alignmentSummary.R

#--------------------------------------------------------------------------------------------
# HybPhyloMaker: PNG picture with histogram and boxplot for alignment summaries
# https://github.com/tomas-fer/HybPhyloMaker
# Based on http://rgraphgallery.blogspot.com/2013/04/rg-plotting-boxplot-and-histogram.html
# Modified for HybPhyloMaker
# v.1.6.0
# Tomas Fer, 2018
# tomas.fer@natur.cuni.cz
#--------------------------------------------------------------------------------------------

#Read table from 'summaryALL.txt' 
x <- read.table("summaryALL.txt", header=TRUE, stringsAsFactors=F)
x <- subset(x, select=c(No_of_taxa, Alignment_length, Missing_percent, Proportion_variable_sites, Proportion_parsimony_informative, GC_content, MstatX_entropy, trimAl_sct))

#Make PNG picture of histogram from values in a table (omitting first column with names)
for (i in 1:length(colnames(x))) {
  png(file=paste(colnames(x[i]), "_histogram.png", sep = ""), width=600, height=600)
  nf <- layout(mat = matrix(c(1,2),2,1, byrow=TRUE),  height = c(1,3))
  par(mar=c(3.1, 3.1, 1.1, 2.1))
  boxplot(x[,i], horizontal=TRUE,  outline=TRUE, ylim=c(min(x[,i]), max(x[,i])), frame=F, axes = FALSE, col = "grey")
  hist(x[,i],xlim=c(min(x[,i]), max(x[,i])), col = "lightblue", main = colnames(x[i]))
  dev.off()
}