GO::View
This perl module generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the GO::TermFinder perl module created by the Stanford Microarray Database (SMD). This module is useful when analyzing experimental or computational results that produce a set of gene products that may have a common function or process.
use GO::View; my $goView = GO::View->new(-goid => $goid, -ontologyProvider => $ontology, -annotationProvider => $annotation, -termFinder => \@pvalues, -aspect => 'P', -configFile => $confFile, -imageDir => "/tmp", -imageUrlRoot => "http://www.ABC.com/tmp", -imageName => "GOview.88.png", -tree => 'up', -nodeUrl => $goUrl, -geneUrl => $geneUrl, -pvalueCutOff => '0.01', -imageLabel => "SGD"); argument required expect data and type ------------------------------------------------------------------------- -goid No A gene ontology ID (GOID). If nothing is passed in, the module will use the top goid of each ontology branch (i.e, goid for molecular_function, biological_process, or cellular_component) -ontologyProvider Yes An ontology provider instance. -annotationProvider No An annotation provider instance. It is required for creating tree for GO Term Finder result. -termFinder No An array of hash references returned from 'findTerms' method of GO::TermFinder module. It is required for creating tree for GO Term Finder result. -aspect No <P|C|F>. The aspect of the ontology provider. It is required for creating tree for GO Term Finder result. -configFile Yes The configuration file for setting the general variables for the graphic display. -imageDir Yes The directory for storing the newly created image file. It must be world (nobody) readable and writable if you want to display the image to the web. -imageUrlRoot No The url root for the -imageDir. It is required if you want to display the image to the web. -imageName No The image file name. By default, the name will be something like 'GOview.xxxx.png'. The 'xxxx' will be the process id. A suffix for the image (.png or .gif) should not be provided, as that will be determined at run time, depending on the capabilities of the GD library. -treeType No <up|down>. The tree type. 1. up => display the ancestor tree for the given goid. 2. down => display the descendant tree for the given goid. By default, it will display the descendant tree. -geneUrl No The URL for each Gene to link to. It needs to have the text <REPLACE_THIS> in the url which will be substituted by the real goid for a node. -nodeUrl No The url for each GO node to link to. It needs to have the text <REPLACE_THIS> in the url which will be substituted by the real goid for a node. -pvalueCutOff No The p-value cutoff for displaying the graphic for GO Term Finder. The default is 0.01 -imageLabel No The image label which will appear at the left bottom corner of the map. ------------------------------------------------------------------------ To display the image on the web: $goView->showGraph; To create and return image file name with full path: my $imageFile = $goView->createImage;
Bug reports can be submitted via email
shuai@genome.stanford.edu
Shuai Weng, shuai@genome.stanford.edu
Copyright (c) 2003 Stanford University. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
The rest of the documentation details each of the public methods.
Title : new Function: Initializes the GO::View object. : Recognized named parameters are -goid, -ontologyProvider, -annotationProvider, -termFinder, -aspect, -configFile, -imageDir, -imageUrlRoot, -imageName, -treeType, -nodeUrl, -imageLabel Returns : a new object Args : named parameters
Title : graph Usage : my $graph = $goView->graph; Function: Gets the newly created Graphviz instance. Returns : a new Graphviz instance.
Title : showGraph Usage : $goView->showGraph; Function: Creates the image and print the map image to a file. Returns : the name of the file to which the image was written Throws : Exception if the imageUrlRoot is not passed to the object.
Title : imageFile Usage : my $imageFile = $goView->imageFile; Function: Gets the newly created image file name (with full path). Returns : image file name.
Title : createImage Usage : $goView->createImage; Function: Creates the GO tree image file. Calls it only if you want to create the image file only and do not want to display the image. Returns : The newly created image file name with full path.
Title : imageMap Usage : my $map = $goView->imageMap; Function : returns the text that constitutes an image map for the created image. Returns : a string
To install GO::TermFinder, copy and paste the appropriate command in to your terminal.
cpanm
cpanm GO::TermFinder
CPAN shell
perl -MCPAN -e shell install GO::TermFinder
For more information on module installation, please visit the detailed CPAN module installation guide.