peEdgeRenderInfo {ROntoTools} | R Documentation

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

### Description

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

### Usage

    peEdgeRenderInfo(x, pos.col = "black", pos.lty = "solid", pos.ah = "vee",
      neg.col = "black", neg.lty = "dashed", neg.ah = "tee",
      zero.col = "lightgray", zero.lty = "dotted", zero.ah = "none")

### Arguments

`x` | an object of class `pePathway-class`
`pos.col` | color of the edges with possitive weight
`pos.lty` | line type of the edges with possitive weight
`pos.ah` | arrow head of the edges with possitive weight
`neg.col` | color of the edges with negative weight
`neg.lty` | line type of the edges with negative weight
`neg.ah` | arrow head of the edges with negative weight
`zero.col` | color of the edges with zero weight
`zero.lty` | color of the edges with zero weight
`zero.ah` | color of the edges with zero weight

### Value

a named list as expected by `edgeRenderInfo`

### Author(s)

Calin Voichita and Sorin Draghici

### See Also

`edgeRenderInfo`,`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 edges in the graph (solid/dashed/dotted)
    renderGraph(g)

[Package ROntoTools version 2.12.0 Index]