CX2

CX2 helpers from annnet.io.cx2_io.

`annnet.io.cx2_io`

CX2 Adapter for AnnNet AnnNet.

Provides: to_cx2(G) -> List[Dict[str, Any]] (CX2 JSON object) from_cx2(cx2_data) -> AnnNet

This adapter maps AnnNet Graphs to the Cytoscape Exchange (CX2) format. It creates a lossless representation by serializing complex features (hyperedges, slices, multilayer) into a 'manifest' stored within the CX2 'networkAttributes'.

Classes

Functions

`to_cx2(G, *, export_name='annnet export', layer=None, include_inter=False, include_coupling=False, hyperedges='skip')`

Convert an AnnNet graph to CX2 compliant JSON format.

The output is a list of aspect dictionaries (CX2 format). Complex AnnNet features (hyperedges, slices, multilayer structure) are serialized into a JSON string stored in networkAttributes under 'AnnNet_Manifest'.

Parameters:

Name	Type	Description	Default
`G`	`AnnNet`	The graph to export.	required
`export_name`	`str`	Name of the exported network (stored in networkAttributes).	`"annnet export"`
`layer`	`tuple of str`	Elementary layer tuple specifying which layer to export. If provided, only the subgraph for that layer is exported. Useful for multilayer graphs where flattening creates unreadable visualizations in Cytoscape (e.g., coupling edges become self-loops). If None, exports the entire graph. Example: layer=("social", "2020") for a 2-aspect multilayer network.	`None`
`hyperedges`	`('skip', 'expand', 'reify')`	How to handle hyperedges in the export: - "skip": Omit hyperedges entirely - "expand": Convert to cartesian product of pairwise edges - "reify": Create explicit hyperedge nodes with membership edges	`"skip"`

Returns:

Type	Description
`list of dict`	CX2-compliant JSON structure (list of aspect dictionaries).

Notes

Cytoscape does not natively support multilayer networks. When exporting multilayer graphs without specifying a layer, coupling edges may appear as self-loops and the visualization becomes cluttered.
Use the layer parameter to export individual elementary layers for clean, interpretable Cytoscape visualizations.
The full multilayer structure is preserved in the manifest regardless of the layer parameter, enabling lossless round-trip via from_cx2().

`from_cx2(cx2_data, *, hyperedges='manifest')`

Fully robust CX2 - AnnNet importer. Supports: - manifest reconstruction (full fidelity) - reified hyperedges - expanded hyperedges - Cytoscape-edited files - sparse attribute tables - arbitrary attribute modifications

`show(G, *, export_name='annnet export', layer=None, include_inter=False, include_coupling=False, hyperedges='skip', port=None, auto_open=True)`

Visualize graph in web browser using Cytoscape.js.

Parameters:

Name	Type	Description	Default
`G`	`AnnNet`	The graph to visualize.	required
`export_name`	`str`	Name of the network display.	`"annnet export"`
`layer`	`tuple of str`	Elementary layer tuple specifying which layer to visualize. If None, shows the entire graph (may include coupling edges as self-loops). Example: layer=("social", "2020") for a 2-aspect multilayer network.	`None`
`include_inter`	`bool`	When layer is specified, whether to include interlayer edges (edges between nodes in different layers but same aspect). Only relevant if layer is not None.	`False`
`include_coupling`	`bool`	When layer is specified, whether to include coupling edges (edges connecting the same node across layers). Only relevant if layer is not None. Warning: Including coupling creates self-loops in the visualization.	`False`
`hyperedges`	`('skip', 'expand', 'reify')`	How to handle hyperedges: - "skip": Omit hyperedges entirely - "expand": Convert to cartesian product of pairwise edges - "reify": Create explicit hyperedge nodes with membership edges	`"skip"`
`port`	`int`	Port for local web server. If None, finds available port automatically.	`None`
`auto_open`	`bool`	If True, automatically open browser.	`True`

Returns:

Type	Description
`str`	Local URL to the visualization.

Notes

For multilayer graphs: - Without layer parameter: shows entire flattened graph with coupling edges appearing as self-loops (messy but shows full structure) - With layer parameter: shows clean single-layer view without coupling edges (recommended for visualization)

Press Ctrl+C in terminal to stop the web server.

Examples:

>>> G.show()  # Show entire graph (all layers flattened)
>>> G.show(layer=("social", "2020"))  # Clean single layer view
>>> G.show(layer=("social", "2020"), include_coupling=True)  # With self-loops