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GO::View.3pm

NAME

GO::View - Creates a gif or png image for visualizing the GO DAG

DESCRIPTION

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          <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.
 
     -maxTopNodeToShow     No          This argument is used to limit the
                                       amount of the graph that might be
                                       shown, for the sake of reducing run-
                                       time.  The default is 6.
 
     ------------------------------------------------------------------------
 
     To display the image on the web:
 
          $goView->showGraph;
     
     To create and return image file name with full path:
     
          my $imageFile = $goView->createImage;
 
 

FEEDBACK

Reporting Bugs

Bug reports can be submitted via email

   shuai@genome.stanford.edu
 
 

AUTHOR

Shuai Weng, shuai@genome.stanford.edu

COPYRIGHT

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.

APPENDIX

The rest of the documentation details each of the public methods.

METHODS

new

  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
 
 

graph

  Title   : graph
  Usage   : my $graph = $goView->graph;
  Function: Gets the newly created Graphviz instance.   
  Returns : a new Graphviz instance.
 
 

showGraph

  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.
 
 

imageFile

  Title   : imageFile
  Usage   : my $imageFile = $goView->imageFile;
  Function: Gets the newly created image file name (with full path).  
  Returns : image file name.
 
 

createImage

  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.
 
 

imageMap

  Title    : imageMap
  Usage    : my $map = $goView->imageMap;
  Function : returns the text that constitutes an image map for the
             created image.
  Returns  : a string