R: Plot LOD curves

plot.scanone {qtl} | R Documentation

## Plot LOD curves

### Description

Plot the LOD curve for a genome scan with a single-QTL model (the output of `scanone`).

### Usage

    ## S3 method for class 'scanone'
    plot(x, x2, x3, chr, lodcolumn=1, incl.markers=TRUE,
         xlim, ylim, lty=1, col=c("black","blue","red"), lwd=2,
         add=FALSE, gap=25, mtick = c("line", "triangle"),
         show.marker.names=FALSE, alternate.chrid=FALSE,
         bandcol=NULL, type="l", cex=1, pch=1, bg="transparent",
         bgrect=NULL, ...)

### Arguments

`x` | An object of class `"scanone"`, as output by `scanone`.
`x2` | Optional second `scanone` object.
`x3` | Optional third `scanone` object.
`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.
`lodcolumn` | An integer, or vector of 3 integers, indicating which of the LOD score columns should be plotted (generally this is 1).
`incl.markers` | Indicate whether to plot line segments at the marker locations.
`xlim` | Limits for x-axis (optional).
`ylim` | Limits for y-axis (optional).
`lty` | Line types; a vector of length 1 or 3.
`col` | Line colors; a vector of length 1 or 3.
`lwd` | Line widths; a vector of length 1 or 3.
`add` | If TRUE, add to a current plot.
`gap` | Gap separating chromosomes (in cM).
`mtick` | Tick mark type for markers (line segments or upward-pointing triangels).
`show.marker.names` | If TRUE, show the marker names along the x axis.
`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.
`bandcol` | Optional color for alternating bands to indicate chromosomes. If NULL (the default), no bands are plotted. A good choice might be `bandcol="gray70"`.
`type` | Type of plot (see `plot`): for example, `type="l"` for lines or `type="p"` for points only, may be of length 1 or 3.
`cex` | Point size expansion, for example if `type="p"` is used. May be of length 1 or 3.
`pch` | Point type, for example if `type="p"` is used. See `points`. May be of length 1 or 3.
`bg` | Background color for points, for example if `type="p"` and `pch=21` are used. See `points`. May be of length 1 or 3.
`bgrect` | Optional background color for the rectangular plotting region.
`...` | Passed to the function `plot` when it is called.

### Details

This function allows you to plot the results of up to three genome scans against one another. Such objects must conform with each other.

One may alternatively use the argument `add` to add the plot of an additional genome scan to the current figure, but some care is required: the same chromosomes should be selected, and the results must concern crosses with the same genetic maps.

If a single `scanone` object containing multiple LOD score columns (for example, from different phenotypes) is input, up to three LOD curves may be plotted, by providing a vector in the argument `lodcolumn`. If multiple `scanone` objects are input (via `x`, `x2` and `x3`), the LOD score columns to be plotted are chosen from the corresponding element of the `lodcolumn` argument.

### Value

None.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`scanone`, `summary.scanone`, `par`, `colors`, `add.threshold`, `xaxisloc.scanone`

### Examples

    data(fake.f2)

    fake.f2 <- calc.genoprob(fake.f2,step=2.5)
    out.mr <- scanone(fake.f2, method="mr")
    out.em <- scanone(fake.f2, method="em")
    plot(out.mr)
    plot(out.mr, out.em, chr=c(1,13), lty=1, col=c("violetred","black"))
    out.hk <- scanone(fake.f2, method="hk")
    plot(out.hk, chr=c(1,13), add=TRUE, col="slateblue")

    plot(out.hk, chr=13, show.marker.names=TRUE)

    plot(out.hk, bandcol="gray70")

    # plot points rather than lines
    plot(out.hk, bandcol="gray70", type="p", cex=0.3, pch=21, bg="slateblue")

[Package qtl version 1.46-2 Index]