How to use the networkx.draw function in networkx

To help you get started, we’ve selected a few networkx examples, based on popular ways it is used in public projects.

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github vpc-ccg / calib / benchmark_aux / draw_cluster.py View on Github external
hamming_avg = float(line[6])

            for neighbor in line[7].rstrip().split(','):
                if len(neighbor) < 1:
                    continue
                fields = neighbor.split('_')
                neighbor_id = int(fields[0])
                left = int(fields[1])
                right = int(fields[2])
                dist = int(fields[3])


                G.add_edge(node_id, neighbor_id, color=colors[dist],weight=(left+right)/5)

            plt.figure(figsize=(30,30))
            nx.draw(G)#, pos, edges=edges, edge_color=colors, width=weights)
            plt.savefig(out_file+"_basic.pdf")

            edges = G.edges()
            colors = [G[u][v]['color'] for u,v in edges]
            weights = [G[u][v]['weight'] for u,v in edges]

            plt.figure(figsize=(30,30))
            pos = nx.spring_layout(G)
            nx.draw(G, pos, edges=edges, edge_color=colors, width=weights, alpha=0.1, node_size=25)
            plt.savefig(out_file+"_spring.pdf")

            plt.figure(figsize=(18,18))
            pos = nx.spectral_layout(G)
            nx.draw(G, pos, edges=edges, edge_color=colors, width=weights)
            plt.savefig(out_file+"_spectral.pdf")
github shogun-toolbox / shogun / examples / undocumented / python_modular / graphical / inverse_covariance_estimation_demo.py View on Github external
# extract nodes from graph
	nodes = set([n1 for n1, n2 in graph] + [n2 for n1, n2 in graph])

    # create networkx graph
	G=nx.Graph()

    # add nodes
	for node in nodes:
		G.add_node(node)

    # add edges
	for edge in graph:
		G.add_edge(edge[0], edge[1])

    # draw graph
	nx.draw(G, ax=subplot)

    # show graph
	return graph
github MUSoC / Visualization-of-popular-algorithms-in-Python / Egocentric Network / egocentric_network_2.py View on Github external
def DrawGraph(G, egocentric_network_edge_list, egocentric_network_node_list, vert):
	pos = nx.spring_layout(G)
	nx.draw(G, pos, with_labels = True, node_color = 'blue', alpha = 0.8)  #with_labels=true is to show the node number in the output graph
	nx.draw_networkx_edges(G, pos, edgelist = egocentric_network_edge_list , width = 2.5, alpha = 0.8, edge_color = 'red')
	nx.draw_networkx_nodes(G,pos, nodelist = egocentric_network_node_list, node_color = 'red', alpha = 0.5)
	nx.draw_networkx_nodes(G,pos,nodelist=[vert],node_color='green',node_size=500,alpha=0.8)
	return pos
github entropicalabs / entropica_qaoa / entropica_qaoa / utilities.py View on Github external
def plot_graph(G):
    """
    Plots a networkx graph.

    Parameters
    ----------
    G:
        The networkx graph of interest.
    """

    weights = np.real([*nx.get_edge_attributes(G, 'weight').values()])
    pos = nx.shell_layout(G)

    nx.draw(G, pos, node_color='#A0CBE2', with_labels=True, edge_color=weights,
            width=4, edge_cmap=plt.cm.Blues)
    plt.show()
github blaze / blaze / blaze / compute / expr / viz.py View on Github external
def view(self):
    import matplotlib.pyplot as plt
    networkx.draw(self)
    plt.show()
github dmlc / dgl / tutorials / basics / 1_first.py View on Github external
G = build_karate_club_graph()
print('We have %d nodes.' % G.number_of_nodes())
print('We have %d edges.' % G.number_of_edges())

###############################################################################
# Visualize the graph by converting it to a `networkx
# `_ graph:

import networkx as nx
# Since the actual graph is undirected, we convert it for visualization
# purpose.
nx_G = G.to_networkx().to_undirected()
# Kamada-Kawaii layout usually looks pretty for arbitrary graphs
pos = nx.kamada_kawai_layout(nx_G)
nx.draw(nx_G, pos, with_labels=True, node_color=[[.7, .7, .7]])

###############################################################################
# Step 2: Assign features to nodes or edges
# --------------------------------------------
# Graph neural networks associate features with nodes and edges for training.
# For our classification example, we assign each node an input feature as a one-hot vector:
# node :math:`v_i`'s feature vector is :math:`[0,\ldots,1,\dots,0]`,
# where the :math:`i^{th}` position is one.
#
# In DGL, you can add features for all nodes at once, using a feature tensor that
# batches node features along the first dimension. The code below adds the one-hot
# feature for all nodes:

import torch

G.ndata['feat'] = torch.eye(34)
github briandconnelly / seeds / contrib / actions / DrawTransitions.py View on Github external
if self.experiment.epoch > 0:
            # Get a list of the colors to use for each edge.
            edge_colors = []
            tmatrix = self.experiment.data['population']['transitions']

            for f in range(self.max_types):
                for t in range(self.max_types):
                    if tmatrix[f][t] > tmatrix[t][f]:
                        edge_colors.append(self.colors[f])
                        wt = tmatrix[f][t] - tmatrix[t][f]
                        graph.add_edge(f, t, weight=wt)

        # Make the figure
        plt.figure()
        nx.draw(graph, with_labels=False, pos=nx.circular_layout(graph),
                edge_color=edge_colors, node_color=self.colors, node_size=node_sizes, labels=self.node_labels)

        if self.display_epoch:
            plt.text(0, -0.05, "Epoch: %d" % (self.experiment.epoch),
                     horizontalalignment='left',
                     size='small')

        filename = "%s-%06d.%s" % (self.filename, self.experiment.epoch, self.format)
        data_file = self.datafile_path(filename)
        plt.savefig(data_file, transparent=self.transparent)
        plt.close()
github dmlc / dgl / graph.py View on Github external
def draw(self):
        from networkx.drawing.nx_agraph import graphviz_layout

        pos = graphviz_layout(self, prog='dot')
        nx.draw(self, pos, with_labels=True)
github networkx / networkx / examples / drawing / plot_ego_graph.py View on Github external
# Create a BA model graph
n = 1000
m = 2
G = nx.generators.barabasi_albert_graph(n, m)

# find node with largest degree
node_and_degree = G.degree()
(largest_hub, degree) = sorted(node_and_degree, key=itemgetter(1))[-1]

# Create ego graph of main hub
hub_ego = nx.ego_graph(G, largest_hub)

# Draw graph
pos = nx.spring_layout(hub_ego)
nx.draw(hub_ego, pos, node_color="b", node_size=50, with_labels=False)

# Draw ego as large and red
options = {"node_size": 300, "node_color": "r"}
nx.draw_networkx_nodes(hub_ego, pos, nodelist=[largest_hub], **options)
plt.show()