RCy3 (version 1.2.0)

makeSimpleGraph: makeSimpleGraph

Description

A 3-node, 3-edge graph, with some biological trappings, useful for demonstrations.

Usage

makeSimpleGraph()

Value

Returns a 3-node, 3-edge graph, with some attributes on the nodes and edges.

Examples

  # first, delete existing windows to save memory:
  deleteAllWindows(CytoscapeConnection())

  g = makeSimpleGraph ()
  
  ## The function is currently defined as
  function () 
  {
      g = new("graphNEL", edgemode = "directed")
      nodeDataDefaults(g, attr = "type") = "undefined"
      attr(nodeDataDefaults(g, attr = "type"), "class") = "STRING"
      nodeDataDefaults(g, attr = "lfc") = 1
      attr(nodeDataDefaults(g, attr = "lfc"), "class") = "DOUBLE"
      nodeDataDefaults(g, attr = "label") = "default node label"
      attr(nodeDataDefaults(g, attr = "label"), "class") = "STRING"
      nodeDataDefaults(g, attr = "count") = "0"
      attr(nodeDataDefaults(g, attr = "count"), "class") = "INTEGER"
      edgeDataDefaults(g, attr = "edgeType") = "undefined"
      attr(edgeDataDefaults(g, attr = "edgeType"), "class") = "STRING"
      edgeDataDefaults(g, attr = "score") = 0
      attr(edgeDataDefaults(g, attr = "score"), "class") = "DOUBLE"
      edgeDataDefaults(g, attr = "misc") = ""
      attr(edgeDataDefaults(g, attr = "misc"), "class") = "STRING"
      g = graph::addNode("A", g)
      g = graph::addNode("B", g)
      g = graph::addNode("C", g)
      nodeData(g, "A", "type") = "kinase"
      nodeData(g, "B", "type") = "transcription factor"
      nodeData(g, "C", "type") = "glycoprotein"
      nodeData(g, "A", "lfc") = "-3.0"
      nodeData(g, "B", "lfc") = "0.0"
      nodeData(g, "C", "lfc") = "3.0"
      nodeData(g, "A", "count") = "2"
      nodeData(g, "B", "count") = "30"
      nodeData(g, "C", "count") = "100"
      nodeData(g, "A", "label") = "Gene A"
      nodeData(g, "B", "label") = "Gene B"
      nodeData(g, "C", "label") = "Gene C"
      g = graph::addEdge("A", "B", g)
      g = graph::addEdge("B", "C", g)
      g = graph::addEdge("C", "A", g)
      edgeData(g, "A", "B", "edgeType") = "phosphorylates"
      edgeData(g, "B", "C", "edgeType") = "synthetic lethal"
      edgeData(g, "A", "B", "score") = 35
      edgeData(g, "B", "C", "score") = -12
      return(g)
    }