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comparison tools/plotting/xy_plot.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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 <command interpreter="bash">r_wrapper.sh $script_file</command>
4
5 <inputs>
6 <param name="main" type="text" value="" size="30" label="Plot Title"/>
7 <param name="xlab" type="text" value="" size="30" label="Label for x axis"/>
8 <param name="ylab" type="text" value="" size="30" label="Label for y axis"/>
9 <repeat name="series" title="Series">
10 <param name="input" type="data" format="tabular" label="Dataset"/>
11 <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/>
12 <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/>
13 <conditional name="series_type">
14 <param name="type" type="select" label="Series Type">
15 <option value="line" selected="true">Line</option>
16 <option value="points">Points</option>
17 </param>
18 <when value="line">
19 <param name="lty" type="select" label="Line Type">
20 <option value="1">Solid</option>
21 <option value="2">Dashed</option>
22 <option value="3">Dotted</option>
23 </param>
24 <param name="col" type="select" label="Line Color">
25 <option value="1">Black</option>
26 <option value="2">Red</option>
27 <option value="3">Green</option>
28 <option value="4">Blue</option>
29 <option value="5">Cyan</option>
30 <option value="6">Magenta</option>
31 <option value="7">Yellow</option>
32 <option value="8">Gray</option>
33 </param>
34 <param name="lwd" type="float" label="Line Width" value="1.0"/>
35 </when>
36 <when value="points">
37 <param name="pch" type="select" label="Point Type">
38 <option value="1">Circle (hollow)</option>
39 <option value="2">Triangle (hollow)</option>
40 <option value="3">Cross</option>
41 <option value="4">Diamond (hollow)</option>
42 <option value="15">Square (filled)</option>
43 <option value="16">Circle (filled)</option>
44 <option value="17">Triangle (filled)</option>
45 </param>
46 <param name="col" type="select" label="Point Color">
47 <option value="1">Black</option>
48 <option value="2">Red</option>
49 <option value="3">Green</option>
50 <option value="4">Blue</option>
51 <option value="5">Cyan</option>
52 <option value="6">Magenta</option>
53 <option value="7">Yellow</option>
54 <option value="8">Gray</option>
55 </param>
56 <param name="cex" type="float" label="Point Scale" value="1.0"/>
57 </when>
58 </conditional>
59 </repeat>
60 </inputs>
61
62 <configfiles>
63 <configfile name="script_file">
64 ## Setup R error handling to go to stderr
65 options( show.error.messages=F,
66 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
67 ## Determine range of all series in the plot
68 xrange = c( NULL, NULL )
69 yrange = c( NULL, NULL )
70 #for $i, $s in enumerate( $series )
71 s${i} = read.table( "${s.input.file_name}" )
72 x${i} = s${i}[,${s.xcol}]
73 y${i} = s${i}[,${s.ycol}]
74 xrange = range( x${i}, xrange )
75 yrange = range( y${i}, yrange )
76 #end for
77 ## Open output PDF file
78 pdf( "${out_file1}" )
79 ## Dummy plot for axis / labels
80 plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" )
81 ## Plot each series
82 #for $i, $s in enumerate( $series )
83 #if $s.series_type['type'] == "line"
84 lines( x${i}, y${i}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} )
85 #elif $s.series_type.type == "points"
86 points( x${i}, y${i}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} )
87 #end if
88 #end for
89 ## Close the PDF file
90 devname = dev.off()
91 </configfile>
92 </configfiles>
93
94 <outputs>
95 <data format="pdf" name="out_file1" />
96 </outputs>
97
98 <tests>
99 <test>
100 <param name="main" value="Example XY Plot"/>
101 <param name="xlab" value="Column 1"/>
102 <param name="ylab" value="Column 2"/>
103 <param name="input" value="2.tabular" ftype="tabular"/>
104 <param name="xcol" value="1"/>
105 <param name="ycol" value="2"/>
106 <param name="type" value="line"/>
107 <param name="lty" value="2"/>
108 <param name="col" value="2"/>
109 <param name="lwd" value="1.0"/>
110 <output name="out_file1" file="XY_Plot_1_out.pdf"/>
111 </test>
112 </tests>
113 <help>
114 .. class:: infomark
115
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.
117
118 -----
119
120 .. class:: warningmark
121
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.
123
124 -----
125
126 **Example**
127
128 Input file::
129
130 1 68 4.1
131 2 71 4.6
132 3 62 3.8
133 4 75 4.4
134 5 58 3.2
135 6 60 3.1
136 7 67 3.8
137 8 68 4.1
138 9 71 4.3
139 10 69 3.7
140
141 Create a two series XY plot on the above data:
142
143 - Series 1: Red Dashed-Line plot between columns 1 and 2
144 - Series 2: Blue Circular-Point plot between columns 3 and 2
145
146 .. image:: ./static/images/xy_example.jpg
147 </help>
148 </tool>