% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot-methods.R
\title{Plot pathway level statistics}
\S4method{plot}{pePathway,missing}(x, y, ..., type = "two.way", eps = 1e-06)

\S4method{plot}{pePathway,character}(x, y, main = "", ..., type = "two.way",
  eps = 1e-06)
\item{x}{an object of type \code{\link{pePathway-class}}}

\item{y}{if provided, the factor to be ploted (either \code{Acc} (default) or \code{Pert}; see \code{\link{pePathway-class}})}

\item{...}{Arguments to be passed to methods, such as \code{\link{par}}}

\item{type}{type of plot (either \code{two.way} (default) or \code{boot})}

\item{eps}{any value smaller than this will be ploted as 0}

Display graphical representation of pathway level statistic like:
i) two way comparison between the measured expression change and one of the 
factors computed by Pathway-Express (\code{\link{pe}}) or ii) the boostrap 
statistics of the same factors.

# 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 (for more accurate results use nboot = 2000)
peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)


plot(peRes@pathways[[50]], "Pert", main = "Perturbation factor")

plot(peRes@pathways[[50]], type = "boot")

plot(peRes@pathways[[50]], "Pert", type = "boot", main = "Perturbation factor")

Calin Voichita and Sorin Draghici
\code{\link{pe}}, \code{\link{plot,peRes,missing-method}}, \code{\link{peNodeRenderInfo}}, \code{\link{peEdgeRenderInfo}}