addGraphToGraph

Description

Given a CytoscapeWindow containing a graph, this method adds new nodes, edges, and their attributes. Thus, it is the way to extend a graph – to merge a new graph with an existing one. A typical use would be to add a second KEGG pathway to a CytoscapeWindow upon discovering that two KEGG pathways overlap, sharing some enzymes and some reactions. No existing attributes are written over.

Usage

addGraphToGraph(obj, other.graph)

Arguments

Value

None.

Author(s)

Paul Shannon

Examples

  window.name <- 'demo addGraphToGraph'
  cw3 <- new.CytoscapeWindow (window.name, graph=makeSimpleGraph ())
  displayGraph (cw3)
  redraw (cw3)
  layoutNetwork (cw3)

    # create a new graph, which adds two nodes, and edges between them
    # and an existing node, A

  g2 <- new("graphNEL", edgemode = "directed")
  g2 <- graph::addNode ('A', g2)
  g2 <- graph::addNode ('D', g2)
  g2 <- graph::addNode ('E', g2)

  g2 <- initNodeAttribute (g2, "label", "char", "default node label")
  g2 <- initEdgeAttribute (g2, "edgeType", "char", "unspecified")
  g2 <- initEdgeAttribute (g2, "probability", "numeric", 0.0)

  nodeData (g2, 'D', 'label') <- 'Gene D'
  nodeData (g2, 'E', 'label') <- 'Gene E'

  g2 <- graph::addEdge ('D', 'E', g2)
  g2 <- graph::addEdge ('A', 'E', g2)

  edgeData (g2, 'D', 'E', 'probability') <- 0.95
  edgeData (g2, 'D', 'E', 'edgeType') <- 'literature'
  edgeData (g2, 'A', 'E', 'edgeType') <- 'inferred'

  addGraphToGraph (cw3, g2)
  redraw (cw3)
  layoutNetwork (cw3)