\name{plotPWF}
\Rdversion{1.1}
\alias{plotPWF}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{
Plot the Probability Weighting Function
}
\description{
Plots the Probability Weighting Function created by \code{\link{nullp}} by binning together genes.
}
\usage{
plotPWF(pwf,binsize="auto",pwf_col=3,pwf_lwd=2,xlab="Biased Data in <binsize> gene bins.",ylab="Proportion DE",...)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{pwf}{
A data frame with 3 columns named DEgenes, bias.data & pwf and row names giving the gene names.  Usually generated by \code{\link{nullp}}.
}
  \item{binsize}{
Calculate and plot the fraction of genes that are DE in bins of this size.  If set to "auto" the best binsize for visualization is attempted to be found automatically.
}
  \item{pwf_col}{
The colour of the probability weighting function
}
  \item{pwf_lwd}{
The width of the probability weighting function
}
  \item{xlab}{
The x-axis label. \code{<binsize>} is replaced by the binsize used.
}
  \item{ylab}{
The y-axis label.
}
  \item{...}{
Extra arguments that are passed to plot.
}
}
\details{
This function is almost always called using the output from the \code{\link{nullp}} function.  However, it can be used to visualize the length (or any other type of quantifyable) bias in ability to detect DE in a data set.  The \code{pwf} arguement needs to be a data frame with 3 columns each containing numeric entries (although NAs are permitted in the bias.data and pwf columns), which must be named "DEgenes", "bias.data" and "pwf", although they can appear in any order.  The row names are taken to be the gene names. The DEgenes column should be 0s or 1s where 1 represents a DE gene, 0 a gene which is not DE.  The bias.data column is a quantification of the quantity for which there is a bias in detecting DE for the associated gene, this is usually gene length or the number of counts associated with a gene.  Finally, the pwf column gives the probability weighting to be applied for a given gene.
}
\value{
Nothing is returned.
}
\references{
  Young, M. D., Wakefield, M. J., Smyth, G. K., Oshlack, A. (2010) \emph{Gene ontology analysis for RNA-seq: accounting for selection bias}
  Genome Biology
  Date: Feb 2010
  Vol: 11
  Issue: 2
  Pages: R14
}
\author{
Matthew D. Young \email{myoung@wehi.edu.au}
}
%\note{
%%  ~~further notes~~
%}

%% ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
\code{\link{nullp}}
}
\examples{
data(genes)
pwf <- nullp(genes, 'hg19', 'ensGene',plot.fit=FALSE)
plotPWF(pwf,binsize=200)
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
%\keyword{ ~kwd1 }
%\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line