Question: Cytoscape: how to show different interactions using different lines or different colors
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gravatar for Bioinformatician_in_trouble
2.1 years ago by

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.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Bioinformatician_in_trouble10
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gravatar for Asaf
2.1 years ago by
Asaf5.3k
Israel
Asaf5.3k wrote:

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.

ADD COMMENTlink written 2.1 years ago by Asaf5.3k

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

ADD REPLYlink written 2.1 years ago by Bioinformatician_in_trouble10
1

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.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by sridhar56100
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