peNodeRenderInfo {ROntoTools} | R Documentation

## Extract node render information from a `pePathway-class` object

### Description

Extract node render information from a `pePathway-class` object

### Usage

    peNodeRenderInfo(x, y = "Pert", input.shape = "box",
      default.shape = "ellipse", pos.col = "red", neg.col = "blue",
      zero.col = "white")

### Arguments

`x` | an object of class `pePathway-class`
`y` | a string representing the factor to be represented (`Pert, Acc` or `input`; see `pePathway-class`)
`input.shape` | shape of nodes that have measured expression change
`default.shape` | shape of all other nodes
`pos.col` | color of nodes with a positive `y` factor
`neg.col` | color of nodes with a negative `y` factor
`zero.col` | color of nodes with the `y` factor equal to zero

### Value

a named list as expected by `nodeRenderInfo`

### Author(s)

Calin Voichita and Sorin Draghici

### See Also

`nodeRenderInfo`,`par`

### Examples

    # load experiment
    load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools"))
    fc <- top$logFC[top$adj.P.Val <= .01]
    names(fc) <- top$entrez[top$adj.P.Val <= .01]
    ref <- top$entrez

    # load the set of pathways
    kpg <- keggPathwayGraphs("hsa")
    kpg <- setEdgeWeights(kpg)
    kpg <- setNodeWeights(kpg, defaultWeight = 1)

    # perform the pathway analysis
    peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)

    p <- peRes@pathways[[50]]
    g <- layoutGraph(p@map, layoutType = "dot")
    graphRenderInfo(g) <- list(fixedsize = FALSE)
    edgeRenderInfo(g) <- peEdgeRenderInfo(p)
    nodeRenderInfo(g) <- peNodeRenderInfo(p)
    # notice the different type of nodes in the graph (box/circle)
    # the color of each node represents the perturbation (red = positive, blue = negative)
    # the shade represents the stregth of the perturbation
    renderGraph(g)

    nodeRenderInfo(g) <- peNodeRenderInfo(p, "Acc")
    # now, the color of each node represents the accumulation (red = positive, blue = negative)
    # notice that square nodes with no parents have no accumulation
    renderGraph(g)

[Package ROntoTools version 2.12.0 Index]