qtl (version 0.92-3)

plot.scantwo: Plot LOD scores for a two-dimensional genome scan

Description

Plot the joint and epistasis LOD scores for a two-dimensional genome scan with a two-QTL model.

Usage

plot.scantwo(x, chr, incl.markers=FALSE, zlim,
             contours=FALSE, main, zscale=TRUE, ...)

Arguments

x

An object of class "scantwo", as output by link[qtl]{scantwo}.

chr

Vector specifying which chromosomes to plot.

incl.markers

If FALSE, plot LOD scores on an evenly spaced grid (not including the results at the markers).

zlim

A vector of length 2 (optional), indicating the z limits for the joint LOD and the epistasis LOD scores, respectively. If missing, the maximum limits are used for each.

contours

If TRUE, add contours to the plot, using a call to contour.

main

An optional title for the plot.

zscale

If TRUE, a color scale is plotted at the right.

...

Ignored at this point.

Value

• None.

Details

Uses image to plot a grid of LOD scores. The upper triangle contains the epistasis LOD scores; the lower triangle contains the joint LOD scores. The diagonal contains either all zeros or the main effects LOD scores.

If a color scale is plotted (zscale=TRUE), the axis on the left indicates the scale for the epistasis LOD scores (the upper triangle), while the axis on the right indicates the joint LOD scores (the lower triangle). Note that the axis labels get screwed up if you change the size of the figure window; you'll need to redo the plot.

Note that the numbers plotted with the contours (if contours=TRUE) are for the joint LOD scores, and may be incorrect for the epistasis LOD scores. It appears to be difficult to fix this.

See Also

scantwo, summary.scantwo, plot.scanone

Examples

data(fake.f2)
fake.f2 <- calc.genoprob(fake.f2, step=10)
out.2dim <- scantwo(fake.f2, method="hk", chr=c(1,6,13))
plot(out.2dim)
plot(out.2dim, zlim=c(7.5,7.5))