annotate Csize_plot.R @ 12:f69fc89bb392 draft

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author mb2013
date Tue, 20 May 2014 03:27:42 -0400
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1 #The Csize tool creates a plot with a Principal Component
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2 #and the centroid size (created with a procrustes analysis)
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3 #MB
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6 #commandline arguments
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7 args <- commandArgs(TRUE)
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9 #inputs
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10 input_PCA <- args[1]
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11 input_Csize <- args[2]
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12 main_title <- args[3]
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13 x_title <- args[4]
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14 y_title <- args[5]
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15 x_column <- args[6]
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16 names <- args [7] #sample names in one file
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17 output <- args[8]
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19 #library geomorph
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20 suppressMessages(library("geomorph"))
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21 #reading of the input files
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22 read <- read.csv(file <- input_PCA, header = TRUE) #principal components
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23 read2 <- read.csv(file <- input_Csize, header = TRUE) #centroid size
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24 read3 <- scan(file <- names, what = "", quiet = TRUE)
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25 pca1 <- read[,as.integer(x_column)] #principal component
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26 read2 <- read2[,1] #centroid size
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28 #output
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29 png(output)
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30
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31 #creating plot with pca and centroid size
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32 suppressMessages(plot(pca1,read2, main = main_title, xlab = x_title, ylab = y_title, pch=20,cex=0.6))
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33 #adding labels to datapoints
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34 text(pca1,read2,labels = read3, pos = 3, cex = 0.6, col = 'red')
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36 graphics.off()