\name{facetPlot}
 \alias{facetPlot}
 \title{
 Plot all chromosomes horizontally next to each other
 }
 \description{
 Plots all chromosomes in horizontal alignment next to each other, 
 with optionally a moving average smoother applied to the data 
 }
 \usage{ 
 facetPlot(datalist,samples=c(1,2),slid=FALSE,combine=FALSE,k=1,file="default")
 }
 \arguments{
 \item{datalist}{
 The CAFE datalist to be analyzed, i.e. the output of \code{\link{ProcessCels}}.
 }
 \item{samples}{
 A vector or sample numbers to be plotted
 }
 \item{slid}{
 If \code{TRUE}, use moving average smoother
 }
 \item{combine}{
 If \code{TRUE}, will plot the unaltered raw data in the background
 }
 \item{k}{
 The sliding window size. Must be a positive integer, smaller than the 
 length of Affy IDs on the chromosome
 }
 \item{file}{
 Specify a file name to store output png file
 }
 }
 \value{
 Plot to file system.
 Return a ggplot2 graph
 }
 \references{
 H. Wickham. ggplot2: elegant graphics for data analysis. 
 Springer New York, 2009.
 }
 \author{
 Sander Bollen
 }
 \note{
 Makes heavy use of the ggplot2 package
 }
 
 
 \seealso{
 \code{\link{slidPlot}}
 \code{\link{rawPlot}}
 \code{\link{discontPlot}}
 }
 \examples{
 data("CAFE_data")
 facetPlot(CAFE_data,samples=9)
 }
 \keyword{dplot}
 \keyword{hplot}