Mercurial > repos > saskia-hiltemann > xy_plot_multiformat
comparison xy_plot.xml @ 0:d43075b3e107 draft default tip
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| author | saskia-hiltemann |
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| date | Fri, 30 Oct 2015 10:46:49 -0400 |
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| -1:000000000000 | 0:d43075b3e107 |
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| 1 <tool id="XY_Plot_1_multiformat" name="Plotting tool" version="1.0.1"> | |
| 2 <description>for multiple series and graph types and multiple output types</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="3.2.1">R</requirement> | |
| 5 <requirement type="package" version="2.11.1">fontconfig</requirement> | |
| 6 </requirements> | |
| 7 <command interpreter="bash">r_wrapper.sh $script_file</command> | |
| 8 | |
| 9 <inputs> | |
| 10 <param name="main" type="text" value="" label="Plot Title"/> | |
| 11 <param name="xlab" type="text" value="" label="Label for x axis"/> | |
| 12 <param name="ylab" type="text" value="" label="Label for y axis"/> | |
| 13 <param name="ftype" type="select" label="File Type"> | |
| 14 <option value="pdf">PDF</option> | |
| 15 <option value="png">PNG</option> | |
| 16 <option value="jpeg">JPEG</option> | |
| 17 <option value="bmp">BMP</option> | |
| 18 <option value="tiff">TIFF</option> | |
| 19 </param> | |
| 20 <repeat name="series" title="Series"> | |
| 21 <param name="input" type="data" format="tabular" label="Dataset"/> | |
| 22 <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/> | |
| 23 <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/> | |
| 24 <conditional name="series_type"> | |
| 25 <param name="type" type="select" label="Series Type"> | |
| 26 <option value="line" selected="true">Line</option> | |
| 27 <option value="points">Points</option> | |
| 28 </param> | |
| 29 <when value="line"> | |
| 30 <param name="lty" type="select" label="Line Type"> | |
| 31 <option value="1">Solid</option> | |
| 32 <option value="2">Dashed</option> | |
| 33 <option value="3">Dotted</option> | |
| 34 </param> | |
| 35 <param name="col" type="select" label="Line Color"> | |
| 36 <option value="1">Black</option> | |
| 37 <option value="2">Red</option> | |
| 38 <option value="3">Green</option> | |
| 39 <option value="4">Blue</option> | |
| 40 <option value="5">Cyan</option> | |
| 41 <option value="6">Magenta</option> | |
| 42 <option value="7">Yellow</option> | |
| 43 <option value="8">Gray</option> | |
| 44 </param> | |
| 45 <param name="lwd" type="float" label="Line Width" value="1.0"/> | |
| 46 </when> | |
| 47 <when value="points"> | |
| 48 <param name="pch" type="select" label="Point Type"> | |
| 49 <option value="1">Circle (hollow)</option> | |
| 50 <option value="2">Triangle (hollow)</option> | |
| 51 <option value="3">Cross</option> | |
| 52 <option value="4">Diamond (hollow)</option> | |
| 53 <option value="15">Square (filled)</option> | |
| 54 <option value="16">Circle (filled)</option> | |
| 55 <option value="17">Triangle (filled)</option> | |
| 56 </param> | |
| 57 <param name="col" type="select" label="Point Color"> | |
| 58 <option value="1">Black</option> | |
| 59 <option value="2">Red</option> | |
| 60 <option value="3">Green</option> | |
