Declutter edges

[Rohan Chodankar]

Hi

I have succesfully created a network pathway in Cytoscape. The colour of the nodes is up reg (red) and down reg(green) genes and size of the node is logFC. Is there a way to declutter all the edges in this network. It was created using the MCODE Plugin.

Thanks for helping

Rohan

[Alex Pico]

Sure, we can share a few network visualization tips for the classic “hairball” problem.

First, the choice of red-green is a common mistake. These can be difficult to distinguish for color-blind folks. Fortunately, Cytoscape makes it easy to pick scientifically-test colors. In the Style panel for Node Fill Color, try using the Palettes: https://cytoscape.org/cytoscape-tutorials/protocols/advanced-palettes/#/

Next, for the edges, I can see you have a gradient of thickness and opacity already. These must be mapped to an Edge Table column value (see the Edge tab in the Style panel to check). This will allow you to use the same values to Filter which edges are viewed. There will be NO WAY to view all of the current edges in any coherent manner. So, you’ll need to explore a threshold cutoff for the edges. See Filter tutorial: https://cytoscape.org/cytoscape-tutorials/protocols/filtering-by-selection/#/

After you have a filtered subset of edges, then you can play with layout. Here’s an intro to layouts: https://cytoscape.org/cytoscape-tutorials/protocols/network-layout/#/. Here’s another example of tuning layouts: https://cytoscape.org/cytoscape-tutorials/protocols/advanced-tuning-layouts/#/1. Here’s a video of some of the same content: https://www.youtube.com/watch?v=YPdbjIDD9vA&list=PLFQS98nmv__zUUAIfU_dGXFi-qZP90VVQ&index=4 

Finally, you can create more space in a given layout using Layout Tools. Here’s a tutorial: https://cytoscape.org/cytoscape-tutorials/protocols/network-layout/#/3   And here’s a video: https://youtu.be/eZv7PojevRI?t=155. 

This is a big topic!  Here are the slides for a 4-hour course we teach on network viz and that just scratches the surface… 

https://cytoscape.org/cytoscape-tutorials/presentations/data-visualization-2020-ucsf.html#/

 - Alex

On Feb 5, 2021, at 8:52 AM, Rohan Chodankar <rohan.c...@gmail.com> wrote:

Hi

I have succesfully created a network pathway in Cytoscape. The colour of the nodes is up reg (red) and down reg(green) genes and size of the node is logFC. Is there a way to declutter all the edges in this network. It was created using the MCODE Plugin.

<Screenshot 2021-02-05 at 16.52.27.png>

Thanks for helping

Rohan

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<Screenshot 2021-02-05 at 16.52.27.png>

[Scooter Morris]

And to add to what Alex said, unless the arrowheads are absolutely critical to the scientific interpretation of the network, dropping those would be another way to declutter. 

-- scooter