Ternary Plots
Ayush Noori | EduSTEM Advanced Biology
Background
A ternary plot is a barycentric plot on three variables which sum to a constant. It graphically depicts the ratios of the three variables as positions in an equilateral triangle. In population genetics, it is often called a de Finetti diagram.
Please see the HardyWeinberg package vignette here.
Setup
Load the requisite libraries.
if(!require(HardyWeinberg)){
install.packages("HardyWeinberg")
library(HardyWeinberg)
}
Set the working directory to where you would like your output data to result.
dir = "<insert appropriate directory address here>"
setwd(dir)
Plotting
AA, AB, and BB are homozygous dominant, heterozygous, and homozygous recessive respectively (i.e. bi-allelic markers). Each row in the column is a different marker or SNP.
Draw random SNPs from a population that is in Hardy-Weinberg Equilibrium.
set.seed(123)
m = 100 # number of markers
n = 100 # sample size
dat = HWData(n,m)
out = HWTernaryPlot(dat, 100, region=1, vertex.cex=2, signifcolour=TRUE)
In this ternary plot, the center parabola represents the ratio p^2+2pq+p^2, or the Hardy-Weinberg Equilibrium. Red loci differ from the ratio by more than a certain p-value, therefore are considered to NOT be in Hardy-Weinberg Equilibrium.
For more information, please see Hardy-Weinberg Equilibrium and the Ternary Plot by Graffelman and Camarena.
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Best Regards,
Ayush Noori
EduSTEM Boston Chapter Founder
Resources:
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