qtl (version 0.85-4)

plot.scanone: Plot output for a single QTL scan

Description

Plot the output from a single QTL scan. One may specify which chromosomes to plot

Usage

plot.scanone(x,output2,output3,chr,incl.markers=TRUE,ylim,
             lty=c(1,2,3),col="black",lwd=2,add=FALSE,gap=25,...)

Arguments

x

A data.frame with at least three columns. The first three columns should be the following:

output2

Data for another genome scan, like output (optional).

output3

Data for another genome scan, like output (optional).

chr

Vector specifying which chromosomes to plot.

incl.markers

Indicate whether to plot line segments at the marker locations.

ylim

Limits for y-axis [optional].

lty

Line type for output1, 2 and 3; this should be a vector of length 1 or 3.

col

Line color for output1, 2 and 3; this should be a vector of length 1 or 3.

lwd

Line width for output1, 2 and 3; this should be a vector of length 1 or 3.

add

If TRUE, add to a current plot.

gap

Gap separating chromosomes.

...

Ignored at this point.

Value

• Plot of the lod score against marker position for the genome scan.

See Also

scanone, vbscan, summary.scanone

Examples

data(fake.f2)
fake.f2 <- argmax.geno(fake.f2)
output <- scanone(fake.f2,method="anova")
output2 <- scanone(pull.chr(fake.f2,1),method="im")
plot(output)
plot(output,output2,chr=1)