\HeaderA{plotSnp}{Plots copy number and genotype calls.}{plotSnp}
\keyword{hplot}{plotSnp}
\begin{Description}\relax
Plots copy number and genotype call versus physical position for
an arbitrary number of samples and chromosomes.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotSnp(object, chromosomes, samples, snpId = c(NA, 1e+06), oma = c(5, 4, 4, 0.5), mar = c(0.5, 0, 0.5, 0.2), width.right = NULL, showLayout = FALSE, plot = TRUE, col = c("royalblue", "red", "royalblue", "green3"), bg = rep("white", 4), cex = c(2, 3, 2, 2), pch = rep(".", 4), col.centromere = c("bisque", NA), bw = FALSE, lwd = 2, col.axis = "brown", cex.axis = 1, cex.main = 1, cex.lab = 1, xlim = NULL, ylim = NULL, log = "", xaxis.side = rep(c(1, 3), length.out = length(chromosomes)), xaxs = "i", xaxt = "n", yaxs = "i", yaxt = "n", xlab = "", ylab = "", lab = c(2, 5, 7), adj = 0, main = "", legend = c(TRUE, TRUE), legend.panel = c(TRUE, FALSE), legend.location = c("topright", "bottomright"), legend.bty = c("n", "n"), legend.col = c("white", "white"), ncol = 2, cex.legend = c(1, 1), digits = 3, pt.cex = cex.legend * 1.5, bty = "n", addCytoband = FALSE, height.cytoband = 0.5, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] Object of class \code{AnnotatedSnpCopyNumberSet} or \code{AnnotatedSnpSet}
\item[\code{chromosomes}] Vector of character strings for chromosome number.
Chromosomes will be plotted in the order given.
\item[\code{samples}] Vector of integers indicating sample number.
\item[\code{snpId}] Not yet implemented.
\item[\code{oma}] See \code{par}
\item[\code{mar}] See \code{par}
\item[\code{width.right}] Width of panel for the legend relative to the width
of the smallest chromosome.
\item[\code{showLayout}] Logical for whether to display the output of
\code{layout} for plotting
\item[\code{plot}] Logical.  If FALSE, only the output from \code{layout} is displayed.
\item[\code{col}] A character or numerical vector indicating the color to plot genotype
call:  AA color, AB color,  BB color, no call color.  For
\code{AnnotatedSnpCopyNumberSet}, only the first color is used.
\item[\code{bg}] A character or numerical vector indicating the background color for the
plotting symbols.  Possible to specify a different background for
each genotype call in the same order as \code{col}.
\item[\code{cex}] A numerical vector of plotting symbol size in the same
order as \code{col}.
\item[\code{pch}] A character or numerical vector of plotting symbol size in the same
order as \code{col}.
\item[\code{col.centromere}] Vector of length two: color of centromere and
color for the centromere border. 
\item[\code{bw}] Converts all colors to grayscale.  
\item[\code{lwd}] See \code{par}
\item[\code{col.axis}] See \code{par}
\item[\code{cex.axis}] See \code{par}
\item[\code{cex.main}] See \code{par}
\item[\code{cex.lab}] See \code{par}
\item[\code{xlim}] See \code{par}
\item[\code{ylim}] See \code{par}
\item[\code{log}] See \code{par}
\item[\code{xaxis.side}] Vector of integers indicating whether to plot the
x-axis on the top (3) or bottom (1) for each sample.  The default is
to alternate top/bottom.
\item[\code{xaxs}] See \code{par}
\item[\code{xaxt}] See \code{par}
\item[\code{yaxs}] See \code{par}
\item[\code{yaxt}] See \code{par}
\item[\code{xlab}] See \code{par}
\item[\code{ylab}] See \code{par}
\item[\code{lab}] See \code{par}
\item[\code{adj}] See \code{par}
\item[\code{main}] See \code{par}
\item[\code{legend}] Logical vector of length 2.  If both are TRUE, a legend
for descriptive statistics (legend 1) and plotting symbols (legend
2) are generated.
\item[\code{legend.panel}] Logical vector of length 2.  Whether to draw the
legends on a separate panel.
\item[\code{legend.location}] Character vector of length 2.  Where to draw
the legends. See \code{legend}.
\item[\code{legend.bty}] Character vector of length 2.  See the argument
\code{bty} in function \code{legend}.
\item[\code{legend.col}] Character vector of length 2. See the argument
\code{bty} in function \code{legend}. 
\item[\code{ncol}] Number of columns in legend for plotting symbols.  See \code{legend}.
\item[\code{cex.legend}] Same as argument \code{cex} in function \code{legend}.
\item[\code{digits}] Rounds values in legend to the number of digits specified.
\item[\code{pt.cex}] See \code{legend}
\item[\code{bty}] See \code{par}
\item[\code{addCytoband}] Logical indicating whether to add a cytoband.
\item[\code{height.cytoband}] Height of cytoband relative to height of samples.
\item[\code{...}] Additional arguments
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\end{Details}
\begin{Value}
\end{Value}
\begin{Note}\relax
\end{Note}
\begin{Author}\relax
Robert Scharpf
\end{Author}
\begin{References}\relax
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{par}{par}}, \code{\LinkA{plot}{plot}}, \code{\LinkA{legend}{legend}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(annSnpset)
plotSnp(annSnpset, chromosomes=c(1:22, "X"), 
        samples=1:4, width.right=10, cex.axis=1, lab=c(3, 3, 5),
        cex.lab=1.2, cex.legend=c(1, 1.2))
\end{ExampleCode}
\end{Examples}

