peNodeRenderInfo {ROntoTools} | R Documentation |
pePathway-class
objectExtract node render information from a pePathway-class
object
peNodeRenderInfo(x, y = "Pert", input.shape = "box", default.shape = "ellipse", pos.col = "red", neg.col = "blue", zero.col = "white")
x |
an object of class |
y |
a string representing the factor to be represented ( |
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 |
neg.col |
color of nodes with a negative |
zero.col |
color of nodes with the |
a named list as expected by nodeRenderInfo
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 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)