Creating CX2Network objects

Below are factories that facilitate creation of CX2Network objects in different ways:

Raw CX2

The RawCX2NetworkFactory is designed to create a CX2Network instance directly from raw CX2 data.

from ndex2.cx2 import RawCX2NetworkFactory, CX2Network

# Sample raw CX2 data
raw_cx2_data = {...}  # Replace with actual raw CX2 data

# Creating an instance of RawCX2NetworkFactory
factory = RawCX2NetworkFactory()

# Creating a CX2Network from raw CX2 data
cx2_network = factory.get_cx2network(raw_cx2_data)

# cx2_network is now a populated CX2Network instance

NetworkX

The NetworkXToCX2NetworkFactory is designed to convert a NetworkX graph into a CX2Network. This conversion is suitable for transferring network data from NetworkX to the CX2 format.

import networkx as nx
from ndex2.cx2 import NetworkXToCX2NetworkFactory, CX2Network

# Add nodes and edges to networkx_graph...
networkx_graph = nx.Graph()
networkx_graph.add_node(1, size=5)
networkx_graph.add_node(2, size=6)
networkx_graph.add_node(3, size=7)
networkx_graph.add_edge(1, 2) weight=1.0)
networkx_graph.add_edge(2, 3, weight=0.9)

# Creating an instance of NetworkXToCX2NetworkFactory
factory = NetworkXToCX2NetworkFactory()

# Converting NetworkX graph to CX2Network
cx2_network = factory.get_cx2network(networkx_graph)

# cx2_network is now a CX2Network instance representing the NetworkX graph
print(cx2_network.to_cx2())

Pandas

The PandasDataFrameToCX2NetworkFactory enables the conversion of a pandas.DataFrame into a CX2Network. This is useful for integrating pandas.DataFrame data into the CX2 network structure.

import pandas as pd
from ndex2.cx2 import PandasDataFrameToCX2NetworkFactory, CX2Network

# DataFrame with source, target, and other columns
data = {'source': [1, 2], 'target': [2, 3],
        'weight': [1.0, 0.9],
        'source_size': [5, 6], 'target_size': [6, 7]}
df = pd.DataFrame(data)

# Creating an instance of PandasDataFrameToCX2NetworkFactory
factory = PandasDataFrameToCX2NetworkFactory()

# Converting DataFrame to CX2Network
cx2_network = factory.get_cx2network(df)

# cx2_network is now a CX2Network instance based on the DataFrame data
print(cx2_network.to_cx2())

Column Naming Convention

The columns named source and target represent the source and target nodes of each edge, respectively.
Node attributes are prefixed according to their node type: - source_ prefix for attributes of the source node (e.g., source_color). - target_ prefix for attributes of the target node (e.g., target_size).
Edge attributes are directly named after the attribute (e.g., weight for an edge’s weight attribute).