GO::View 0.72

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;