1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
|
\name{plot.cross}
\alias{plot.cross}
\title{Plot various features of a cross object}
\description{
Plots grid of the missing genotypes, genetic map, and histograms or
barplots of phenotypes for the data from an experimental cross.
}
\usage{
\method{plot}{cross}(x, auto.layout=TRUE, pheno.col,
alternate.chrid=TRUE, \dots)
}
\arguments{
\item{x}{An object of class \code{cross}. See
\code{\link[qtl]{read.cross}} for details.}
\item{auto.layout}{If TRUE, \code{par(mfrow)} is set so that all plots
fit within one figure.}
\item{pheno.col}{Vector of numbers or character strings corresponding to
phenotypes that should be plotted. If unspecified, all phenotypes are
plotted.}
\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}{Ignored at this point.}
}
\value{None.}
\details{
Calls \code{\link[qtl]{plot.missing}}, \code{\link[qtl]{plot.map}} and
\code{\link[qtl]{plot.pheno}} to plot the missing genotypes, genetic
map, and histograms or barplots of all phenotypes.
If \code{auto.format=TRUE}, \code{par(mfrow)} is used with
\code{ceiling(sqrt(n.phe+2))} rows and the minimum number of columns
so that all plots fit on the plotting device.
Numeric phenotypes are displayed as histograms or barplots by calling
\code{\link[qtl]{plot.pheno}}.
}
\examples{
data(fake.bc)
plot(fake.bc)
}
\seealso{ \code{\link[qtl]{plot.missing}}, \code{\link[qtl]{plot.map}},
\code{\link[qtl]{plot.pheno}} }
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu}; Brian Yandell }
\keyword{hplot}
|
