AmiGO Manual: RG Graphical View

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Introduction

The interactive graph browser is an application for viewing the structure of the ontology crossed with information from the Reference Genome project.

The application is under heavy development; please read all of the documentation before contacting GO help.

Rgv2.png

Requirements

This viewer has only been tested in Safari 3.x, FireFox 2.x, FireFox 3.x, and Opera 9.x.

Graph Layout

Hopefully most of the graph is self-explanatory. However, there are several items that may be confusing at first:

  • Under the terms in the graph, annotations that are direct are written in blue, while indirect annotations are written in black. This is true in both the static (PNG) and interactive (SVG) graphs.
  • In the interactive (SVH) graphs, next to every species name in the Control Panel, for example, in the image at the top of this page: C. elegans (4/11). This would mean that there are 4 direct annotations for C. elegans and 11 indirect ones.

Interactive Graph Usage

Graph Controls

  • Hovering over a node brings up detailed term information.
  • The graph can be clicked and dragged to change the view (panning).
  • The mouse wheel zooms in and out. On many laptops, the very right side of the mouse pad may be used as a mouse wheel. If using OS X, the "two-fingered slide" can be used for this purpose. The zoom may also be controlled by ctrl-a and ctrl-z (if the browser does not use these for other functions).

Control Panel

  • Checking a species checkbox causes the all direct annotations to be highlighted with a pie wedge in the graph. A circle on the pie wedge will either represent direct experimental evidence or direct ISS evidence depending on color (green and blue respectively).
  • The "All" checkbox will either check or uncheck all of the species checkboxes.
  • The "Coverage" selection at the bottom of the panel will highlight all indirect/inferred annotations for all of the checked species.

Also, under the control panel, are two blue links:

  • "return to homolog set details page" will send you back to the table view of the homolog set.
  • "view graph help pages" will bring you to this page in the AmiGO Manual.

Troubleshooting

  • Currently, the initial graph may start out zoomed in to a blank area. If you initially can see nothing after the graph is loaded, try zooming out using the controls (see above).
  • Depending on your platform, the mouseover events in the interactive (SVG) can be extremely finicky. If a node details box does not come up for you the first time, try moving the mouse away from the node and then move back and try again.
  • Some builds of Opera attempt to keep a minimum font size, which means that when zoomed out far enough, the text in nodes becomes an illegible singularities.
  • Safari is known to override the font suggestions in the SVG document, which can cause illegibility in some cases when zoomed out. Some users have had success with changing the default document font.