boxes.R

#!/usr/bin/env Rscript

library(reshape)
library(ggplot2)

# set the work directory
setwd('~/Downloads')

# matrix-boxplots.txt should be a three-column, TAB-delimited matrix with a header for 'region', 'haplotype', and 'ratio'.
m <- data.frame(read.table('matrix-boxplots.txt', header = TRUE, sep="\t"))

m$region = factor(m$region, levels=c("MED", "ASW", "PSE", "PSW", "PON", "RED", "ION", "IOS"))

g <- ggplot(m, aes(x=haplotype, y=ratio, fill=haplotype, group=haplotype))
g <- g + geom_boxplot(outlier.alpha = 0.0)
g <- g + geom_jitter(width=0.05, alpha=0.5)
g <- g + facet_grid(. ~ region)
g <- g + theme_bw() + theme(axis.text.x = element_text(angle = 90, hjust = 1))

pdf('boxes.pdf', width=12, height=4)
print(g)
dev.off()

matrix-boxplots.txt

region	haplotype	ratio
ASW	HP_02	0.373024136
ASW	HP_02	0.471918075
ASW	HP_02	0.271837848
ASW	HP_03	0.248834262
ASW	HP_03	0.082462621
ASW	HP_03	0.1187625
ASW	HP_04	0.209962772
ASW	HP_04	9.41E-06
ASW	HP_04	0.143162351
(...)