GO Visualizer Tutorial

Part1: How to Use

Go to http://kiharalab.org/web/vis. User can click on the initial three categroies to expand the GO tree. The visualization can be zoomed in/out by using the mouse wheel and drag around by using the left mouse button. The configuration sidebar of GO visualizer is on the right part of the screen.

When mouse is over the rectangle of a GO term, the information of GO term will be shown in the GO Term ID and GO Name boxes.
User can change the orientation of the graph by clicking the button in the Graph Direction section.
By checking the box before "No parent recomputation", the renderer of the graph will only connect the sub nodes to the expanded node and speed up the rendering..

Part2: Visualization of PFP/ESG Results

To view the visualization of a certain PFP/ESG job, user can click the link "Visualization of Predicted GO Terms" below the input sequence section inside job result page. Currently the number of nodes are limited. For PFP, the score lower than 10% of max score is cutted off. For ESG, the score lower than 5% is cutted off.

The browser will pop up a new window for visualization and user can change the color scheme by clicking the button inside the Color Scheme section.

"Number of Pred. Nodes": Colors are based on number of predicted child nodes in the path.

"Score": Colors are based on the prediction score of PFP/ESG.

User can also change the configuration in Part1.

Part3: Download Visualization Figure

To download the snapshot of the current figure in the visualization tool, user can click the button "Download Figure Preview", this will show a preview box of what the image will look like below the button. User can zoom in/out and move around the visualization to fit the preview box. Clicking the "Download Figure Preview" button will re-render the preview box. The download hyperlink will generated and user can click and download the image.
This feature is not supported by all browsers. Currently only available in Firefox.

In the result page of PFP and ESG, if real-time rendering is too slow, user can click the link below each Category name "Download Static XX Figure" to view the visualization offline.

Part4: Network Problem

If user find the tool not generating visualization or timeout, we have provide the static image of visualization below the redirect link at the PFP/ESG result page.

Part5: Cytoscape Visualization

We provide same interface as the original visualization and user has to download the Flash Plugin first in order to use Cytoscape. By using Cytoscape, user can select multiple nodes and move them around. We also provide three different graph presentation: Tree, Circle and Radial.

Figure of Circle and Radial

Part6: Browser Support

Currently the GO visualizer only support Chrome and Firefox. The Cytoscape version supports IE10+, Chrome, and Firefox. If both versions of the visualizer fail, please consider to download static visualization figures from the result page.

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