R: Plot QTL locations

plot.qtl {qtl} | R Documentation

## Plot QTL locations

### Description

Plot the locations of the QTL against a genetic map

### Usage

    ## S3 method for class 'qtl'
    plot(x, chr, horizontal=FALSE, shift=TRUE,
         show.marker.names=FALSE, alternate.chrid=FALSE, justdots=FALSE,
         col="red", ...)

### Arguments

`x` | An object of class `"qtl"`, as produced by `makeqtl`.
`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.
`horizontal` | Specifies whether the chromosomes should be plotted horizontally.
`shift` | If TRUE, shift the first marker on each chromosome to be at 0 cM.
`show.marker.names` | If TRUE, marker names are included.
`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.
`justdots` | If FALSE, just plot dots at the QTL, rather than arrows and QTL names.
`col` | Color used to plot indications of QTL
`...` | Passed to `plotMap`.

### Details

Creates a plot, via `plotMap`, and indicates the locations of the QTL in the input QTL object, `x`.

### Value

None.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`plotMap`, `makeqtl`

### Examples

    data(fake.f2)

    # take out several QTLs and make QTL object
    qc <- c("1", "6", "13")
    qp <- c(25.8, 33.6, 18.63)
    fake.f2 <- subset(fake.f2, chr=qc)

    fake.f2 <- calc.genoprob(fake.f2, step=2, err=0.001)
    qtl <- makeqtl(fake.f2, qc, qp, what="prob")
    plot(qtl)
    plot(qtl, justdots=TRUE, col="seagreen")

[Package qtl version 1.46-2 Index]