Export network data with Cytoscape visualization — exportNetworkToHTML • MSstatsBioNet

Convenience function that takes nodes and edges data directly and creates both the configuration and HTML export in one step.

Usage

exportNetworkToHTML(
  nodes,
  edges,
  filename = "network_visualization.html",
  displayLabelType = "id",
  nodeFontSize = 12,
  ...
)

nodes: Data frame with at minimum an id column. Optional columns: logFC (numeric), entity_name (character; may be semicolon-joined for multi-grounded rows), entity_id (character), site (character, underscore-separated PTM site list), and the node status columns of validate_network(): entity_type sets the node shape (e.g. a hexagon for "metabolite"); measured = FALSE draws a node with no fill and a dashed grey border ("not in input data"); included_in_query = FALSE fades it. A node with an NA logFC has no fill. A protein with site rows takes its colour from its row with no site; without one, only its sites are coloured. Missing status columns count as TRUE.
edges: Data frame with columns source, target, interaction. Optional: directed (an edge with FALSE has no arrow and is drawn once for both directions; without the column, Complex and Association edges are undirected), site, evidence_url, opened when an edge is clicked.
filename: Output HTML filename
displayLabelType: "id" (default) or "entity_name": which column is used as the visible node label. "entityName" is deprecated and is treated as "entity_name" with a warning.
nodeFontSize: Font size (px) for node labels. Default 12.
...: Additional arguments passed to exportCytoscapeToHTML()

Invisibly returns the file path of the created HTML file