Mercurial > repos > mb2013 > nepenthes_3dpca

comparison Procrustes.R @ 11:064592f816c6 draft

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author mb2013
date Tue, 20 May 2014 03:27:28 -0400
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10:c27d951d5136 11:064592f816c6
1 #Procrustes tool for performing procrustes analysis on landmark data
2 #MB
3
4 #commandline arguments
5 args <- commandArgs(TRUE)
6 #input
7 input <- args[1]
8 nb_landmarks <- args[2]
9 nb_dimension <- 3
10 output <- args[3]
11 outputcentroid <- args[4]
12
13 #package geomorph
14 suppressMessages(library("geomorph"))
15
16 #reading input file (landmark coordinates)
17 read <- read.csv(file <- input,header = FALSE)
18
19 #creating good array with arrayspecs
20 new_array <- arrayspecs(read,as.integer(nb_landmarks),as.integer(nb_dimension))
21
22 #perform procrustes with gpagen
23 output_procrustes <- gpagen(A=new_array, ShowPlot= FALSE)
24 #turn array for PCA
25 output_procrustes_coo <- t(two.d.array(output_procrustes$coords))
26 #output procrustes coordinates
27 write.csv(output_procrustes_coo,output, row.names = FALSE)
28 #output procrustes centroid size
29 write.csv(output_procrustes$Csize,outputcentroid, row.names = FALSE)