Plot QTL locations
Plot the locations of the QTL against a genetic map
## S3 method for class 'qtl'
plot(x, chr, horizontal=FALSE, shift=TRUE,
show.marker.names=FALSE, alternate.chrid=FALSE, justdots=FALSE,
col="red", ...)x |
An object of class |
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 |
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 |
Creates a plot, via plotMap, and indicates the
locations of the QTL in the input QTL object, x.
None.
Karl W Broman, broman@wisc.edu
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")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.