\name{plot.pePathway}
\alias{plot,pePathway,character-method}
\alias{plot,pePathway,missing-method}
\alias{plot.pePathway}
\title{Plot pathway level statistics}
\arguments{

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

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

\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}
}
\description{
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.
}
\examples{
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[])

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

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

plot(peRes@pathways[], "Pert", type = "boot", main = "Perturbation factor")
}
\author{
Calin Voichita and Sorin Draghici
}
\seealso{