| plot.rf {qtl} | R Documentation |
Plot a grid showing the recombination fractions for all pairs of markers, and/or the LOD scores for tests of linkage between pairs of markers.
plot.rf(x, chr, what=c("both","lod","rf"), alternate.chrid=FALSE,
zmax=12, ...)
x |
An object of class cross. See
read.cross for details. |
chr |
Optional vector indicating the chromosomes to plot.
This should be a vector of character strings referring to chromosomes
by name; numeric values are converted to strings. Refer to
chromosomes with a preceding - to have all chromosomes but
those considered. A logical (TRUE/FALSE) vector may also be used. |
what |
Indicate whether to plot LOD scores, recombination fractions or both. |
alternate.chrid |
If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished. |
zmax |
Maximum LOD score plotted; values above this are all thresholded at this value. |
... |
Generally ignored, but you can include main to
change or omit the title of the figure. |
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(log2(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.
None.
Karl W Broman, kbroman@biostat.wisc.edu
est.rf, image,
badorder, ripple
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, what="rf") # plot just the LOD scores, and just for chr 2 and 3 plot.rf(badorder, chr=2:3, what="lod")