\HeaderA{plotGenome}{Plots the genome}{plotGenome}
\aliasA{maPalette}{plotGenome}{maPalette}
\aliasA{plotCGH.func}{plotGenome}{plotCGH.func}
\aliasA{plotGene}{plotGenome}{plotGene}
\aliasA{plotGeneSign}{plotGenome}{plotGeneSign}
\keyword{hplot}{plotGenome}
\begin{Description}\relax
Basic plot of the log2 ratios for each array ordered along the genome.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotGenome(aCGH.obj, samples = 1:num.samples(aCGH.obj), naut = 22,
           Y = TRUE, X = TRUE, data = log2.ratios(aCGH.obj),
           chrominfo = human.chrom.info.Jul03,
           yScale = c(-2, 2), samplenames = sample.names(aCGH.obj),
           ylb = "Log2Ratio")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{aCGH.obj}] an object of class aCGH
\item[\code{samples}] vector containing indeces of the samples to be plotted.
\item[\code{naut}] number of autosomes in the organism
\item[\code{Y}] TRUE if chromosome Y is to be plotted, FALSE otherwise
\item[\code{X}] TRUE if chromosome X is to be plotted, FALSE otherwise
\item[\code{data}] a matrix containing values to use for plotting. defaults to the \code{log2.ratios(aCGH.obj)}.
\item[\code{chrominfo}] a chromosomal information associated with the mapping
of the data.
\item[\code{yScale}] Minimum y-scale to use for plotting. Scale is expanded if any of the
values exceed the positive or negative limit.

\item[\code{samplenames}] sample names.
\item[\code{ylb}] label for the Y-axis.
\end{ldescription}
\end{Arguments}
\begin{SeeAlso}\relax
\code{\LinkA{aCGH}{aCGH}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

#plot samples in the order of descending quality 
data(colorectal)
order.quality <- order(sd.samples(colorectal)$madGenome)
pdf("plotGenome.orderByQuality.pdf")
par(mfrow=c(2,1))
for(i in order.quality)
   plotGenome(colorectal, samples = i, Y = FALSE)
dev.off()

\end{ExampleCode}
\end{Examples}

