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.

Author(s)

Paul Shannon

Examples

g = makeSimpleGraph ()

## The function is currently defined as
function () 
{
    g = new("graphNEL", edgemode = "directed")
    g = initNodeAttribute(g, "type", "char", "undefined")
    g = initNodeAttribute(g, "lfc", "numeric", 1)
    g = initNodeAttribute(g, "label", "char", "default node label")
    g = initNodeAttribute(g, "count", "integer", 0)
    g = initEdgeAttribute(g, "edgeType", "char", "undefined")
    g = initEdgeAttribute(g, "score", "numeric", 0)
    g = initEdgeAttribute(g, "misc", "char", "default misc")
    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
    nodeData(g, "B", "lfc") = 0
    nodeData(g, "C", "lfc") = 3
    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)
  }