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\name{plot.missing}
\alias{plot.missing}
\title{Plot grid of missing genotypes}
\description{
Plot a grid showing which genotypes are missing.
}
\usage{
plot.missing(x, chr, reorder=FALSE, main="Missing genotypes",
alternate.chrid=FALSE, \dots)
}
\arguments{
\item{x}{An object of class \code{cross}. See
\code{\link[qtl]{read.cross}} for details. }
\item{chr}{Vector of chromosomes to plot. If missing, plot all
chromosomes.}
\item{reorder}{Specify whether to reorder individuals according to
their phenotypes.
\tabular{ll}{
FALSE \tab Don't reorder \cr
TRUE \tab Reorder according to the sum of the phenotypes \cr
n \tab Reorder according to phenotype n}}
\item{main}{Title to place on plot.}
\item{alternate.chrid}{If TRUE and more than one chromosome is
plotted, alternate the placement of chromosome
axis labels, so that they may be more easily distinguished.}
\item{\dots}{Ignored at this point.}
}
\details{
Uses \code{\link[graphics]{image}} to plot a grid with black pixels where the
genotypes are missing. For intercross and 4-way cross data, gray
pixels are plotted for the partially missing genotypes (for example,
``not AA'').
}
\value{None.}
\examples{
data(fake.f2)
plot.missing(fake.f2)
}
\seealso{ \code{\link[qtl]{plot.cross}}, \code{\link[qtl]{geno.image}},
\code{\link[graphics]{image}} }
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu} }
\keyword{hplot}
|
