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31
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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 'size', 's', 2, 'double',
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23 'xlab', 'x', 2, 'character',
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24 'ylab', 'y', 2, 'character',
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25 'binwidth', 'b', 2, 'double',
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26 'xaxismin', 'e', 2, 'integer',
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27 'xaxismax', 'f', 2, 'integer',
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28 'yaxismin', 'g', 2, 'integer',
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29 'yaxismax', 'h', 2, 'integer',
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30 'colors', 'q', 2, 'character',
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31 'colorscheme', 'z', 2, 'character',
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32 'colororder', 'r', 2, 'integer',
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33 'facet', 'a', 2, 'character',
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34 'transform', 'c', 2, 'character',
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35 'woutputdim', 'w', 2, 'integer',
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36 'houtputdim', 'd', 2, 'integer',
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37 'dim', 'k', 2, 'character',
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38 'scaling', 'j', 2, 'character',
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39 'legend', 'l', 2, 'character',
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40 'density', 'm', 2, 'character',
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41 'output', 'o', 2, 'character'
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42 ), byrow=TRUE, ncol=4);
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43
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44 # Parse options
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45 options = getopt(option_specification);
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46
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47
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48
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49 # Print options to see what is going on
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50 cat("\n input: ",options$input)
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51 cat("\n title: ",options$title)
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52 cat("\n size: ",options$size)
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53 cat("\n transform: ",options$alpha)
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54 cat("\n xlab: ",options$xlab)
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55 cat("\n xlab: ",options$xlab)
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56 cat("\n binwidth: ",options$binwidth)
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57 cat("\n output: ",options$output)
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58
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59 integrated <- read.csv(options$input,sep='\t',header=TRUE)
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60 input <- melt(integrated)
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61
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62 #Show/hide legend
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63 if(options$legend == "yes"){
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64 gg_legend = NULL
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65 } else {
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66 gg_legend = theme(legend.position="none")
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67 }
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68
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69 #density
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70 if(options$density == "counts"){
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71 gg_density = ggplot(input,aes(value, color=variable))
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72 gg_freq = NULL
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73 }else if(options$density == "nfreq"){
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74 gg_density = ggplot(input,aes(value, ..ncount.., color=variable))
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75 gg_freq = NULL
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76 }else if(options$density == "freq"){
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77 gg_density = ggplot(input,aes(value, color=variable))
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78 gg_freq = aes(y=..count../sum(..count..))
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79 }else {
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80
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81 }
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82
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83 #Choose between automatically scaled x and y axis or user defined
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84 if(options$scaling == "Automatic"){
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85 gg_scalex = NULL
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86 gg_scaley = NULL
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87 } else {
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88 gg_scalex = xlim(options$xaxismin,options$xaxismax)
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89 gg_scaley = ylim(options$yaxismin,options$yaxismax)
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90 cat("\n xaxismin: ",options$xaxismin)
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91 cat("\n xaxismax: ",options$xaxismax)
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92 cat("\n yaxismin: ",options$yaxismin)
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93 cat("\n yaxismax: ",options$yaxismax)
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94 }
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95
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96 #Choose dimensions of output pdf
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97 if(options$dim == "Default"){
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98 gg_width = 7
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99 gg_height = 7
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100 } else {
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101 gg_width = options$woutputdim
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102 gg_height = options$houtputdim
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103 }
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104
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105
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106 if(options$transform == "log2"){
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107 input["value"] <- log2(input["value"])
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108 }else if(options$transform == "log2plus1"){
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109 input["value"] <- log2(input["value"]+1)
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110 }else if(options$transform == "log10"){
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111 input["value"] <- log10(input["value"])
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112 }else if(options$transform == "log10plus1"){
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113 input["value"] <- log10(input["value"]+1)
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114 }else{
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115 }
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116
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117
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118 if(options$facet == "facet"){
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119 gg_facet = facet_wrap(~ variable)
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120 } else {
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121 gg_facet = NULL
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122 }
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123
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124 if(options$colorscheme == "Default"){
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125 gg_colorscale = NULL
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126 } else {
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127 gg_colorscale = scale_color_brewer(palette=options$colors, direction=options$colororder)
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128 }
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129
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130 gg_density +
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131 geom_freqpoly(gg_freq,binwidth=options$binwidth,size=options$size)+gg_facet+gg_colorscale+
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132 gg_scalex+gg_scaley+theme_bw()+xlab(options$xlab)+ylab(options$ylab)+gg_legend+
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133 ggtitle(options$title)
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134
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135 ggsave(file=options$output)
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