ploidyNGS_generateHistogram.R

#!/usr/bin/env -S Rscript --vanilla
#ploidyNGS_generateHistogram.R

# __author__      = "Diego Mauricio Riano-Pachon & Renato Augusto Correa dos Santos"
# __copyright__   = "Copyright 2016,2017"
# __license__     = "GPL v3.0"
# __maintainer__  = "Diego Mauricio Riano-Pachon"
# __email__       = "diriano@gmail.com"

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

#First argument must be the TAB file with allele frequencies generated by ploidyNGS
#Second argument must be the name of a PDF that will be used as output
#Third argument is xmin in a scale of 0 to 1. It is 1-AllowedMaxAlleleFreq from ploidyNGS
#Fourth argument is xmax in a scale of 0 to 1. It is AllowedMaxAlleleFreq in ploidyNGS

#Usage: Rscript --vanilla ploidyNGS_generateHistogram.R test_depth100.tab test.pdf

args = commandArgs(trailingOnly=TRUE)
xmin=as.numeric(args[3])*100
xmax=as.numeric(args[4])*100
suppressMessages(library(ggplot2))
datain<-read.table(args[1],header=F)
colnames(datain)<-c('Chrom','Pos','Type','Freq')
datain$Typt = factor(datain$Type)
hist_plot<-ggplot(datain,aes(x=Freq, fill=Type)) +
  theme_bw()+
  geom_histogram(binwidth = 0.5, alpha=0.4) +
  ggtitle(args[1]) +
  ylab("Number of heteromorphic positions") +
  xlab("Allele Frequency") +
  scale_x_continuous(limits=c(xmin,xmax))+
  scale_fill_manual(values=c("#920000", 
                             "#24FF24", 
                             "#6DB6FF", 
                             "#FFFF6D")) 
#Friendly to colour-blind users: 
#http://www.somersault1824.com/tips-for-designing-scientific-figures-for-color-blind-readers/
pdf(file=args[2])
suppressWarnings(print(hist_plot))
invisible(dev.off())