GO::View GO::View is a Perl module that creates a gif or png image for visualizing the GO DAG.
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JPG GIF creates gif creates jpg GO DAG

GO::View Description

GO::View is a Perl module that creates a gif or png image for visualizing the GO DAG. 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 => "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 . 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: · Perl

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