propVarPlot.r

# R script that plots cumulative proportion of variance and save a figure in pdf format
args <- commandArgs(TRUE)
library(RColorBrewer)

N <- length(args)
L <- length(t(read.table(as.character(args[1]))))
if (N < 3) {
  cl <- colorRampPalette(brewer.pal(3, "Dark2"))(3)
}
if (N >= 3) {
  cl <- colorRampPalette(brewer.pal(N, "Dark2"))(N)
}
lt <- 1
# line-type
LG <- c()
for (k in 1:length(args)) {
  LG[k] <- strsplit(x = args[k], split = "_")[[1]][1]
}
Titl <- paste(strsplit(x = args[1], split = "_")[[1]][2:3], sep = "-")
pdf(file = "propVarPlot.pdf", width = 5, height = 5)
plot(1:L, 100 * cumsum(t(read.table(as.character(args[1])))), type = "l", col = cl[1], xlab = "Component", ylab = "Cumulative sum (%)", main = Titl, lwd = 2, ylim = c(0, 100), lty = lt, log = "x")
for (j in 2:N) {
  points(1:L, 100 * cumsum(t(read.table(as.character(args[j])))), type = "l", col = cl[j], lwd = 2, lty = lt, log = "x")
}
legend("bottomright", legend = LG, col = cl, bty = "n", lty = lt, cex = 1, lwd = 2)