qtl (version 1.01-9)

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

Description

Plot the results of a two-dimensional, two-QTL genome scan.

Usage

## S3 method for class 'scantwo':
plot(x, chr, incl.markers=FALSE, zlim,
             lower=c("joint","add","cond-int","cond-add"), nodiag=TRUE, 
             contours=FALSE, main, zscale=TRUE, point.at.max=FALSE,
             col.scheme = c("redblue","cm","gray","heat","terrain","topo"),
             gamma=1, ...)

Arguments

x

An object of class "scantwo", as output by 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.

lower

Indicates which LOD scores should be plotted in the lower triangle. See the details below.

nodiag

If TRUE, suppress the plot of the scanone output (which is normally along the diagonal.)

contours

If TRUE, add a contour to the plot at 1.5-LOD below its maximum, using a call to contour. If a numeric vector, contours are drawn at these values below the maximum LOD.

main

An optional title for the plot.

zscale

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

point.at.max

If TRUE, plot an X at the maximum LOD.

col.scheme

Name of color pallet.

gamma

Parameter affecting range of colors when col.scheme="gray" or ="redblue".

...

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 content in the lower triangle depends on the input argument lower. The diagonal contains either all zeros or the main effects LOD scores (from scanone).

The scantwo function calculates, for each pair of putative QTLs, $(q_1,q_2)$, the likelihood undering the null model $L_0$, the likelihood under each of the single-QTL models, $L(q_1)$ and $L(q_2)$, the likelihood under an additive QTL model, $L_a(q_1,q_2)$, and the likelihood under a full QTL model (including QTL-QTL interaction), $L_f(q_1,q_2)$. The upper triangle in plot from this function contains the epistasis LOD scores, $LOD_i = \log_{10} L_f(q_1,q_2) - \log_{10} L_a(q_1,q_2)$.

If lower="joint", the lower triangle will contain the joint LOD scores, $LOD_j = \log_{10} L_f(q_1,q_2) - \log_{10} L_0$.

If lower="add", the lower triangle will contain the additive LOD scores, $LOD_a = \log_{10} L_a(q_1,q_2) - \log_{10} L_0$.

If lower="cond-int", the lower triangle will contain LOD scores comparing the two-QTL joint likelihood to the best of the single-QTL models, $LOD_{ci} = \log_{10} L_f(q_1,q_2) - \log_{10} \max(L(q_1), L(q_2))$.

If lower="cond-add", the lower triangle will contain LOD scores comparing the two-QTL additive likelihood to the best of the single-QTL models, $LOD_{ca} = \log_{10} L_a(q_1,q_2) - \log_{10} \max(L(q_1), L(q_2))$. 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 scale for 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.

See Also

scantwo, summary.scantwo, plot.scanone

Examples

data(fake.f2)
fake.f2 <- calc.genoprob(fake.f2, step=5)
out.2dim <- scantwo(fake.f2, method="hk", chr=c(1,8,13,14))
plot(out.2dim)
plot(out.2dim, nodiag=FALSE)
plot(out.2dim, lower="joint", nodiag=FALSE)