gg.ldplot

Plot a pairwise LD matrix from vcftools with ggplot2

Install with devtools

# library(devtools)
install_github("timknut/gg.ldplot")

Run without devtools installing on the CIGENE cluster

module load R/3.2.3

Example R-script. This will make a *.png with your plot in working dir.

.libPaths( c( .libPaths(), "/mnt/users/tikn/R/x86_64-pc-linux-gnu-library/3.2")) ## Dependencies
library(gg.ldplot, lib.loc = "/mnt/users/tikn/R/x86_64-pc-linux-gnu-library/3.2")
data("bovine_vcf")
png("test_LD.png")
plot_LDmatrix(bovine_vcf)
dev.off()

vcftools

Create the input data.frame with vcftools from a phased vcf with eg:

vcftools --gzvcf phased_vcf.vcf.gz --out bovine_vcf --hap-r2

WARNING vcftools outputs a malformatted table. Fix it with sed -i "s/\s*$//" bovine_vcf.ld"

Now read the file into R.

bovine_vcf <- read.table("bovine_vcf.ld", header = TRUE, stringsAsFactors = F)

Example

The package includes a small example dataset.

data("bovine_vcf")
plot_LDmatrix(bovine_vcf)