plot_event_count_vs_chr_length.R

#!/usr/bin/env Rscript

##############################################################
#  script: plot_event_count_vs_chr_length.R
#  author: Jia-Xing Yue (GitHub ID: yjx1217)
#  last edited: 2019.10.11
#  description: plot the relationship between recombination event count and chromosome lengths
#  example: Rscript --vanilla plot_event_count_vs_chr_length.R  --input prefix.event_count_vs_chr_length.summary.txt --output prefix.event_count_vs_chr_length.summary.pdf
###############################################################

library(ggplot2)
library(optparse)
library(scales)

option_list <- list(
  make_option(c("--input"), type = "character", default = NULL, 
              help = "the summary table generated by event_count_vs_chr_length.plreference genome [default=%default]", metavar = "character"),
  make_option(c("--output"), type = "character", default = "out.pdf", 
              help = "the file name for the ouput plot [default=%default]", metavar = "character")
); 

opt_parser <- OptionParser(option_list = option_list)
opt <- parse_args(opt_parser)


data <- read.table(opt$input,
                   sep = "\t",
                   header = TRUE)

ggplot(data, aes(x = chr_length/1000, y = event_count_mean, color = chr)) +
  geom_point() + 
  geom_errorbar(aes(ymin = event_count_mean - event_count_stderr, ymax = event_count_mean + event_count_stderr)) +
  scale_x_continuous("Chromosome length (kb)") +
  scale_y_continuous("Recombination event count per chromosome per tetrad") +
  facet_wrap(~ event_type) +
  theme_bw()

ggsave(filename = opt$output, device = "pdf", width = 8, height = 6, limitsize = FALSE)