| 61 <option value="4">Blue</option> | |
| 62 <option value="5">Cyan</option> | |
| 63 <option value="6">Magenta</option> | |
| 64 <option value="7">Yellow</option> | |
| 65 <option value="8">Gray</option> | |
| 66 </param> | |
| 67 <param name="cex" type="float" label="Point Scale" value="1.0"/> | |
| 68 </when> | |
| 69 </conditional> | |
| 70 </repeat> | |
| 71 </inputs> | |
| 72 | |
| 73 <configfiles> | |
| 74 <configfile name="script_file"> | |
| 75 ## Setup R error handling to go to stderr | |
| 76 options( show.error.messages=F, | |
| 77 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
| 78 ## Determine range of all series in the plot | |
| 79 xrange = c( NULL, NULL ) | |
| 80 yrange = c( NULL, NULL ) | |
| 81 #for $i, $s in enumerate( $series ) | |
| 82 s${i} = read.table( "${s.input.file_name}" ) | |
| 83 x${i} = s${i}[,${s.xcol}] | |
| 84 y${i} = s${i}[,${s.ycol}] | |
| 85 xrange = range( x${i}, xrange ) | |
| 86 yrange = range( y${i}, yrange ) | |
| 87 #end for | |
| 88 ## Open output PDF file | |
| 89 #if $ftype.value == "pdf" | |
| 90 pdf("outfile.pdf") | |
| 91 #else | |
| 92 "${ftype}"( "outfile.${ftype}" , type="cairo") | |
| 93 #end if | |
| 94 ## Dummy plot for axis / labels | |
| 95 plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" ) | |
| 96 ## Plot each series | |
| 97 #for $i, $s in enumerate( $series ) | |
| 98 #if $s.series_type['type'] == "line" | |
| 99 lines( x${i}, y${i}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} ) | |
| 100 #elif $s.series_type.type == "points" | |
| 101 points( x${i}, y${i}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} ) | |
| 102 #end if | |
| 103 #end for | |
| 104 ## Close the PDF file | |
| 105 devname = dev.off() | |
| 106 </configfile> | |
| 107 </configfiles> | |
| 108 | |
| 109 <outputs> | |
| 110 <data format="pdf" name="out_file1" from_work_dir="outfile.pdf" > | |
| 111 <filter>(ftype == 'pdf') </filter> | |
| 112 </data> | |
| 113 <data format="png" name="out_file2" from_work_dir="outfile.png"> | |
| 114 <filter>(ftype == 'png') </filter> | |
| 115 </data> | |
| 116 <data format="jpg" name="out_file3" from_work_dir="outfile.jpeg"> | |
| 117 <filter>(ftype == 'jpeg') </filter> | |
| 118 </data> | |
| 119 <data format="bmp" name="out_file4" from_work_dir="outfile.bmp"> | |
| 120 <filter>(ftype == 'bmp') </filter> | |
| 121 </data> | |
| 122 <data format="tiff" name="out_file5" from_work_dir="outfile.tiff"> | |
| 123 <filter>(ftype == 'tiff') </filter> | |
| 124 </data> | |
| 125 </outputs> | |
| 126 | |
| 127 <tests> | |
| 128 <test> | |
| 129 <param name="main" value="Example XY Plot PDF"/> | |
| 130 <param name="xlab" value="Column 1"/> | |
| 131 <param name="ylab" value="Column 2"/> | |
| 132 <param name="ftype" value="pdf"/> | |
| 133 <param name="input" value="2.tabular" ftype="tabular"/> | |
| 134 <param name="xcol" value="1"/> | |
| 135 <param name="ycol" value="2"/> | |
| 136 <param name="type" value="line"/> | |
| 137 <param name="lty" value="2"/> | |
| 138 <param name="col" value="2"/> | |
| 139 <param name="lwd" value="1.0"/> | |
| 140 <output name="out_file1" file="XY_Plot_1_multi_out.pdf" format="pdf" /> | |
| 141 </test> | |
| 142 <test> | |
| 143 <param name="main" value="Example XY Plot PNG"/> | |
