Easy Graph Initialization

The CytoscapeWidget accepts an optional graph parameter, using this we can pass the graph’s data and initialise a graph. We can pass data as:

• A json file (wither the filename or the json object itself)

• A networkx graph

• A pandas Dataframe

• A neo4j graph

• A ipycytoscape Graph

import ipycytoscape

# 1. a cytoscape graph from json file
json_from_filename = ipycytoscape.CytoscapeWidget("concentricData.json")
json_from_filename

# 1. a cytoscape graph from json object

import json
with open("concentricData.json") as fi:
    json_file = json.load(fi)

json_from_object = ipycytoscape.CytoscapeWidget(json_file)
json_from_object

# A networkx graph
import networkx as nx

G = nx.complete_graph(5)
graph_from_nx = ipycytoscape.CytoscapeWidget(G)
graph_from_nx

# A pandas Dataframe

import pandas as pd

graphFrame = pd.read_csv("https://raw.githubusercontent.com/nextstrain/ncov/fe5a7ed1f92af63d6d1d43d0307e4b2620108aaa/data/metadata.tsv", sep = '\t')
ipycytoscape.CytoscapeWidget(graphFrame[:30], groupby_cols=['country'], attribute_list=['age', 'virus'])

# NBVAL_SKIP
# A neo4j graph

from py2neo import Graph, Node, Relationship

g = graph = Graph("bolt://132.249.238.185:7687", user="reader", password="demo")

ipycytoscape.CytoscapeWidget(g)

# A ipycytoscape graph
ipycytoscape.CytoscapeWidget(json_from_object.graph)