peEdgeRenderInfo: Extract edge render information from a 'pePathway-class'...
In ROntoTools: R Onto-Tools suite

Description Usage Arguments Value Author(s) See Also Examples

Extract edge render information from a pePathway-class object

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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")

`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

a named list as expected by edgeRenderInfo

Calin Voichita and Sorin Draghici

edgeRenderInfo,par

# 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)