Uses image to plot a grid of LOD scores. The
particular LOD scores plotted in the upper-left and lower-right
triangles are selected via upper and lower,
respectively. By default, the upper-left triangle contains the
epistasis LOD
scores ("int"), and the lower-right triangle contains the LOD
scores for the full model ("full").
The diagonal contains either all zeros or the main effects LOD scores
(from scanone). The scantwo function calculates, for each pair of
putative QTLs, $(q1,q2)$, the likelihood under the
null model $L0$, the likelihood under each of the single-QTL
models, $L(q1)$ and $L(q2)$, the likelihood
under an additive QTL model, $La(q1,q2)$, and the
likelihood under a full QTL model (including QTL-QTL interaction),
$Lf(q1,q2)$.
The five possible LOD scores that may be plotted are the following.
The epistasis LOD scores ("int") are $LODi = log10 Lf(q1,q2) -
log10 La(q1,q2)$.
The full LOD scores ("full") are
$
LODj = log10 Lf(q1,q2) - log10 L0$.
The additive LOD scores ("add") are
$
LODa = log10 La(q1,q2) - log10 L0$.
In addition, we may calculate, for each pair of
chromosomes, the difference between the full LOD score and the
maximum single-QTL LOD scores for that pair of chromosomes
("cond-int").
Finally, we may calculate, for each pair of
chromosomes, the difference between the additive LOD score and the
maximum single-QTL LOD scores for that pair of chromosomes
("cond-add").
If a color scale is plotted (zscale=TRUE), the axis on the
left indicates the scale for the upper-left triangle,
while the axis on the right indicates the scale for the
lower-right triangle. Note that the axis labels can get screwed up
if you change the size of the figure window; you'll need to redo the
plot.