Mercurial > repos > stevecassidy > vowelplot

annotate phonR_tool.R @ 1:4c17593167f0 draft

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author stevecassidy
date Thu, 13 Oct 2016 15:41:12 -0400
parents 3d068b7441be
children 24f05f509f09
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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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8
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9 #create options
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10 option_specification = matrix(c(
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11 'outdir', 'f', 1, 'character',
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12 'htmlfile', 'h', 1, 'character',
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13 'inputfile', 'i', 1, 'character',
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14 'column1', 'y', 1, 'integer',
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15 'column2', 'z', 1, 'integer',
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16 'columnvowels', 'x', 1, 'integer',
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17 'pretty', 'p', 1, 'logical',
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18 'ellipse', 'e', 1, 'logical',
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19 'tokens', 't', 1, 'logical',
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20 'means', 'm', 1, 'logical',
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21 'cextokens', 'c', 1, 'numeric',
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22 'alphatokens', 'a', 1, 'numeric',
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23 'cexmeans', 'b', 1, 'numeric'
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24 ), byrow=TRUE, ncol=4);
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25
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26 # Parse options
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27 options = getopt(option_specification);
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28
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29 if (!is.null(options$outdir)) {
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30 # Create the directory
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31 dir.create(options$outdir,FALSE)
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32 }
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33
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34 pngfile <- gsub("[ ]+", "", paste(options$outdir,"/pngfile.png"))
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35 htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
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36
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37 data = read.table(options$inputfile,sep="\t", header=TRUE);
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38
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39 png(pngfile);
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40
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41 plotVowels(data[,options$column1], data[,options$column2], data[,options$columnvowels], plot.tokens = options$tokens,
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42 pch.tokens = data[,options$columnvowels], cex.tokens = options$cextokens, alpha.tokens = options$alphatokens,
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43 plot.means = options$means, pch.means = data[,options$columnvowels], cex.means = options$cexmeans,
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44 var.col.by = data[,options$columnvowels], ellipse.line = options$ellipse, pretty = options$pretty)
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45 dev.off();
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46
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47 htmlfile_handle <- file(htmlfile)
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48 html_output = c('<html><body>',
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49 '<h3>Result:</h3><img src="pngfile.png"/>',
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50 '</html></body>');
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51 writeLines(html_output, htmlfile_handle);
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52 close(htmlfile_handle);