Graph a Cluster Filtered Network in Cytoscape — GraphCfn • PTMsToPathways

Creates a Cytoscape network from CFN edge and node tables, then applies the PTMsToPathways node shape/color and edge color/width visual mappings. Requires Cytoscape to be open and RCy3 to be installed.

Usage

GraphCfn(
  cfn.edges,
  cfn.nodes,
  Network.title = "CFN",
  Network.collection = "PTMsToPathways",
  visual.style.name = "PTMsToPathways.style"
)

Arguments

cfn.edges: A data frame of CFN edges (source, target, interaction, Weight).
cfn.nodes: A data frame of CFN node attributes with an id column.
Network.title: Character string title for the new Cytoscape network; defaults to "CFN".
Network.collection: Character string name for the Cytoscape collection; defaults to "PTMsToPathways".
visual.style.name: Character string name for the visual style to create; defaults to "PTMsToPathways.style".

Value

Called for its side effects; creates a styled network in Cytoscape.