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\name{plot.pxg}
\alias{plot.pxg}
\title{Plot phenotypes versus marker genotypes.}
\description{
Plot the phenotype values versus the genotypes at a marker or markers.
}
\usage{
plot.pxg(x, marker, pheno.col=1, jitter=1, infer=TRUE,
pch, ylab, main, col, \dots)
}
\arguments{
\item{x}{An object of class \code{cross}. See
\code{\link[qtl]{read.cross}} for details. }
\item{marker}{Marker name (a character string; can be a vector).}
\item{pheno.col}{Column number in the phenotype matrix which should be
used as the phenotype. One may also give a character string matching
a phenotype name.}
\item{jitter}{A positive number indicating how much to spread out the
points horizontally. (Larger numbers correspond to greater spread.)}
\item{infer}{If TRUE, missing genotypes are filled in with a single
random imputation and plotted in red; if FALSE, only individuals
typed at the specified marker are plotted.}
\item{pch}{Plot symbol.}
\item{ylab}{Label for y-axis.}
\item{main}{Main title for the plot. If missing, the names of the
markers are used.}
\item{col}{A vector of colors to use for the confidence intervals
(optional).}
\item{\dots}{Ignored at this point.}
}
\details{
Plots the phenotype data against the genotypes at the specified
marker. If infer=TRUE, the genotypes of individuals that were not
typed is inferred based the genotypes at linked markers via a single
imputation from \code{\link[qtl]{sim.geno}}; these points are plotted
in red. For each genotype, the phenotypic mean is plotted, with error
bars at \eqn{\pm}{+/-} 1 SE.
}
\value{
A data.frame with initial columns the marker genotypes, then the
phenotype data, then a column indicating whether any of the marker
genotypes were inferred (1=at least one genotype inferred, 0=none were
inferred).
}
\examples{
data(listeria)
mname <- find.marker(listeria, 5, 28) # marker D5M357
plot.pxg(listeria, mname)
mname2 <- find.marker(listeria, 13, 26) # marker D13Mit147
plot.pxg(listeria, c(mname, mname2))
plot.pxg(listeria, c(mname2, mname))
data(fake.f2)
mname <- find.marker(fake.f2, 1, 37) # marker D1M437
plot.pxg(fake.f2, mname)
mname2 <- find.marker(fake.f2, "X", 14) # marker DXM66
plot.pxg(fake.f2, mname2)
plot.pxg(fake.f2, c(mname,mname2))
plot.pxg(fake.f2, c(mname2,mname))
}
\seealso{ \code{\link[qtl]{find.marker}}, \code{\link[qtl]{effectplot}},
\code{\link[qtl]{find.flanking}}, \code{\link[qtl]{effectscan}} }
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu}; Brian Yandell }
\keyword{hplot}
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