carnival_visNet visualization in part 05

[ulrmu]

Hi there,

Visualizing the network in the last part of part 05 using carnival_visNetproduces a a network where all nodes are aligned into one straight line. Using the html file in a browser, the nodes cannot be disentangled.

Is anyone else experiencing this issue? Is there any way to use the html file in a network visualization program similar to Cytoscape?

Thank you for any advice!

[adugourd]

Hi,

I'm not sure why this bug occur tbh, this has to do with the visnetwork package I assume.

If you want you can indeed visualise the network in cytoscape as well, all you need to do is to write carnival_result$weightedSIF and carnival_result$nodesAttributes tables in csv files and import them in cytoscape :)

Cheers

Aurelien

[ulrmu]

Thank you, @adugourd ! Could you explain how to properly import/use the two files to visualize the data?

[adugourd]

You can use the write_csv function in R to export the carnival_result$weightedSIF and carnival_result$nodesAttributes tables

The you can check this video to learn how to import csv files in cytoscape :)

https://www.youtube.com/watch?v=Z8jUmJL2HFw

Cheers,

Aurelien

[CheyennedeVriend]

Hi,

I'm having the same exact problem. I did watch the youtube tutorial but I do not understand how to combine these files into cytoscape. Could you please explain how to use the WeightedSIF and NodeAttribute tables into cytoscape?

Thanks in advance!

Kind regards, Cheyenne