1GO::View(3) User Contributed Perl Documentation GO::View(3)
2
6 GO::View - Creates a gif or png image for visualizing the GO DAG
7
9 This perl module generates a graphic that displays the parent and child
10 relationships of a selected GO term. It also provides the visualization
11 for the GO::TermFinder perl module created by the Stanford Microarray
12 Database (SMD). This module is useful when analyzing experimental or
13 computational results that produce a set of gene products that may have
14 a common function or process.
15
17 use GO::View;
18 my $goView =
20 GO::View->new(-goid => $goid,
22 -ontologyProvider => $ontology,
23 -annotationProvider => $annotation,
24 -termFinder => \@pvalues,
25 -aspect => 'P',
26 -configFile => $confFile,
27 -imageDir => "/tmp",
28 -imageUrlRoot => "http://www.ABC.com/tmp",
29 -imageName => "GOview.88.png",
30 -tree => 'up',
31 -nodeUrl => $goUrl,
32 -geneUrl => $geneUrl,
33 -pvalueCutOff => '0.01',
34 -imageLabel => "SGD");
35 argument required expect data and type
38 -------------------------------------------------------------------------
39 -goid No A gene ontology ID (GOID).
40 If nothing is passed in, the module
41 will use the top goid of each ontology
42 branch (i.e, goid for
43 molecular_function, biological_process,
44 or cellular_component)
45 -ontologyProvider Yes An ontology provider instance.
47 -annotationProvider No An annotation provider instance. It is
49 required for creating tree for GO Term
50 Finder result.
51 -termFinder No An array of hash references returned
53 from 'findTerms' method of
54 GO::TermFinder module. It is required
55 for creating tree for GO Term Finder
56 result.
57 -aspect No <P|C|F>. The aspect of the ontology
59 provider. It is required for creating
60 tree for GO Term Finder result.
61 -configFile Yes The configuration file for setting the
63 general variables for the graphic
64 display.
65 -imageDir Yes The directory for storing the newly
67 created image file. It must be
68 world (nobody) readable and writable
69 if you want to display the image to
70 the web.
71 -imageUrlRoot No The url root for the -imageDir. It is
73 required if you want to display the
74 image to the web.
75 -imageName No The image file name. By default, the
77 name will be something like
78 'GOview.xxxx.png'. The 'xxxx' will be
79 the process id. A suffix for the image (.png
80 or .gif) should not be provided, as that will
81 be determined at run time, depending on the
82 capabilities of the GD library.
83 -treeType No <up|down>. The tree type.
85 1. up => display the ancestor tree
87 for the given goid.
88 2. down => display the descendant tree
89 for the given goid.
90 By default, it will display the
91 descendant tree.
92 -geneUrl No The URL for each Gene to link to.
94 It needs to have the text <REPLACE_THIS> in
95 the url which will be substituted
96 by the real goid for a node.
97 -nodeUrl No The url for each GO node to link to.
99 It needs to have the text <REPLACE_THIS> in
100 the url which will be substituted
101 by the real goid for a node.
102 -pvalueCutOff No The p-value cutoff for displaying
104 the graphic for GO Term Finder.
105 The default is 0.01
106 -imageLabel No The image label which will appear at
108 the left bottom corner of the map.
109 -maxTopNodeToShow No This argument is used to limit the
111 amount of the graph that might be
112 shown, for the sake of reducing run-
113 time. The default is 6.
114 ------------------------------------------------------------------------
116 To display the image on the web:
118 $goView->showGraph;
120 To create and return image file name with full path:
122 my $imageFile = $goView->createImage;
124
126 Reporting Bugs
127 Bug reports can be submitted via email
128 shuai@genome.stanford.edu
130
132 Shuai Weng, shuai@genome.stanford.edu
133
135 Copyright (c) 2003 Stanford University. All Rights Reserved. This
136 module is free software; you can redistribute it and/or modify it under
137 the same terms as Perl itself.
138
140 The rest of the documentation details each of the public methods.
141
143 new
144 Title : new
145 Function: Initializes the GO::View object.
146 : Recognized named parameters are -goid, -ontologyProvider,
147 -annotationProvider, -termFinder, -aspect, -configFile,
148 -imageDir, -imageUrlRoot, -imageName, -treeType, -nodeUrl,
149 -imageLabel
150 Returns : a new object
151 Args : named parameters
152 graph
154 Title : graph
155 Usage : my $graph = $goView->graph;
156 Function: Gets the newly created Graphviz instance.
157 Returns : a new Graphviz instance.
158 showGraph
160 Title : showGraph
161 Usage : $goView->showGraph;
162 Function: Creates the image and print the map image to a file.
163 Returns : the name of the file to which the image was written
164 Throws : Exception if the imageUrlRoot is not passed to the object.
165 imageFile
167 Title : imageFile
168 Usage : my $imageFile = $goView->imageFile;
169 Function: Gets the newly created image file name (with full path).
170 Returns : image file name.
171 createImage
173 Title : createImage
174 Usage : $goView->createImage;
175 Function: Creates the GO tree image file. Calls it only if you
176 want to create the image file only and do not want to
177 display the image.
178 Returns : The newly created image file name with full path.
179 imageMap
181 Title : imageMap
182 Usage : my $map = $goView->imageMap;
183 Function : returns the text that constitutes an image map for the
184 created image.
185 Returns : a string
186perl v5.28.0 2007-07-19 GO::View(3)