Mercurial > repos > mb2013 > landtool
changeset 14:be66787b414c draft
Uploaded
author | mb2013 |
---|---|
date | Wed, 20 Nov 2013 07:19:33 -0500 |
parents | 1f8a453d1a64 |
children | 0cef5c0382c8 |
files | plotPCACsize.R |
diffstat | 1 files changed, 33 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plotPCACsize.R Wed Nov 20 07:19:33 2013 -0500 @@ -0,0 +1,33 @@ +#The plotPCACsize tool creates a plot with a principle component and the centroid size created with procrustes analysis +#developer: M.Baak +#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) #principle components +read2 <- read.csv(file <- input_Csize, header = TRUE) #centroid size +read3 <- scan(file <- names, what = "", quiet = TRUE) +pca1 <- read[,as.integer(x_column)] #principle 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()