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