AmiGO 2 Manual: Visualize

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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 the full specification and an example, see the AmiGO_2_Manual:_JSON#Node_Description_Format.

Example results (click to enlarge)

Amigo-vis-graph.png

Caveats

  • Node 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.

Color

The ontology relation colors are as follows:

relation color example
is_a blue
part_of lightblue
develops_from brown
regulates black
negatively_regulates red
positively_regulates green