| plot.scanone {qtl} | R Documentation |
Plot the LOD curve for a genome scan with a single-QTL model (the
output of scanone).
## 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, ...)
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. |
... |
Passed to the function plot when it
is called. |
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.
None.
Karl W Broman, kbroman@biostat.wisc.edu
scanone,
summary.scanone, par,
colors
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)