% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/renderInfo-methods.R
\title{Extract node render information from a \code{pePathway-class} object}
peNodeRenderInfo(x, y = "Pert", input.shape = "box",
  default.shape = "ellipse", pos.col = "red", neg.col = "blue",
  zero.col = "white")
\item{x}{an object of class \code{\link{pePathway-class}}}

\item{y}{a string representing the factor to be represented (\code{Pert, Acc} or \code{input}; see \code{\link{pePathway-class}})}

\item{input.shape}{shape of nodes that have measured expression change}

\item{default.shape}{shape of all other nodes}

\item{pos.col}{color of nodes with a positive \code{y} factor}

\item{neg.col}{color of nodes with a negative \code{y} factor}

\item{zero.col}{color of nodes with the \code{y} factor equal to zero}
a named list as expected by \code{\link{nodeRenderInfo}}
Extract node render information from a \code{pePathway-class} object

# 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 

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

Calin Voichita and Sorin Draghici