AmiGO Manual: Visualize: Difference between revisions
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=Overview= | =Overview= | ||
This page is | This page allows the users to specify specify an arbitrary GO graph using either of two different input formats: the default/simple one and an advanced one. In both cases, the output is the minimal GO graph containing the inputted GO terms and their closure to the root(s). The user may either select the output as a PNG image or SVG markup (please see caveats below). | ||
=Default format= | |||
The default input format is a list of GO IDs (e.g. GO:0002244) separated by whitespace. | |||
=Advanced | =Advanced format= | ||
The advanced format is actually a simple [http://json.org JSON] description of nodes in the graph. While the user cannot specify what nodes appear in the graph beyond the ones used to seed it, they may completely specify the contents of those nodes (e.g. add additional annotation, change the names, or alter coloration). | |||
For example: | |||
===Example JSON=== | |||
{"GO:0002244":{"title": "foo", | {"GO:0002244":{"title": "foo", | ||
Line 20: | Line 24: | ||
"GO:0033060":{}} | "GO:0033060":{}} | ||
===Example results=== | |||
[[File:Amigo-vis-graph.png|300px]] | |||
=Caveats= | |||
* Titles, if supplied, must be unique | * Titles, if supplied, must be unique | ||
* There are bugs in GraphViz--if you get too fancy, strange things might start happening. | * There are bugs in GraphViz--if you get too fancy, strange things might start happening. | ||
* The SVG+XML output is not supported by Microsoft web browsers. | * The SVG+XML output is not supported by Microsoft web browsers. | ||
=Miscellaneous= | |||
This page is a light wrapper around a RESTful graphing component, and is the same one that is used by the Term Enrichment tool and Term Details pages. | |||
[[Category:AmiGO_Manual]] | [[Category:AmiGO_Manual]] | ||
[[Category:AmiGO]] | [[Category:AmiGO]] |
Revision as of 17:20, 11 December 2009
Overview
This page allows the users to specify specify an arbitrary GO graph using either of two different input formats: the default/simple one and an advanced one. In both cases, the output is the minimal GO graph containing the inputted GO terms and their closure to the root(s). The user may either select the output as a PNG image or SVG markup (please see caveats below).
Default format
The default input format is a list of GO IDs (e.g. GO:0002244) separated by whitespace.
Advanced format
The advanced format is actually a simple JSON description of nodes in the graph. While the user cannot specify what nodes appear in the graph beyond the ones used to seed it, they may completely specify the contents of those nodes (e.g. add additional annotation, change the names, or alter coloration).
For example:
Example JSON
{"GO:0002244":{"title": "foo", "body": "bar", "fill": "#ccccff", "font": "#0000ff", "border":"red"}, "GO:0005575":{"title":"alone", "body":""}, "GO:0033060":{}}
Example results
Caveats
- Titles, if supplied, must be unique
- There are bugs in GraphViz--if you get too fancy, strange things might start happening.
- The SVG+XML output is not supported by Microsoft web browsers.
Miscellaneous
This page is a light wrapper around a RESTful graphing component, and is the same one that is used by the Term Enrichment tool and Term Details pages.