if label_flag is True:
        nx.draw_networkx_labels(G, pos, alpha=0.5)
    #nx.draw_graphviz(G)
    plt.show()

    return G