R: Plot recombination fractions

plotRF {qtl} | R Documentation

## 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"), ...)

### 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.

### 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(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.

### Value

None.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`est.rf`, `pull.rf`, `plot.rfmatrix`, `image`, `badorder`, `ripple`

### Examples

    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")

[Package qtl version 1.46-2 Index]