R: Get x-axis locations in scanone plot

xaxisloc.scanone {qtl} | R Documentation

## Get x-axis locations in scanone plot

### Description

Get x-axis locations for given cM positions on given chromosomes in a plot from `plot.scanone`)

### Usage

    xaxisloc.scanone(out, thechr, thepos, chr, gap=25)

### Arguments

`out` | An object of class `"scanone"`, as output by `scanone`. This must be identical to what was used in the call to `plot.scanone`.
`thechr` | Chromosome IDs at which x-axis locations are to be determined.
`thepos` | Chromosome positions at which x-axis locations are to be determined.
`chr` | Optional vector specifying which chromosomes were plotted. This must be identical to what was used in the call to `plot.scanone`.
`gap` | Gap separating chromosomes (in cM). This must be identical to what was used in the call to `plot.scanone`.

### Details

This function allows you to identify the x-axis locations in a plot of genome scan results, produced by `plot.scanone`. This is useful for adding annotations, such as text or arrows.

The arguments `out`, `chr`, and `gap` must match what was used in the call to `plot.scanone`.

The arguments `thechr` and `thepos` indicate the genomic positions for which x-axis locations are desired. If they both have length > 1, they must have the same length. If one has length > 1 and one has length 1, the one with length 1 is expanded to match.

### Value

A numeric vector of x-axis locations.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`plot.scanone`, `add.threshold`

### Examples

    data(hyper)

    hyper <- calc.genoprob(hyper)
    out <- scanone(hyper, method="hk")
    plot(out, chr=c(1, 4, 6, 15))

    # add arrow and text to indicate peak LOD score
    mxout <- max(out)
    x <- xaxisloc.scanone(out, mxout$chr, mxout$pos, chr=c(1,4,6,15))
    arrows(x+30, mxout$lod, x+5, mxout$lod, len=0.1, col="blue")
    text(x+35, mxout$lod, "the peak", col="blue", adj=c(0, 0.5))

[Package qtl version 1.46-2 Index]