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GO::View 0.72

  Date Added: April 23, 2010  |  Visits: 729


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GO::View is a Perl module that creates a gif or png image for visualizing the GO DAG. 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. SYNOPSIS use GO::View; my $goView = GO::View->new(-goid => $goid, -ontologyProvider => $ontology, -annotationProvider => $annotation, -termFinder => @pvalues, -aspect => P, -configFile => $confFile, -imageDir => "/tmp", -imageUrlRoot => "", -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 . 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 . 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 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 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;.

Requirements: No special requirements
Platforms: Linux
Keyword: Dag Display Go Dag Go Term Go Term Finder Goview Image Module No The Perl Perl Module Png Image Required Tree Will Be
Users rating: 0/10

License: Freeware Size: 870.4 KB
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