plot.mpprob: Plot summary of founder probabilities and haplotype blocks

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description

Plot the percentage of each chromosome inherited from each founder

Usage

## S3 method for class 'mpprob'
plot(x, chr, locations, compositionPercent = TRUE,
  lines = TRUE, nlines, colours, ...)

Arguments

x	Object of class mpprob
chr	Chromosomes to plot. Default is all.
locations	Locations to plot. Default is all.
compositionPercent	Flag for whether to plot the percent alleles inherited from each founder
lines	Flag for whether to plot haplotype reconstructions
nlines	Number of most recombinant lines to plot
colours	Colours for lines. Default is rainbow.
...	Additional arguments to plot function

Value

Barplot of the percentage of each founder on each chromosome; individual heatmaps of which chunks of each chromosome are inherited from each founder.

See Also

mpprob, summary.mpprob

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)
mpp.dat <- mpprob(sim.dat, program="qtl")
plot(mpp.dat)

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