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comparison xy_plot.xml @ 0:1cdc54f92956 draft

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author devteam
date Wed, 21 Aug 2013 11:10:58 -0400
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1 <tool id="XY_Plot_1" name="Plotting tool" version="1.0.1">
2 <description>for multiple series and graph types</description>
3 <requirements>
4 <requirement type="package" version="2.11.0">R</requirement>
5 </requirements>
6 <command interpreter="bash">r_wrapper.sh $script_file</command>
7
8 <inputs>
9 <param name="main" type="text" value="" size="30" label="Plot Title"/>
10 <param name="xlab" type="text" value="" size="30" label="Label for x axis"/>
11 <param name="ylab" type="text" value="" size="30" label="Label for y axis"/>
12 <repeat name="series" title="Series">
13 <param name="input" type="data" format="tabular" label="Dataset"/>
14 <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/>
15 <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/>
16 <conditional name="series_type">
17 <param name="type" type="select" label="Series Type">
18 <option value="line" selected="true">Line</option>
19 <option value="points">Points</option>
20 </param>
21 <when value="line">
22 <param name="lty" type="select" label="Line Type">
23 <option value="1">Solid</option>
24 <option value="2">Dashed</option>
25 <option value="3">Dotted</option>
26 </param>
27 <param name="col" type="select" label="Line Color">
28 <option value="1">Black</option>
29 <option value="2">Red</option>
30 <option value="3">Green</option>
31 <option value="4">Blue</option>
32 <option value="5">Cyan</option>
33 <option value="6">Magenta</option>
34 <option value="7">Yellow</option>
35 <option value="8">Gray</option>
36 </param>
37 <param name="lwd" type="float" label="Line Width" value="1.0"/>
38 </when>
39 <when value="points">
40 <param name="pch" type="select" label="Point Type">
41 <option value="1">Circle (hollow)</option>
42 <option value="2">Triangle (hollow)</option>
43 <option value="3">Cross</option>
44 <option value="4">Diamond (hollow)</option>
45 <option value="15">Square (filled)</option>
46 <option value="16">Circle (filled)</option>
47 <option value="17">Triangle (filled)</option>
48 </param>
49 <param name="col" type="select" label="Point Color">
50 <option value="1">Black</option>
51 <option value="2">Red</option>
52 <option value="3">Green</option>
53 <option value="4">Blue</option>
54 <option value="5">Cyan</option>
55 <option value="6">Magenta</option>
56 <option value="7">Yellow</option>
57 <option value="8">Gray</option>
58 </param>
59 <param name="cex" type="float" label="Point Scale" value="1.0"/>
60 </when>
61 </conditional>
62 </repeat>
63 </inputs>
64
65 <configfiles>
66 <configfile name="script_file">
67 ## Setup R error handling to go to stderr
68 options( show.error.messages=F,
69 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
70 ## Determine range of all series in the plot
71 xrange = c( NULL, NULL )
72 yrange = c( NULL, NULL )
73 #for $i, $s in enumerate( $series )
74 s${i} = read.table( "${s.input.file_name}" )
75 x${i} = s${i}[,${s.xcol}]
76 y${i} = s${i}[,${s.ycol}]
77 xrange = range( x${i}, xrange )
78 yrange = range( y${i}, yrange )
79 #end for
80 ## Open output PDF file
81 pdf( "${out_file1}" )
82 ## Dummy plot for axis / labels
83 plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" )
84 ## Plot each series
85 #for $i, $s in enumerate( $series )
86 #if $s.series_type['type'] == "line"
87 lines( x${i}, y${i}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} )
88 #elif $s.series_type.type == "points"
89 points( x${i}, y${i}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} )
90 #end if
91 #end for
92 ## Close the PDF file
93 devname = dev.off()
94 </configfile>
95 </configfiles>
96
97 <outputs>
98 <data format="pdf" name="out_file1" />
99 </outputs>
100
101 <tests>
102 <test>
103 <param name="main" value="Example XY Plot"/>
104 <param name="xlab" value="Column 1"/>
105 <param name="ylab" value="Column 2"/>
106 <param name="input" value="2.tabular" ftype="tabular"/>
107 <param name="xcol" value="1"/>
108 <param name="ycol" value="2"/>
109 <param name="type" value="line"/>
110 <param name="lty" value="2"/>
111 <param name="col" value="2"/>
112 <param name="lwd" value="1.0"/>
113 <output name="out_file1" file="XY_Plot_1_out.pdf"/>
114 </test>
115 </tests>
116 <help>
117 .. class:: infomark
118
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.
120
121 -----
122
123 .. class:: warningmark
124
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.
126
127 -----
128
129 **Example**
130
131 Input file::
132
133 1 68 4.1
134 2 71 4.6
135 3 62 3.8
136 4 75 4.4
137 5 58 3.2
138 6 60 3.1
139 7 67 3.8
140 8 68 4.1
141 9 71 4.3
142 10 69 3.7
143
144 Create a two series XY plot on the above data:
145
146 - Series 1: Red Dashed-Line plot between columns 1 and 2
147 - Series 2: Blue Circular-Point plot between columns 3 and 2
148
149 .. image:: ${static_path}/images/xy_example.jpg
150 </help>
151 </tool>