Cytoscape JSON file format and STYLE storage
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4 months ago
Akash D ▴ 10

I have made a particular network in some style (Gradient/3D marble type)in Cystoscape and have exported the network to .cyjs or JSON format. However when try to import the .cyjs file, the style (Gradient/3D marble type) gets lost and the network comes back to its bare minimum attributed format.

According to Cytoscape manual, The style attributes need to be exported differently as some_style.xml format as because .cyjs are not made to handle this (style) parameter.

  1. How can I visualize my .cyjs file just as the way I saved it and its style?
  2. Do I need to integrate the some_style.xml and .cyjs format ?

Any help please?

Styles format File JSON Cytoscape • 256 views
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4 months ago
Scooter ▴ 160

Greetings Akash,

First, note that cytoscape.js and cytoscape desktop are not 100% compatible in terms of the styling. For example, I don't think that your gradients will show up in cytoscape.js (you can do the same thing using SVG for cytoscape.js, but you have to do that yourself). I have two recommendations that will get you closer, however:

  1. Export your network to NDEx and visualize it there. That will preserve as much of your styling information as possible.
  2. Export your network to the Web (File->Export network->To Web Page...). That will give you a zip file with a simple HTML application you can push up to a web site. It should preserve most of your styling.

-- scooter

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Thank you so very much. Will try it out and get back.

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