# HG changeset patch # User mb2013 # Date 1384949940 18000 # Node ID c4c40e20871c478142b342ce69fea4b4d8e27d58 # Parent 719a2d230fa284b39f1d0df70c8cbd00d4850df2 Uploaded diff -r 719a2d230fa2 -r c4c40e20871c Plottool.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Plottool.R Wed Nov 20 07:19:00 2013 -0500 @@ -0,0 +1,40 @@ +#Plottool makes a graph of Principle Components created with a Principle Component analysis. +#developer: M.Baak + +#commands extracting of commandline +args <- commandArgs(TRUE) + +#input files and options +input <- args[1] +main_title <- args[2] +x_title <- args[3] +y_title <- args[4] +x_column <- args[5] +y_column <- args[6] +names <- args [7] #name of every sample in one file +#output file +output <- args[8] + +suppressMessages(library("geomorph")) #package geomorph + +#reading of input files +read <- read.csv(file <- input,header = TRUE) +read2 <- scan(file <- names, what = "", quiet = TRUE) + +pca1 <- read[,as.integer(x_column)] #principle component +pca2 <- read[,as.integer(y_column)] #principle component + +png(output) #output in png format + +#axis boundaries +minpca1 = min(pca1) - max(pca1) +maxpca1 = max(pca1) + max(pca1) +minpca2 = min(pca2) - max(pca2) +maxpca2 = max(pca2) + max(pca2) + +#creating the plot with principle components and titels +suppressMessages(plot(pca1,pca2, main = main_title, xlab = x_title, ylab = y_title, pch=20,cex=0.6, xlim = c(minpca1,maxpca1), ylim=c(minpca2,maxpca2))) +#add labels to data points +text(pca1,pca2,labels = read2, pos = 2, cex = 0.9,col = heat.colors(35:40)) + +graphics.off()