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1 # The tool PCA creates a Principal Component Analysis on Procrustes coordinates.
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2 # MB
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3
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4 #commands of commandline
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5 args <- commandArgs(TRUE)
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6 #input file: procrustes coordinates
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7 input <- args[1]
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8 #output file
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9 output <- args[2]
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10 output2 <- args[3]
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11
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12 #package geomorph
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13 suppressMessages(library("geomorph"))
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14
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15 #reading of coordinates
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16 read <- read.csv(file <- input,header = TRUE)
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17 #principal component analysis with princomp, using covariance matrix of coordinates
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18 pca <- princomp(x=cov(read))
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19
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20 #output pca scores
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21 write.csv(pca$scores,output, row.names = FALSE)
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22 write.csv(pca$sdev, output2, row.names = FALSE)
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