peEdgeRenderInfo {ROntoTools} | R Documentation |
pePathway-class
objectExtract edge render information from a pePathway-class
object
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 |
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
# 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)