Description Usage Arguments Details Value Author(s) See Also Examples
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.
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x |
An object of class |
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 |
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. |
mark.diagonal |
If TRUE, include black line segments around the pixels along the diagonal, to better separate the upper left triangle from the lower right triangle. |
... |
Generally ignored, but you can include |
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
, pull.rf
, plot.rfmatrix
,
image
,
badorder
, ripple
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