plot.scanone {qtl}R Documentation

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.

Author(s)

Karl W Broman, kbroman@jhsph.edu
http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html

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)
[Package Contents]