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\name{plot.map}
\alias{plot.map}
\title{Plot genetic map}
\description{
Plot genetic map of marker locations for all chromosomes.
}
\usage{
\method{plot}{map}(x, map2, chr, horizontal=FALSE, shift=TRUE,
show.marker.names=FALSE, alternate.chrid=FALSE, \dots)
}
\arguments{
\item{x}{A list whose components are vectors of marker locations. A
\code{cross} object may be given instead, in which case the genetic
map it contains is used.}
\item{map2}{An optional second genetic map with the same number of
chromosomes and markers as the first. As with the first argument, a
\code{cross} object may be given instead. If this argument is
given, a comparison of the two genetic maps is plotted.}
\item{chr}{Optional vector specifying which chromosomes to plot. (The
chromosomes must be specified by name.)}
\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[graphics]{plot}}.}
}
\value{None.}
\details{
Plots the genetic map for each chromosome, or a comparison of the
genetic maps if two maps are given.
For a sex-specific map, female and male maps are plotted against one
another. For two sex-specific maps, the two female maps are plotted
against one another and the two male maps are plotted against one
another.
}
\examples{
data(fake.bc)
\dontshow{fake.bc <- subset(fake.bc, chr=18:19)}
plot.map(fake.bc)
plot.map(fake.bc,horizontal=TRUE)
newmap <- est.map(fake.bc)
plot(newmap)
plot.map(fake.bc, newmap)
plot.map(fake.bc, show.marker.names=TRUE)
}
\seealso{ \code{\link[qtl]{est.map}}, \code{\link[qtl]{plot.cross}} }
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu} }
\keyword{hplot}
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