I would like to change the sizes of the selected nodes in Cytoscape app. Also, for large networks when manual selection is very tedious, then is it also possible to set the sizes of source and target nodes differently?
1 Answers
There are a few ways to set the sizes of selected nodes in Cytoscape:
- While selected, you can open the Style tab and set a "bypass" value for Node Size (the third column of settings). This will override any default or mapped values (the first two columns).
- While selected, you can create a new Node Table columns (plus icon). Make it a string or boolean, for example. Then enter a value for one of rows, then right-click on it and choose "Apply to all selected rows". This will fill all selected nodes with the same value. Now you can use a Node Size mapping in the Style panel. This approach is preferred as the selection is now permanently indicated by a Node Table column and will save/export/convert better.
- You could also define the select in a table (e.g., in Excel) with a column of node names and a new column (like the one you made manually in option 2). Then simply import the table.
- You could also use RCy3 if you like R...
Regarding sizing source and targets: Cytoscape's style pane does not have access to this model information. The best approach is probably #3 above. You likely already have a table defining source and target nodes outside of Cytoscape. You can use that to create explicit table columns and then create a mapping to Node Size.
Hope this helps!
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