plot.scanone {qtl}R Documentation

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, lodcolumn=3, incl.markers=TRUE,
             xlim, ylim, lty=1, col=c("black","blue","red"), lwd=2,
             add=FALSE, gap=25, main, mtick = c("line", "triangle"),
             ...)

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.)
lodcolumn An integer, or vector of 3 integers, indicating which columns of the input should be plotted (generally column 3).
incl.markers Indicate whether to plot line segments at the marker locations.
xlim Limits for x-axis (optional).
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.
mtick Tick mark type for markers (line segments or upward-pointing triangels).
... Passed to the function plot when it is called.

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.

Value

None.

Author(s)

Karl W Broman, kbroman@jhsph.edu

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

[Package qtl version 0.98-57 Index]