Mercurial > repos > mb2013 > nepenthes_3dpca
view Csize_plot.R @ 16:fea55f4efcce draft
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author | mb2013 |
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date | Tue, 20 May 2014 03:29:11 -0400 |
parents | f3b7f86db21e |
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#The Csize tool creates a plot with a Principal Component #and the centroid size (created with a procrustes analysis) #MB #commandline arguments args <- commandArgs(TRUE) #inputs input_PCA <- args[1] input_Csize <- args[2] main_title <- args[3] x_title <- args[4] y_title <- args[5] x_column <- args[6] names <- args [7] #sample names in one file output <- args[8] #library geomorph suppressMessages(library("geomorph")) #reading of the input files read <- read.csv(file <- input_PCA, header = TRUE) #principal components read2 <- read.csv(file <- input_Csize, header = TRUE) #centroid size read3 <- scan(file <- names, what = "", quiet = TRUE) pca1 <- read[,as.integer(x_column)] #principal component read2 <- read2[,1] #centroid size #output png(output) #creating plot with pca and centroid size suppressMessages(plot(pca1,read2, main = main_title, xlab = x_title, ylab = y_title, pch=20,cex=0.6)) #adding labels to datapoints text(pca1,read2,labels = read3, pos = 3, cex = 0.6, col = 'red') graphics.off()