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1 <tool id="XY_Plot_1" name="Plotting tool" version="1.0.1">
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2 <description>for multiple series and graph types</description>
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3 <requirements>
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4 <requirement type="package" version="2.11.0">R</requirement>
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5 </requirements>
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6 <command interpreter="bash">r_wrapper.sh $script_file</command>
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7
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8 <inputs>
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9 <param name="main" type="text" value="" size="30" label="Plot Title"/>
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10 <param name="xlab" type="text" value="" size="30" label="Label for x axis"/>
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11 <param name="ylab" type="text" value="" size="30" label="Label for y axis"/>
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12 <repeat name="series" title="Series">
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13 <param name="input" type="data" format="tabular" label="Dataset"/>
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14 <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/>
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15 <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/>
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16 <conditional name="series_type">
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17 <param name="type" type="select" label="Series Type">
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18 <option value="line" selected="true">Line</option>
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19 <option value="points">Points</option>
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20 </param>
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21 <when value="line">
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22 <param name="lty" type="select" label="Line Type">
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23 <option value="1">Solid</option>
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24 <option value="2">Dashed</option>
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25 <option value="3">Dotted</option>
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26 </param>
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27 <param name="col" type="select" label="Line Color">
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28 <option value="1">Black</option>
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29 <option value="2">Red</option>
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30 <option value="3">Green</option>
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31 <option value="4">Blue</option>
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32 <option value="5">Cyan</option>
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33 <option value="6">Magenta</option>
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34 <option value="7">Yellow</option>
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35 <option value="8">Gray</option>
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36 </param>
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37 <param name="lwd" type="float" label="Line Width" value="1.0"/>
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38 </when>
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39 <when value="points">
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40 <param name="pch" type="select" label="Point Type">
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41 <option value="1">Circle (hollow)</option>
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42 <option value="2">Triangle (hollow)</option>
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43 <option value="3">Cross</option>
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44 <option value="4">Diamond (hollow)</option>
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45 <option value="15">Square (filled)</option>
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46 <option value="16">Circle (filled)</option>
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47 <option value="17">Triangle (filled)</option>
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48 </param>
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49 <param name="col" type="select" label="Point Color">
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50 <option value="1">Black</option>
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51 <option value="2">Red</option>
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52 <option value="3">Green</option>
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53 <option value="4">Blue</option>
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54 <option value="5">Cyan</option>
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55 <option value="6">Magenta</option>
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56 <option value="7">Yellow</option>
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57 <option value="8">Gray</option>
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58 </param>
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59 <param name="cex" type="float" label="Point Scale" value="1.0"/>
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60 </when>
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61 </conditional>
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62 </repeat>
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63 </inputs>
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64
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65 <configfiles>
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66 <configfile name="script_file">
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67 ## Setup R error handling to go to stderr
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68 options( show.error.messages=F,
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69 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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70 ## Determine range of all series in the plot
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71 xrange = c( NULL, NULL )
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72 yrange = c( NULL, NULL )
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73 #for $i, $s in enumerate( $series )
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74 s${i} = read.table( "${s.input.file_name}" )
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75 x${i} = s${i}[,${s.xcol}]
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76 y${i} = s${i}[,${s.ycol}]
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77 xrange = range( x${i}, xrange )
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78 yrange = range( y${i}, yrange )
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79 #end for
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80 ## Open output PDF file
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81 pdf( "${out_file1}" )
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82 ## Dummy plot for axis / labels
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83 plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" )
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84 ## Plot each series
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85 #for $i, $s in enumerate( $series )
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86 #if $s.series_type['type'] == "line"
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87 lines( x${i}, y${i}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} )
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88 #elif $s.series_type.type == "points"
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89 points( x${i}, y${i}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} )
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90 #end if
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91 #end for
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92 ## Close the PDF file
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93 devname = dev.off()
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94 </configfile>
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95 </configfiles>
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96
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97 <outputs>
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98 <data format="pdf" name="out_file1" />
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99 </outputs>
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100
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101 <tests>
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102 <test>
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103 <param name="main" value="Example XY Plot"/>
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104 <param name="xlab" value="Column 1"/>
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105 <param name="ylab" value="Column 2"/>
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106 <param name="input" value="2.tabular" ftype="tabular"/>
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107 <param name="xcol" value="1"/>
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108 <param name="ycol" value="2"/>
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109 <param name="type" value="line"/>
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110 <param name="lty" value="2"/>
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111 <param name="col" value="2"/>
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112 <param name="lwd" value="1.0"/>
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113 <output name="out_file1" file="XY_Plot_1_out.pdf"/>
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114 </test>
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115 </tests>
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116 <help>
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117 .. class:: infomark
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118
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119 This tool allows you to plot values contained in columns of a dataset against each other and also allows you to have different series corresponding to the same or different datasets in one plot.
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120
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121 -----
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122
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123 .. class:: warningmark
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124
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125 This tool throws an error if the columns selected for plotting are absent or are not numeric and also if the lengths of these columns differ.
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126
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127 -----
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128
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129 **Example**
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130
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131 Input file::
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132
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133 1 68 4.1
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134 2 71 4.6
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135 3 62 3.8
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136 4 75 4.4
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137 5 58 3.2
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138 6 60 3.1
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139 7 67 3.8
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140 8 68 4.1
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141 9 71 4.3
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142 10 69 3.7
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143
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144 Create a two series XY plot on the above data:
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145
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146 - Series 1: Red Dashed-Line plot between columns 1 and 2
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147 - Series 2: Blue Circular-Point plot between columns 3 and 2
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148
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149 .. image:: ${static_path}/images/xy_example.jpg
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150 </help>
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151 </tool>
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