aaFreqByPos.R

## load the tidyverse packages, incl. dplyr, readr, ggplot2, tidyr, tibble, purrr, stringr, forcats
library(tidyverse)
library(ggplot2)
# get data from command line:
args <- commandArgs(trailingOnly=TRUE)
# args affectations for testing into interactive R :
# args <- c("-i", "GCA_900095815.1.csv", "-s", "Methanothermobacter wolfeii ATCC43096", "-t", "(55.0°C, 1792 CDS)")
if (length(args)==0) {
  stop("Arguments to be supplied: -i inputFile.csv -s \"speciesNameForGarphTitle\" -t \"OgtAndTempForGarphTitle\"", call.=FALSE)
} else {
  for (i in seq(1,length(args))) {
    if(args[i]=="-i") { inFile <- args[i+1] } 
    if(args[i]=="-s") {species <- args[i+1] }
    if(args[i]=="-t") {ogtTemp <- args[i+1] }
  }
}
# output definitions:
graphTitle <- paste(species,"\n",ogtTemp)
position <- seq(1,20) # add a "position" column to graphical managment of positions
 
# get data:
aa <- read_csv(inFile)

# graph creation:
# dashed: +geom_line(aes(y=G,color="G"),linetype="dashed"))+
aaGraph <- ggplot(cbind(position,aa),aes(x=position))+
   geom_line(aes(y=H,color="H"))+ # #CCBB44
   geom_line(aes(y=I,color="I"))+ # darkorange
   geom_line(aes(y=K,color="K"),linewidth=1)+ # red
   geom_line(aes(y=N,color="N"))+ # green
   geom_line(aes(y=R,color="R"),linewidth=1)+ # blue #4477AA
   geom_line(aes(y=Y,color="Y"))+ # #AA3377
   scale_color_manual(values=c("#CCBB44","darkorange","red","green4","blue","#AA3377"))+
   labs(title = graphTitle, x = "aa position", y = "aa frequency", color="legend")+
   theme_bw()

# graph save (pdf and png formats):
outFilePdf <- str_replace_all(inFile, "csv", "pdf")
pdf(paste0(outFilePdf))
print(aaGraph)
dev.off()

outFilePng <- str_replace_all(inFile, "csv", "png")
ggsave(plot=aaGraph, filename=outFilePng, width=14, height=8, units = "cm")