AmiGO 2 Manual: Visualize: Difference between revisions

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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).
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).


So far, the following keys are recognized:
For the full specification and an example, see the [[AmiGO_2_Manual:_JSON#Node_Description_Format]].
 
* "title": The title of the node (must be unique).
* "body": The text appearing under the title.
* "fill": The color of the node.
* "font": The color of the font.
* "border": The border color around the text of the node.
 
While the body tag should be able to take simple psuedo-HTML as [http://www.graphviz.org/doc/info/shapes.html#html GraphViz does], the HTML support in GraphViz is fiddly (e.g. spaces *do count* and some tags don't work in certain combinations)--it takes a little experimentation.
 
===Example JSON===
 
{"GO:0002244":{"title": "foo",
                "body":  "bar",
                "fill":  "#ccccff",
                "font":  "#0000ff",
                "border":"red"},
"GO:0005575":{"title":"alone",
              "body":""},
"GO:0033060":{}}


===Example results (click to enlarge)===
===Example results (click to enlarge)===

Latest revision as of 17:32, 17 October 2013

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)

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
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