Other graph formats interface

PyViPR uses NetworkX functions and cytoscape.js extensions to enable the visualization of the following graph formats:

• nx.Graph, nx.DiGraph, nx.MultiDiGraph

• GRAPHML

• SIF

• SBGN XML

• GEXF

• GML

• YAML

• CYTOSCAPE JSON

Networkx graph

import networkx as nx
import pyvipr.network_viz as nviz
from pyvipr.util_networkx import network_dynamic_data

G = nx.Graph()
G.add_edge(1, 2)
e = (2, 3)
G.add_edge(*e)  # unpack edge tuple*

node_rel = {1:[50, 100, 0],
            2:[50, 100, 0],
            3:[50, 100, 0]}

edge_colors = {(1,2):['#2b913a', '#2b913a', '#2b913a'],
                (2, 3):['#2b913a', '#2b913a', '#2b913a'],
                (1, 3):['#2b913a', '#2b913a', '#2b913a']}

nviz.nx_graph_dyn_view(G, tspan=[1,2,3], node_rel=node_rel,
                     edge_colors=edge_colors, layout_name='fcose')

GRAPHML format

nviz.graphml_view('graphs_formats/graphml_example2.graphml', layout_name='fcose')

SIF format

nviz.sif_view('graphs_formats/bid_network.sif', layout_name='fcose')

SBGN XML format

nviz.sbgn_xml_view('graphs_formats/activated_stat1alpha_induction_of_the_irf1_gene.xml', layout_name='fcose')

GEXF format

nviz.gexf_view('graphs_formats/gexf_network.gexf')

GML format

nviz.gml_view('graphs_formats/karate.gml', label='id')

YAML format

nviz.yaml_view('graphs_formats/yaml_network.yaml')

CYTOSCAPE JSON format

nviz.json_view('graphs_formats/earm.json', layout_name='fcose')