How to use the pygraphviz.AGraph function in pygraphviz

SELECT DISTINCT ?parent ?node
FROM 
WHERE {
?node skos:broader ?parent
} ORDER BY ?parent
""")

resultsEdges = sparql.query().convert()

for y in resultsEdges["results"]["bindings"]:
    g1.add_edge(("/".join(y["parent"]["value"].split("/")[5:]), "/".join(y["node"]["value"].split("/")[5:])))

# Draw as PNG
# print "Writing plot..."
dot = write(g1)
G = pgv.AGraph(dot)
G.layout(prog='dot')
G.draw('../output/foo.png')
print G.string()
# gvv = gv.readstring(dot)

def visualize(data, processes, root):
    G = pgv.AGraph(directed=False, strict=False)
    G.node_attr['shape']='box'
    for pid, p in processes.iteritems():

        if pid == root.pid:
            G.add_node(p.name() + "\n" + str(pid), color="black")            
        else:
            G.add_node(p.name() + "\n" + str(pid), color="green")

        #node = G.get_node(p.name() + "\n" + str(pid))

    for el in data:
        if el["dst_pid"] != 0:
            G.add_edge(el["src_prog"] + "\n" + str(el["src_pid"]), el["dst_prog"] + "\n" + str(el["dst_pid"]), color="blue", len="1.5")
        else:
            G.add_node(el["dst_prog"] + "\nExternal", color="red")
            G.add_edge(el["src_prog"] + "\n" + str(el["src_pid"]), el["dst_prog"] + "\nExternal", color="red", len="1.5")

def build_fat_graph():
    """Build http://www.graphviz.org/content/twopi2"""
    G = pgv.AGraph('graph_coloring_z3_example_fat_graph.gv')
    return (G, 'twopi2_fat_graph', 'twopi')

def orBox(bioNumber):
    with open('orBox{0}.dump'.format(bioNumber),'rb') as f:
        boxes = pickle.load(f)        
    fileName = 'image'
    graph = pgv.AGraph(directed=False,concentrate=True)
    print boxes[0]
    for element in boxes[0]:
        graph.add_node(element,shape='diamond',color='pink',style='filled')
        s = set()
        edges = set()
        rootEdges = set()
        for component in boxes[0][element]:
            s.add('{0}'.format(component[0]))
            s.add('{0}'.format(component[1]))
            #if boxes[0][element][component]:
            #    edges.add(('{0}-{1}'.format(element,component[0]),'{0}-{1}'.format(element,component[1])))

            rootEdges.add((element,'{0}-{1}'.format(element,component[0])))
            rootEdges.add((element,'{0}-{1}'.format(element,component[1])))
        for item in s:
            graph.add_node('{0}-{1}'.format(element,item),label=item)

def build_peternson_3_coloring_graph():
    """Build http://en.wikipedia.org/wiki/File:Petersen_graph_3-coloring.svg"""
    G = pgv.AGraph()
    G.node_attr['style'] = 'filled'
    # Hum, the attribute 'directed' (in AGraph constructor) doesn't seem to work, so that's my workaround.
    G.edge_attr['dir'] = 'none'

    edges = [
        (0, 2), (0, 1), (0, 5), (0, 4), (1, 6), (1, 7),
        (2, 3), (2, 8), (3, 4), (3, 7), (4, 5), (4, 6),
        (5, 9), (6, 8), (7, 9), (8, 9), (9, 3)
    ]

    for i in range(10):
        G.add_node(i)

    for src, dst in edges:
        G.add_edge(src, dst)

Notes
    -----
    If N has an dict N.graph_attr an attempt will be made first
    to copy properties attached to the graph (see from_agraph)
    and then updated with the calling arguments if any.

    """
    try:
        import pygraphviz
    except ImportError:
        raise ImportError('requires pygraphviz ',
                          'http://pygraphviz.github.io/')
    directed = N.is_directed()
    strict = nx.number_of_selfloops(N) == 0 and not N.is_multigraph()
    A = pygraphviz.AGraph(name=N.name, strict=strict, directed=directed)

    # default graph attributes
    A.graph_attr.update(N.graph.get('graph', {}))
    A.node_attr.update(N.graph.get('node', {}))
    A.edge_attr.update(N.graph.get('edge', {}))

    A.graph_attr.update((k, v) for k, v in N.graph.items()
                        if k not in ('graph', 'node', 'edge'))

    # add nodes
    for n, nodedata in N.nodes(data=True):
        A.add_node(n)
        if nodedata is not None:
            a = A.get_node(n)
            a.attr.update({k: str(v) for k, v in nodedata.items()})

def __init_graph(self, resdir):
        graphdir     = os.path.abspath(os.path.join(resdir, os.pardir))
        self.svgfile = os.path.join(graphdir, "graph.svg")
        self.graph   = pygraphviz.AGraph(strict   = False,
                                         directed = True,
                                         rankdir  = 'LR')

def request_relayout(self):

        if self.graph is None:
            return

        # remove all edges
        for p in self._edge_paths:
            self.scene.removeItem(p)

        # remove all nodes
        self.remove_all_children()
        self._edge_paths = []

        g = pygraphviz.AGraph(directed=True)
        g.graph_attr['nodesep'] = 100
        g.graph_attr['ranksep'] = 50
        g.node_attr['shape'] = 'rect'

        for node in self.graph.nodes_iter():
            scene_proxy = self._proxy(node)
            size = node.size()
            width, height = size.width(), size.height()
            scene_proxy.setGeometry(QRectF(0.0, 0.0, width, height))
            g.add_node(node, width=width, height=height)

        for from_, to in self.graph.edges_iter():
            g.add_edge(from_, to)

        g.layout(prog='dot')

def draw_BN(g, path):
    graph = pgv.AGraph(directed=True, strict=True, fontname='Helvetica', arrowtype='open')
    label_dict = dict(zip(range(2, 10), 'ASTLBEXD'))
    pos_dict = dict(zip(range(2, 10), ['0, 3!', '2.75, 3!', '0, 2!', '2, 2!', '3.5, 1!', '1.5, 1!', '1.5, 0!', '3.5, 0!']))

    def add_node(graph, node_id, label, shape='circle', style='filled'):
        if label in {0, 1}:
            return
        else:
            label, pos = label_dict[label], pos_dict[label]
        graph.add_node(
                node_id, label=label, color='black', fillcolor='white',
                shape=shape, style=style, pos=pos, fontsize=27,
        )
        return

    if g is None:
        graph.add_node(