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annotate phonR_tool.R @ 4:0c6aea9fe490 draft default tip

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author stevecassidy
date Wed, 14 Dec 2016 21:54:31 -0500
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1 #
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2 # Galaxy tool that plots Vowels using the phonR package.
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3 # Accepts 8 inputs of the form <tsv data file> <output file name> <column1> <column2> <optPretty> <optEllipse> <optTokens> <optMeans>
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4 # Created by Michael Bauer
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5 #
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6 library(phonR)
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7 library(getopt)
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9 #create options
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10 option_specification = matrix(c(
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11 'pdffile', 'h', 1, 'character',
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12 'inputfile', 'i', 1, 'character',
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13 'column1', 'y', 1, 'integer',
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14 'column2', 'z', 1, 'integer',
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15 'columnvowels', 'x', 1, 'integer',
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16 'pretty', 'p', 1, 'logical',
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17 'ellipse', 'e', 1, 'logical',
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18 'tokens', 't', 1, 'logical',
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19 'means', 'm', 1, 'logical',
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20 'cextokens', 'c', 1, 'numeric',
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21 'alphatokens', 'a', 1, 'numeric',
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22 'cexmeans', 'b', 1, 'numeric'
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23 ), byrow=TRUE, ncol=4);
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25 # Parse options
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26 options = getopt(option_specification);
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28 pdffile <- gsub("[ ]+", "", paste(options$pdffile))
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30 data = read.table(options$inputfile,sep="\t", header=TRUE);
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32 pdf(pdffile);
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34 plotVowels(data[,options$column1], data[,options$column2], data[,options$columnvowels], plot.tokens = options$tokens,
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35 pch.tokens = data[,options$columnvowels], cex.tokens = options$cextokens, alpha.tokens = options$alphatokens,
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36 plot.means = options$means, pch.means = data[,options$columnvowels], cex.means = options$cexmeans,
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37 var.col.by = data[,options$columnvowels], ellipse.line = options$ellipse, pretty = options$pretty)
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38 dev.off();