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1 # Setup R error handling to go to stderr
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2 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
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3
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4 # We need to not crash galaxy with an UTF8 error on German LC settings.
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5 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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6
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7
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8 # Import library
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9 library("getopt")
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10 library("reshape2")
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11 library("ggplot2")
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12 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
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13 # Take in trailing command line arguments
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14 args <- commandArgs(trailingOnly = TRUE)
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15
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16
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17 # get options, using the spec as defined by the enclosed list.
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18 # we read the options from the default: commandArgs(TRUE).
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19 option_specification = matrix(c(
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20 'input', 'i', 2, 'character',
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21 'title', 't',2, 'character',
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22 'ggfill', 's', 2, 'character',
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23 'ggcolor', 'z', 2, 'character',
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24 'xlab', 'x', 2, 'character',
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25 'ylab', 'y', 2, 'character',
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26 'drawquartiles', 'a', 2, 'character',
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27 'transform', 'w', 2, 'character',
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28 'xaxismin', 'e', 2, 'integer',
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29 'xaxismax', 'f', 2, 'integer',
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30 'yaxismin', 'g', 2, 'integer',
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31 'yaxismax', 'h', 2, 'integer',
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32 'scaling', 'b', 2, 'character',
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33 'output', 'o', 2, 'character'
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34 ), byrow=TRUE, ncol=4);
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35
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36 # Parse options
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37 options = getopt(option_specification);
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38
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39
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40
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41 # Print options to see what is going on
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42 cat("\n input: ",options$input)
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43 cat("\n title: ",options$title)
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44 #cat("\n size: ",options$size)
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45 cat("\n xlab: ",options$xlab)
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46 cat("\n ylab: ",options$ylab)
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47 cat("\n output: ",options$output)
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48
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49
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50 if(options$scaling == "Automatic"){
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51 gg_scaley = NULL
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52 } else {
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53 gg_scaley = ylim(options$yaxismin,options$yaxismax)
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54 cat("\n yaxismin: ",options$yaxismin)
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55 cat("\n yaxismax: ",options$yaxismax)
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56 }
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57
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58
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59 integrated <- read.csv(options$input,sep='\t',header=TRUE)
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60 input <- melt(integrated)
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61
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62
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63
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64 if(options$transform == "log2"){
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65 input["value"] <- log2(input["value"])
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66 }else if(options$transform == "log2plus1"){
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67 input["value"] <- log2(input["value"]+1)
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68 }else if(options$transform == "log10"){
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69 input["value"] <- log10(input["value"])
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70 }else if(options$transform == "log10plus1"){
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71 input["value"] <- log10(input["value"]+1)
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72 }else{
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73 }
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74
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75 if(options$drawquartiles == "none"){
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76 gg_quartile = NULL
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77 } else {
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78 gg_quartile = c(0.25, 0.5, 0.75)
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79 }
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80
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81
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82
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83 ggplot(input,aes(variable,value)) +geom_violin(scale = "area", colour = options$ggcolor, fill = options$ggfill, draw_quantiles = gg_quartile) +
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84 gg_scaley+theme_bw()+xlab(options$xlab)+ylab(options$ylab)+ggtitle(options$title)
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85
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86 ggsave(file=options$output)
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