LEAPFrOG_plot: LEAPFrOG plotting function

In LEAPFrOG: Likelihood Estimation of Admixture in Parents From Offspring Genotypes

Description

Plots offspring and parental admiture proportions in the style of STRUCTURE, the popular population genetic software.

Usage

LEAPFrOG_plot(Results,PopNames,SampNames=NULL)

Arguments

Results	Array of dimensions 3*Npopulations*Noffspring. The first row is for the genotyped offspring and the second two for the unobserved parents. Each cell contains an admixture proportion.
PopNames	Character vector of length J (number of reference populations), Eg. c("Africa","Asia","Europe"). Order of names should correspond with order of parameters in Results.
SampNames	Character vector of sample names, equal to number of rows in Results, or NULL (detault), which will be printed underneath the admixture bars. Most useful when dealing with a small number of samples with distinct identity e.g. c("Hair","Blood","Door Handle","Ballroom","Lead Piping"). If NULL then no labels are printed beneath the plot (more appropriate for simulations or large population samples)

Author(s)

Daniel Crouch & Michael Weale, Department of Medical and Molecular Genetics, King's College London

See Also

LEAPFrOG,LEAPFrOG_EM,BEAPFrOG

Examples

#Example with nonsense data -
#10000 random SNP genotypes 
#...and uniform, random allele frequencies from two populations.
library(LEAPFrOG)
#Get LEAPFrOG parameter estimates  for 10 simulated individuals
Results=array(dim=c(3,2,10))
for(i in 1:10){
z1=LEAPFrOG(sample(0:2,10000,replace=TRUE),cbind(runif(10000,0,1),runif(10000,0,1)))
Results[1,,i]=z1$m    #Offspring 
Results[2,,i]=z1$P1 #Parent 'A'
Results[3,,i]=z1$P2 #Parent 'B
}
#Now plot these 10 individuals
LEAPFrOG_plot(Results,PopNames=c("PopA","PopB"))
#With sample names:
names=c("Hair","Blood","Door Handle","Ballroom","Lead Piping")
names=c(names,"Briefcase","Toothbrush","Sock","Shirt","Skin")
LEAPFrOG_plot(Results,PopNames=c("PopA","PopB"),SampNames=names)

LEAPFrOG documentation built on May 2, 2019, 12:38 p.m.