ROntoTools (version 2.0.0)

peEdgeRenderInfo: 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

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)