[2] | 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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