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qtl (version 1.70)

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.

Author

Danny Arends danny.arends@gmail.com

See Also

  • The MQM tutorial: https://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

Run this code
data(multitrait)
multitrait <- subset(multitrait, chr=1:2, ind=!apply(multitrait$pheno, 1, function(a) any(is.na(a))))
multitrait$pheno <- multitrait$pheno[,1:3]
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")

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