plot.mpcross: Plot summary of mpcross object

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description

Plots summary of phenotypes and genetic map for mpcross object. If calculated, plots a heatmap of recombination fraction estimates and transformed LOD scores with legend.

Usage

## S3 method for class 'mpcross'
plot(x, chr, ask = TRUE, ...)

Arguments

x	Object of class mpcross
chr	Selected chromosomes. Default is all
ask	Flag for whether to pause between plots
...	Additional arguments to plot functions

Value

Phenotype distributions are plotted as histograms or barplots depending on the variable type.

Genetic maps are plotted using a version of plotlink.map for all genetic maps included in the object (may be both a simulated version and an estimated version).

If recombination fractions have been estimated, a heatmap with recombination fraction estimates below the diagonal and scaled LOD scores above the diagonal is also plotted. LOD scores are transformed to 2^(-(LOD/4+1)) in order to be on the same scale as the theta values.

See Also

mpestrf, mpcross.object, plotlink.map

Examples

sim.map <- qtl::sim.map(len=rep(100, 2), n.mar=11, include.x=FALSE, eq.spacing=TRUE)
sim.ped <- sim.mpped(4, 1, 500, 6, 1)
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, 
	qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), 
	nrow=2, ncol=6, byrow=TRUE), seed=1)
plot(sim.dat)

behuang/mpMap documentation built on May 12, 2019, 10:53 a.m.