How to merge the edited KEGG pathways in cytoscape

I have learnt to import KEGG pathways to cytoscape and merge the pathways without any edits. but I want to differentiate the nodes of each pathways with different colours to understand the pathways of particular gene or molecule. when I try to merge pathways after editing, only the source data is getting merged not the edited one. could someone please guide me with tips to merging the edited pathways in cytoscape in detail ?

I assume that when you say “editing” you are referring to editing the visual properties (i.e. color). You are correct that merging networks does not attempt to merge the visual properties. On the other hand, this isn’t really hard — just add a node column in one of your pathways and fill that column with a values (doesn’t matter what value). When you do the merge, that column will be preserved. Now since only one of your pathways has values in the that column, you can set up a discrete mapping and change the color of only those nodes with a value in the column. This is covered in the Basic Data Visualization tutorial at tutorials.cytoscape.org.

— scooter