| 144 <param name="xlab" value="Column 1"/> | |
| 145 <param name="ylab" value="Column 2"/> | |
| 146 <param name="ftype" value="png"/> | |
| 147 <param name="input" value="2.tabular" ftype="tabular"/> | |
| 148 <param name="xcol" value="1"/> | |
| 149 <param name="ycol" value="2"/> | |
| 150 <param name="type" value="line"/> | |
| 151 <param name="lty" value="2"/> | |
| 152 <param name="col" value="2"/> | |
| 153 <param name="lwd" value="1.0"/> | |
| 154 <output name="out_file2" md5="c2762c725f80fe4419e35768cac5d11b" /> | |
| 155 </test> | |
| 156 <test> | |
| 157 <param name="main" value="Example XY Plot JPEG"/> | |
| 158 <param name="xlab" value="Column 1"/> | |
| 159 <param name="ylab" value="Column 2"/> | |
| 160 <param name="ftype" value="jpeg"/> | |
| 161 <param name="input" value="2.tabular" ftype="tabular"/> | |
| 162 <param name="xcol" value="1"/> | |
| 163 <param name="ycol" value="2"/> | |
| 164 <param name="type" value="line"/> | |
| 165 <param name="lty" value="2"/> | |
| 166 <param name="col" value="2"/> | |
| 167 <param name="lwd" value="1.0"/> | |
| 168 <output name="out_file3" md5="5c89f4e87bb5f2a809877b471f9c2d69" /> | |
| 169 </test> | |
| 170 <test> | |
| 171 <param name="main" value="Example XY Plot BMP"/> | |
| 172 <param name="xlab" value="Column 1"/> | |
| 173 <param name="ylab" value="Column 2"/> | |
| 174 <param name="ftype" value="bmp"/> | |
| 175 <param name="input" value="2.tabular" ftype="tabular"/> | |
| 176 <param name="xcol" value="1"/> | |
| 177 <param name="ycol" value="2"/> | |
| 178 <param name="type" value="line"/> | |
| 179 <param name="lty" value="2"/> | |
| 180 <param name="col" value="2"/> | |
| 181 <param name="lwd" value="1.0"/> | |
| 182 <output name="out_file4" md5="74ea4b29bd7de44c1b6377c6c26671e7"/> | |
| 183 </test> | |
| 184 <test> | |
| 185 <param name="main" value="Example XY Plot TIFF"/> | |
| 186 <param name="xlab" value="Column 1"/> | |
| 187 <param name="ylab" value="Column 2"/> | |
| 188 <param name="ftype" value="tiff"/> | |
| 189 <param name="input" value="2.tabular" ftype="tabular"/> | |
| 190 <param name="xcol" value="1"/> | |
| 191 <param name="ycol" value="2"/> | |
| 192 <param name="type" value="line"/> | |
| 193 <param name="lty" value="2"/> | |
| 194 <param name="col" value="2"/> | |
| 195 <param name="lwd" value="1.0"/> | |
| 196 <output name="out_file5" md5="7ebf7d201ad9cdf0fc6995639749ae7d"/> | |
| 197 </test> | |
| 198 </tests> | |
| 199 <help> | |
| 200 .. class:: infomark | |
| 201 | |
| 202 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. | |
| 203 | |
| 204 ----- | |
| 205 | |
| 206 .. class:: warningmark | |
| 207 | |
| 208 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. | |
| 209 | |
| 210 ----- | |
| 211 | |
| 212 **Example** | |
| 213 | |
| 214 Input file:: | |
| 215 | |
| 216 1 68 4.1 | |
| 217 2 71 4.6 | |
| 218 3 62 3.8 | |
| 219 4 75 4.4 | |
| 220 5 58 3.2 | |
| 221 6 60 3.1 | |
| 222 7 67 3.8 | |
| 223 8 68 4.1 | |
| 224 9 71 4.3 | |
| 225 10 69 3.7 | |
| 226 | |
| 227 Create a two series XY plot on the above data: | |
| 228 | |
| 229 - Series 1: Red Dashed-Line plot between columns 1 and 2 | |
| 230 - Series 2: Blue Circular-Point plot between columns 3 and 2 | |
| 231 | |
| 232 .. image:: xy_example.jpg | |
| 233 </help> | |
| 234 </tool> |