Positional Data Missing?

[Terrence Ernst]

I am wondering why positional data is missing when running exportNetwork, using RCy3.

I am specifically looking at the 'wine and cheese' example, from the cytoscape.js page. (http://www.wineandcheesemap.com/) (https://github.com/cytoscape/wineandcheesemap)

This example uses a flat (json) file that I am assuming was exported via the thick client (v=https://github.com/cytoscape/wineandcheesemap/blob/gh-pages/data.json) Note the positional data, for each node.

When trying to duplicate this example, using RCy3, I notice that the positional data is not exported.

[Alex Pico]

Positional data is exported by RCy3. Here's a short demo script:

library(RCy3)
openSession()
exportNetwork("test", "CX")

You'll find the data in chunks that looks like this:

{
    "node" : 211,
    "view" : 768,
    "x" : 1835.5062515151699,
    "y" : 1306.3731574723454
  }

It's no longer explicitly called "position" like in the example json you pointed to. That's from 2016, maybe the format changed?

 - Alex

[Terrence Ernst]

I should note that I am referring specifically to the creation of the CYJS file, not the CX version.

[Alex Pico]

Ack. Good catch! Turns out that Cytoscape Commands and CyREST both exclude position from their CYJS exports. I’ll file bugs for those. Once it’s fixed at the source, then it will automatically work in RCy3 as well. RCy3 simply calls the ‘network export’ command, in this case.

 - Alex

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