qtl (version 0.92-3)

plot.scanone: Plot LOD curves

Description

Plot the LOD curve for a genome scan with a single-QTL model (the output of scanone).

Usage

plot.scanone(x, x2, x3, chr, incl.markers=TRUE, ylim,
             lty=c(1,2,3), col="black", lwd=2, add=FALSE,
             gap=25, main, ...)

Arguments

x

A data.frame with at least three columns. The first three columns should be the following (any further columns are ignored):

x2

data.frame for a second genome scan (optional)

x3

data.frame for a third genome scan (optional)

chr

Vector specifying which chromosomes to plot. (The chromosomes must be specified by name.)

incl.markers

Indicate whether to plot line segments at the marker locations.

ylim

Limits for y-axis (optional).

lty

Line types; a vector of length 1 or 3.

col

Line colors; a vector of length 1 or 3.

lwd

Line widths; a vector of length 1 or 3.

add

If TRUE, add to a current plot.

gap

Gap separating chromosomes (in cM).

main

An optional title for the plot.

...

Passed to the function 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 add to add the plot of an additional genome scan to the current figure, but some care is required.

See Also

scanone, summary.scanone, par, colors

Examples

data(fake.f2)
fake.f2 <- calc.genoprob(fake.f2,step=2.5)
out.mr <- scanone(fake.f2, method="mr")
out.im <- scanone(fake.f2, chr=c(1,13), method="em")
plot(out.mr)
plot(out.mr, out.im, chr=c(1,13))
plot(out.mr, out.im, , c(1,13), lty=1, col=c("violetred","black"))
out.hk <- scanone(fake.f2, chr=c(1,13), method="hk")
plot(out.hk, , , c(1,13), add=TRUE, col="slateblue")