Mercurial > repos > mb2013 > nepenthes_3dpca
view Procrustes.R @ 11:064592f816c6 draft
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author | mb2013 |
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date | Tue, 20 May 2014 03:27:28 -0400 |
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#Procrustes tool for performing procrustes analysis on landmark data #MB #commandline arguments args <- commandArgs(TRUE) #input input <- args[1] nb_landmarks <- args[2] nb_dimension <- 3 output <- args[3] outputcentroid <- args[4] #package geomorph suppressMessages(library("geomorph")) #reading input file (landmark coordinates) read <- read.csv(file <- input,header = FALSE) #creating good array with arrayspecs new_array <- arrayspecs(read,as.integer(nb_landmarks),as.integer(nb_dimension)) #perform procrustes with gpagen output_procrustes <- gpagen(A=new_array, ShowPlot= FALSE) #turn array for PCA output_procrustes_coo <- t(two.d.array(output_procrustes$coords)) #output procrustes coordinates write.csv(output_procrustes_coo,output, row.names = FALSE) #output procrustes centroid size write.csv(output_procrustes$Csize,outputcentroid, row.names = FALSE)