plot.qtl: Plot QTL locations

Description

Plot the locations of the QTL against a genetic map

Usage

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

Arguments

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.

Value

None.

Details

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

Examples

Run this code

# NOT RUN {
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)
# }
# NOT RUN {
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")
# }