(Cytoscape) What is advantage of grouping and nesting?
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2.6 years ago
hslee97 • 0

I draw many networks using cytoscape. But, really I need not use grouping and nesting systems. What their's main advantage in cytoscape?

Cytoscape • 584 views
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2.6 years ago
scooter ▴ 590

Well, there are two ways to think about grouping. First, grouping a set of nodes into a compound node can help visualize some distinct aspect of those nodes. For example, a group of proteins might form a complex. Second, in very dense networks, you may want to abstract a set of nodes and collapse them -- in sequence similarity networks, for example, it's not uncommon to collapse a set of very similar sequences into a single node. Here are two papers you can look at that have suggestions for when you might want to use grouping:

  1. Ten simple rules to create biological network figures for communication
  2. Visualization of omics data for systems biology

-- scooter

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Thanks Scooter, I will try two papers that you suggest.

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