plotRF: Plot recombination fractions

Description

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.

Usage

plotRF(x, chr, what=c("both","lod","rf"), alternate.chrid=FALSE,
        zmax=12, mark.diagonal=FALSE,
        col.scheme=c("viridis", "redblue"), ...)

Value

None.

Arguments

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.
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.
col.scheme: The color palette. The default is "viridis"; see Option D at https://bids.github.io/colormap/
...: Generally ignored, but you can include main to change or omit the title of the figure.

Author

Karl W Broman, broman@wisc.edu

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.

With col.scheme="viridis" (the default), purple corresponds to a large LOD score or a small recombination fraction, while yellow is the reverse. With col.scheme="redblue", 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.

Examples

Run this code

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

# plot just chr 1
plotRF(badorder, chr=1)

# plot just the recombination fractions
plotRF(badorder, what="rf")

# plot just the LOD scores, and just for chr 2 and 3
plotRF(badorder, chr=2:3, what="lod")

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