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\name{plot.scanone}
\alias{plot.scanone}
\title{Plot LOD curves}
\description{
Plot the LOD curve for a genome scan with a single-QTL model (the
output of \code{\link[qtl]{scanone}}).
}
\usage{
\method{plot}{scanone}(x, x2, x3, chr, lodcolumn=1, incl.markers=TRUE,
xlim, ylim, lty=1, col=c("black","blue","red"), lwd=2,
add=FALSE, gap=25, mtick = c("line", "triangle"),
show.marker.names=FALSE, alternate.chrid=FALSE, \dots)
}
\arguments{
\item{x}{An object of class \code{"scanone"}, as output by
\code{\link[qtl]{scanone}}.}
\item{x2}{Optional second \code{scanone} object.}
\item{x3}{Optional third \code{scanone} object.}
\item{chr}{Optional vector specifying which chromosomes to plot. (The
chromosomes must be specified by name.)}
\item{lodcolumn}{An integer, or vector of 3 integers, indicating which
of the LOD score columns should be plotted (generally this is 1).}
\item{incl.markers}{Indicate whether to plot line segments at the
marker locations.}
\item{xlim}{Limits for x-axis (optional).}
\item{ylim}{Limits for y-axis (optional).}
\item{lty}{Line types; a vector of length 1 or 3.}
\item{col}{Line colors; a vector of length 1 or 3.}
\item{lwd}{Line widths; a vector of length 1 or 3.}
\item{add}{If TRUE, add to a current plot.}
\item{gap}{Gap separating chromosomes (in cM).}
\item{mtick}{Tick mark type for markers (line segments or
upward-pointing triangels).}
\item{show.marker.names}{If TRUE, show the marker names along the x axis.}
\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 the function \code{\link[graphics]{plot}} when it
is called.}
}
\value{None.}
\details{
This function allows you to plot the results of up to three genome
scans against one another. Such objects must conform with each
other.
One may alternatively use the argument \code{add} to add the plot of
an additional genome scan to the current figure, but some care is
required: the same chromosomes should be selected, and the results
must concern crosses with the same genetic maps.
If a single \code{scanone} object containing multiple LOD score
columns (for example, from different phenotypes) is input, up to three
LOD curves may be plotted, by providing a vector in the argument
\code{lodcolumn}. If multiple \code{scanone} objects are input (via
\code{x}, \code{x2} and \code{x3}), the LOD score columns to be
plotted are chosen from the corresponding element of the
\code{lodcolumn} argument.
}
\examples{
data(fake.f2)
\dontshow{fake.f2 <- subset(fake.f2, chr=c(1,13))}
fake.f2 <- calc.genoprob(fake.f2,step=2.5)
out.mr <- scanone(fake.f2, method="mr")
out.em <- scanone(fake.f2, method="em")
plot(out.mr)
plot(out.mr, out.em, chr=c(1,13), lty=1, col=c("violetred","black"))
out.hk <- scanone(fake.f2, method="hk")
plot(out.hk, chr=c(1,13), add=TRUE, col="slateblue")
plot(out.hk, chr=13, show.marker.names=TRUE)
}
\seealso{ \code{\link[qtl]{scanone}},
\code{\link[qtl]{summary.scanone}}, \code{\link[graphics]{par}},
\code{\link[grDevices]{colors}} }
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu} }
\keyword{hplot}
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