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plot.scanPhyloQTL.Rd
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plot.scanPhyloQTL.Rd
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\name{plot.scanPhyloQTL}
\alias{plot.scanPhyloQTL}
\title{Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree}
\description{
Plot the LOD curves for each partition for a genome scan with a single
diallelic QTL (the
output of \code{\link{scanPhyloQTL}}).
}
\usage{
\method{plot}{scanPhyloQTL}(x, chr, incl.markers=TRUE,
col, xlim, ylim, lwd=2, gap=25, mtick=c("line", "triangle"),
show.marker.names=FALSE, alternate.chrid=FALSE, legend=TRUE, \dots)
}
\arguments{
\item{x}{An object of class \code{"scanPhyloQTL"}, as output by
\code{\link{scanPhyloQTL}}.}
\item{chr}{Optional vector indicating the chromosomes to plot.
This should be a vector of character strings referring to chromosomes
by name; numeric values are converted to strings. Refer to
chromosomes with a preceding \code{-} to have all chromosomes but
those considered. A logical (TRUE/FALSE) vector may also be used.}
\item{incl.markers}{Indicate whether to plot line segments at the
marker locations.}
\item{col}{Optional vector of colors to use for each partition.}
\item{xlim}{Limits for x-axis (optional).}
\item{ylim}{Limits for y-axis (optional).}
\item{lwd}{Line width.}
\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{legend}{Indicates whether to include a legend in the plot.}
\item{\dots}{Passed to the function \code{\link{plot.scanone}} when it
is called.}
}
\value{None.}
%\details{
%}
\examples{
\dontrun{
# example map; drop X chromosome
data(map10)
map10 <- map10[1:19]
# simulate data
x <- simPhyloQTL(4, partition="AB|CD", crosses=c("AB", "AC", "AD"),
map=map10, n.ind=150,
model=c(1, 50, 0.5, 0))
# run calc.genoprob on each cross
x <- lapply(x, calc.genoprob, step=2)
# scan genome, at each position trying all possible partitions
out <- scanPhyloQTL(x, method="hk")
# maximum peak
max(out, format="lod")
# approximate posterior probabilities at peak
max(out, format="postprob")
# all peaks above a threshold for LOD(best) - LOD(2nd best)
summary(out, threshold=1, format="lod")
# all peaks above a threshold for LOD(best), showing approx post'r prob
summary(out, format="postprob", threshold=3)
# plot of results
plot(out)
}
}
\seealso{ \code{\link{scanPhyloQTL}}, \code{\link{max.scanPhyloQTL}},
\code{\link{summary.scanPhyloQTL}}, \code{\link{plot.scanone}},
\code{\link{inferredpartitions}},
\code{\link{simPhyloQTL}},
\code{\link[graphics]{par}}, \code{\link[grDevices]{colors}} }
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu} }
\references{
Broman, K. W., Kim, S., An\'e, C. and Payseur, B. A. Mapping
quantitative trait loci to a phylogenetic tree. In preparation.
}
\keyword{hplot}