Visualize Networks Online and Offline

Metascape provides intuitive visualizations for either pathway enrichment networks or protein-protein interaction networks. By default, we do not display labels for the nodes within the .png and .pdf outputs, because displaying them will make both networks and labels unreadable (Figure 1).

Figure 1. Displaying labels tend to make the network visualization unpublishable.

In order to interpret the network, we recommend users to open the network .cys file within Cytoscape application. For those users who do not have Cytoscape installed or just want a quick examination of the networks, Metascape now provides an easy alternative to display networks within the browser.

Visualization within Browser

On the Analysis Report web page. Users can click on the Web icon (Figure 2) to open an interactive browser page. The network is displayed using CytoscapeJS, a simplified Cytoscape web client.

Figure 2. Click on the Web icon to open the network in a new browser window.

In the web view, one can use mouse scroll to zoom in/out. The labels for the nodes can be displayed when they are mouse selected (Figure 3). The application seems to be buggy (at least when the labels have not been displayed yet), if you do not see labels, try to click on the background to unselect nodes first, then mouse select the nodes again.

Figure 3. Select nodes (by mouse boxing them, yellow highlighted) will have their descriptions displayed.

We also included CytoscapeJS application in the Zip package. The AnalysisReport.html file contained with the zip file provides the same Web icon that can lead to the similar web view (works without Internet connection).

Cytoscape AutoAnnotate

Better visualization options are available by opening the .cys session file within the Cytoscape application. AutoAnnotate is a Cytoscape app preinstalled in Cytoscape (if not, upgrade your Cytoscape or use menu Apps > App Manager to install).

To run AutoAnnotate, choose menu Apps > AutoAnnotate > New Annotation Set … (Figure 4).

Figure 4. Launch AutoAnnotate

Configure the Advanced options like the following (Figure 5). This is for the GO enrichment network. There is no need to use AutoAnnotate for protein-protein interaction network, as we display gene symbols for all MCODE networks by default.

Figure 5. Configuration options.

The result is shown below (Figure 6). There are settings (shown on the right panel) to adjust colors and font sizes. Notice that AutoAnnotate nicely extracts keywords for each cluster to provide a functional overview. Since the default effect can be rather crowded, AutoAnnotate is not used by Metascape to produce publishable graphics.

Figure 6. The result of AutoAnnotate.

If you would like move clusters apart for a clearer view, it is important to use menu Layout > Clear All Edge Bends to unbundle edges first.

Figure 7. Unbundle all edges.

Then select nodes and move them to desirable locations:

Figure 8. Separate clusters with edge bundle off.

Then bundle the edges afterwards for a more aesthetic view using menu Layout > Bundle Edges > All Nodes and Edges.

Figure 9. Bundle edges

We turn Figure 9 into Figure 10:

Figure 10. Edge bundle on.

If you would like to publish the final graph, use menu File > Export > Network to Image …

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