\name{genoPlot}
\alias{genoPlot,-method}
\alias{genoPlot}
\title{genoPlot,-method}
\alias{genoPlot,-method}
\alias{genoPlot}
\alias{genoPlot-methods}
\alias{genoPlot}
\description{Plot data along the genome}
\details{\code{genoPlot-methods}: For a GenoSet object, data for a specified sample in a specified assayDataElement
can be plotted along the genome.  One chromosome can be specified if desired. If
more than one chromosome is present, the chromosome boundaries will be marked.
Alternatively, for a numeric x and a
numeric or Rle y, data in y can be plotted at genome positions y. In this case,
chromosome boundaries can be taken from the argument locs. If data for y-axis comes
from a Rle, either specified directly or coming from the specified assayData
element and sample, lines are plotted representing segments.

}
\value{\code{genoPlot-methods}: nothing

}
\author{Peter M. Haverty}
\arguments{\item{sample}{A index or sampleName to plot}
\item{element}{character, name of element in assayData to plot}
\item{x}{GenoSet (or descendant) or numeric with chromosome or genome positions}
\item{y}{numeric or Rle, values to be used for y-dimension, run start and stop indices or numeric with all values mapped to values in x for x-dimension or index of sample to be plotted if x is a GenoSet.}
\item{element}{character, when x is a GenoSet, the name of the assayDataElement to plot from.}
\item{locs}{RangedData, like locData slot of GenoSet}
\item{chr}{Chromosome to plot, NULL by default for full genome}
\item{add}{Add plot to existing plot}
\item{xlab}{character, label for x-axis of plot}
\item{ylab}{character, label for y-axis of plot}
\item{col}{character, color to plot lines or points}
\item{lwd}{numeric, line width for segment plots from an Rle}
\item{pch}{character or numeric, printing charactater, see points}
\item{...}{Additional plotting args}
}
\examples{data(genoset)
genoPlot( baf.ds,1,element="lrr")
genoPlot( genoPos(baf.ds), assayDataElement(baf.ds,"lrr")[,1], locs=locData(baf.ds) ) # The same
genoPlot( 1:10, Rle(c(rep(0,5),rep(3,4),rep(1,1))) )}
\alias{genoPlot,-method}
\alias{genoPlot}
\alias{genoPlot,-method}
\alias{genoPlot}
\alias{genoPlot,-method}
\alias{genoPlot}