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\name{plot.rf}
\alias{plot.rf}
\title{Plot recombination fractions}
\description{
Plot a grid showing the recombination fractions for all pairs of
markers, and/or the LOD scores for tests of linkage between pairs of
markers.
}
\usage{
plot.rf(x, chr, what=c("both","lod","rf"), alternate.chrid=FALSE,
zmax=12, \dots)
}
\arguments{
\item{x}{An object of class \code{cross}. See
\code{\link[qtl]{read.cross}} for details.}
\item{chr}{Vector specifying which chromosomes to plot
(optional)}
\item{what}{Indicate whether to plot LOD scores, recombination
fractions or both.}
\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{zmax}{Maximum LOD score plotted; values above this are all
thresholded at this value.}
\item{\dots}{Ignored at this point.}
}
\value{None.}
\details{
Uses \code{\link[graphics]{image}} to plot a grid showing the
recombination fractions and/or LOD scores for all pairs of markers.
(The LOD scores are for a test of \eqn{r = 1/2}.)
If both are plotted, the recombination fractions are in the upper left
triangle while the LOD scores are in the lower right triangle.
Red corresponds to a large LOD or a small recombination fraction,
while blue is the reverse. Note that missing values appear in light
gray.
Recombination fractions are transformed by \eqn{-4(\log_2{r}+1)}{%
-4(log2(r)+1)} to make them on the same sort of scale as LOD
scores. Values of LOD or the transformed recombination fraction that
are above 12 are set to 12.
}
\examples{
data(badorder)
badorder <- est.rf(badorder)
plot.rf(badorder)
# plot just chr 1
plot.rf(badorder, chr=1)
# plot just the recombination fractions
plot.rf(badorder, what="rf")
# plot just the LOD scores, and just for chr 2 and 3
plot.rf(badorder, chr=2:3, what="lod")
}
\seealso{ \code{\link[qtl]{est.rf}}, \code{\link[graphics]{image}},
\code{\link[qtl]{badorder}}, \code{\link[qtl]{ripple}} }
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu} }
\keyword{hplot}
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