Visualization of SSNs in Cytoscape - ahvdk/SSNpipe GitHub Wiki

The following visualization examples requires that Cytoscape is installed as well as the yFiles layout algorithms. yFiles layouts can be installed through Cytoscape: Apps in the top menu > App Manager… > Middle selection pane > Scroll down to “yFiles layout Algorithms” > Install.

Visualize networks from “Create SSNs” or “Refine SSNs”

This visualization example requires that you have files created from: 2. SSNpipe Usage Examples.

1. File > Import > Networks from File… > Select the file NETWORK_cs_ev_0_.txt in the networks subfolder > Open > OK.
2. File > Import > Table from File… > Select the file NodeTable_cs.txt in the results folder > Open > OK.
3. File > Import > Table from File… > Select the file Analysis_5_Info.txt in the analysis subfolder > Open > OK.

Now, a network and associated information is imported into Cytoscape. To style the network according to the imported files from SSNPipe:

4. Click Style in the left side panel.
5. Fill color > Select “Subgroup” in Column > Select “Discrete mapping” in Mapping type > Select colors.
6. Label > Select “Label” as column > Select “Passthrough mapping” in Mapping type.
7. Set the width and height to 100.
8. Set border width to 3, and border paint to black.
9. Select Eclipse as shape.
10. In the top menu, select Layout and select “yFiles Organic Layout”.

Networks imported into the current network collection will take the same style, try by importing a filtered network:

11. File > Import > Networks from File > Select the file NETWORK_cs_ev_55_.txt in the networks subfolder > Open > OK.

To export the figures:

12. Click File > Export > Network to Image.

 

Visualize a network from “Create Metanodes”

This visualization example requires that you have files created from: 2. SSNpipe Usage Examples.

1. File > Import > Networks from File… > NETWORK_cs_ev_0_5_.txt in the metanodes subfolder > Open > OK.
2. File > Import > Table from File… > Select the file NodeTable_cs.txt in the results folder > Open > OK.
3. File > Import > Table from File… > Select the file Analysis_5_Info.txt in the analysis subfolder > Open > OK.
4. File > Import > Table from File… > Select the file Metanodes_5_info.txt in the metanodes subfolder > Open > OK.

Now, a metanode network and associated information is imported into Cytoscape. To style the network according to the imported files from SSNPipe:

5. Click Style in the left side panel.
6. Fill color > Select “Subgroup” in Column > Select “Discrete mapping” in Mapping type > Select colors
7. Label > Select “Label” as column > Select “Passthrough mapping” in Mapping type
8. Set border width to 3, and border paint to black.
9. Select Eclipse as shape.
10. Height > Set default to 10 and Select “Size” in Column > Select “Passthrough mapping” in Mapping type.
11. Width > Set default to 10 and Select “Size” in Column > Select “Passthrough mapping” in Mapping type.
12. In the top menu, select Layout and select “yFiles Organic Layout”.

To export the figures:

13. Click File > Export > Network to Image.