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.
------------------------------------------------------------------------
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.eduAUTHOR
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 parametersgraph
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