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