qtl (version 1.01-9)

plot.rf: Plot recombination fractions

Description

Plot a grid showing the recombination fractions for all pairs of markers, or of the LOD scores between pairs of markers.

Usage

plot.rf(x, chr, which=c("both","lod","rf"), ...)

Arguments

x

An object of class cross. See read.cross for details.

chr

Vector specifying which chromosomes to plot (optional)

which

Indicate whether to plot LOD scores, recombination fractions or both.

...

Ignored at this point.

Value

• None.

Details

Uses image to plot a grid showing the recombination fractions and/or LOD scores for all pairs of markers. (The LOD scores are for a test of $r = 1/2$.) If both are plotted, the recombination fractions are in the upper left triangle while the LOD scores are in the lower right triangle. Red corresponds to a large LOD or a small recombination fraction, while blue is the reverse. Note that missing values appear in light gray.

Recombination fractions are transformed by $-4(\log_2{r}+1)$ to make them on the same sort of scale as LOD scores. Values of LOD or the transformed recombination fraction that are above 12 are set to 12.

See Also

est.rf, image, badorder, ripple

Examples

data(badorder)
badorder <- est.rf(badorder)
plot.rf(badorder)

# plot just chr 1
plot.rf(badorder,chr=1)

# plot just the recombination fractions
plot.rf(badorder,which="rf") 

# plot just the LOD scores, and just for chr 2 and 3
plot.rf(badorder,which="lod")