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.
- File > Import > Networks from File… > Select the file NETWORK_cs_ev_0_.txt in the networks subfolder > Open > OK.
- File > Import > Table from File… > Select the file NodeTable_cs.txt in the results folder > Open > OK.
- 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:
- Click Style in the left side panel.
- Fill color > Select “Subgroup” in Column > Select “Discrete mapping” in Mapping type > Select colors.
- Label > Select “Label” as column > Select “Passthrough mapping” in Mapping type.
- Set the width and height to 100.
- Set border width to 3, and border paint to black.
- Select Eclipse as shape.
- 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:
- File > Import > Networks from File > Select the file NETWORK_cs_ev_55_.txt in the networks subfolder > Open > OK.
To export the figures:
- 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.
- File > Import > Networks from File… > NETWORK_cs_ev_0_5_.txt in the metanodes subfolder > Open > OK.
- File > Import > Table from File… > Select the file NodeTable_cs.txt in the results folder > Open > OK.
- File > Import > Table from File… > Select the file Analysis_5_Info.txt in the analysis subfolder > Open > OK.
- 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:
- Click Style in the left side panel.
- Fill color > Select “Subgroup” in Column > Select “Discrete mapping” in Mapping type > Select colors
- Label > Select “Label” as column > Select “Passthrough mapping” in Mapping type
- Set border width to 3, and border paint to black.
- Select Eclipse as shape.
- Height > Set default to 10 and Select “Size” in Column > Select “Passthrough mapping” in Mapping type.
- Width > Set default to 10 and Select “Size” in Column > Select “Passthrough mapping” in Mapping type.
- In the top menu, select Layout and select “yFiles Organic Layout”.
To export the figures:
- Click File > Export > Network to Image.