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

Notes

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. In the case of the Term Enrichment tool, it adds a p-value annotation to each node as well as changing its color in relation to the p-value.

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.

AmiGO Manual: Visualize

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