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\name{plot.qtl}
\alias{plot.qtl}
\title{Plot QTL locations}
\description{
Plot the locations of the QTL against a genetic map
}
\usage{
\method{plot}{qtl}(x, chr, horizontal=FALSE, shift=TRUE,
show.marker.names=FALSE, alternate.chrid=FALSE, \dots)
}
\arguments{
\item{x}{An object of class \code{"qtl"}, as produced by
\code{\link[qtl]{makeqtl}}.}
\item{chr}{Vector specifying which chromosomes to plot. (The
chromosomes must be specified by name.) If missing, all chromosomes
are plotted.}
\item{horizontal}{Specifies whether the chromosomes should be
plotted horizontally.}
\item{shift}{If TRUE, shift the first marker on each chromosome to be
at 0 cM.}
\item{show.marker.names}{If TRUE, marker names are included.}
\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}{Passed to \code{\link[qtl]{plot.map}}.}
}
\value{None.}
\details{
Creates a plot, via \code{\link[qtl]{plot.map}}, and indicates the
locations of the QTL in the input QTL object, \code{x}.
}
\examples{
data(fake.f2)
# take out several QTLs and make QTL object
qc <- c("1", "6", "13")
qp <- c(25.8, 33.6, 18.63)
fake.f2 <- subset(fake.f2, chr=qc)
\dontshow{fake.f2 <- subset(fake.f2, ind=1:50)}
fake.f2 <- sim.geno(fake.f2, n.draws=2, step=2, err=0.001)
qtl <- makeqtl(fake.f2, qc, qp, what="draws")
plot(qtl)
}
\seealso{ \code{\link[qtl]{plot.map}}, \code{\link[qtl]{makeqtl}} }
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu} }
\keyword{hplot}
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