qtl (version 1.44-9)

mqmplot.multitrait: Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes

Description

Plotting routine to display the results from a multiple-QTL model on multiple phenotypes. It supports four different visualizations: a contourmap, heatmap, 3D graph or a multiple QTL plot created by using plot.scanone on the mqmmulti object

Usage

mqmplot.multitrait(result, type=c("lines","image","contour","3Dplot"),
                   group=NULL, meanprofile=c("none","mean","median"),
                   theta=30, phi=15, …)

Arguments

result

Result object from mqmscanall

type

Selection of the plot method to visualize the data: "lines" (defaut plotting option), "image", "contour" and "3Dplot"

group

A numeric vector indicating which traits to plot. NULL means no grouping

meanprofile

Plot a mean/median profile from the group selected

theta

Horizontal axis rotation in a 3D plot

phi

Vertical axis rotation in a 3D plot

…

Additional arguments passed to plot.

See Also

• The MQM tutorial: http://rqtl.org/tutorials/MQM-tour.pdf

• MQM - MQM description and references

• mqmscan - Main MQM single trait analysis

• mqmscanall - Parallellized traits analysis

• mqmaugment - Augmentation routine for estimating missing data

• mqmautocofactors - Set cofactors using marker density

• mqmsetcofactors - Set cofactors at fixed locations

• mqmpermutation - Estimate significance levels

• scanone - Single QTL scanning

Examples

# NOT RUN {
data(multitrait)
# }
# NOT RUN {
multitrait <- fill.geno(multitrait) # impute missing genotype data
result <- mqmscanall(multitrait, logtransform=TRUE)
mqmplot.multitrait(result,"lines")
mqmplot.multitrait(result,"contour")
mqmplot.multitrait(result,"image")
mqmplot.multitrait(result,"3Dplot")
# }