This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Cytoscape: how to show different interactions using different lines or different colors

Hi All, I am trying to create a network in cytoscape 3.4.0 where my source and target are genes and my interaction would be "activates" or "Inhibits". My question is, I want to show the interactions either by using different line color or different line type. How can I do this. ? Looking forward for a response. Thank you in advance.

cytoscape network gene-gene interactions
• 3,757 views • link
written by Bioinformatician_in_trouble • Bioinformatician_in_trouble

1 answer

You should import edges attributes file to Cytoscape if they are not defined at network loading and then change display settings. You can do it using several formats, simplest is excel file.

• 0 views • link
written by Asaf Asaf

Hi asaf, Thank you for your reply.I am not sure how to add attributes( saw the attribute file format from cytoscape manual, but could not follow) This is how i have placed the columns in the excel sheet that I used to create network Gene 1 Gene 2 Interaction ATM TP53 Activates CHEK1 CDC25 Inhibits

How do i add attributes to this?Looking forward for your answer.Thank you

• 0 views • link
written by Bioinformatician_in_trouble • Bioinformatician_in_trouble

Importing the attribute file is also part of the initial import step. Check the import options closely, Cytoscape initially has a learning curve, once you get used to it, it will be simpler.

Following this link should be helpful,

http://www.cytoscape.org/manual/Cytoscape2_6Manual.html#Import Attribute Table Files

Also, I would suggest using some example datasets to play with and that will help you get a hang of it.

• 0 views • link
written by sridhar56 sridhar56

Log in to answer this question.

More posts like this