| Previous changeset 6:7012f7336e61 (2014-05-20) Next changeset 8:0cb68fb9010f (2014-05-20) |
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Commit message:
Uploaded |
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added:
PCA.R |
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| diff -r 7012f7336e61 -r 5aaede6275f9 PCA.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PCA.R Tue May 20 03:26:37 2014 -0400 |
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| @@ -0,0 +1,22 @@ +# The tool PCA creates a Principal Component Analysis on Procrustes coordinates. +# MB + +#commands of commandline +args <- commandArgs(TRUE) +#input file: procrustes coordinates +input <- args[1] +#output file +output <- args[2] +output2 <- args[3] + +#package geomorph +suppressMessages(library("geomorph")) + +#reading of coordinates +read <- read.csv(file <- input,header = TRUE) +#principal component analysis with princomp, using covariance matrix of coordinates +pca <- princomp(x=cov(read)) + +#output pca scores +write.csv(pca$scores,output, row.names = FALSE) +write.csv(pca$sdev, output2, row.names = FALSE) |