Question: Bayesian Network from R to visualize in cytoscape
gravatar for Maria
5.5 years ago by
United States
Maria0 wrote:

Hello all,

I have a bayesian network that I created in R and wants to visualize it in cytoscape. Does anyone know how to do it.



cytoscape bayesian network R • 2.2k views
ADD COMMENTlink modified 3.0 years ago by sugus40 • written 5.5 years ago by Maria0
gravatar for Natasha Latysheva
5.5 years ago by
United Kingdom
Natasha Latysheva50 wrote:

Cytoscape is quite friendly to start using, it simply requires at least 2 columns denoting interactions (i.e. for each row, item in column A 'interacts' with column B in some meaningful way) and any optional values for mapping edge values (e.g. interaction strengths, confidence in interaction validity). As long as you have that information in a tsv file, you can use Cytoscape's import function

ADD COMMENTlink written 5.5 years ago by Natasha Latysheva50


I try using bayelvira plugin in cytoscape, but having trouble importing my data. I'm not sure what file format is compatible with this plugin. thanks for the response.

ADD REPLYlink written 5.5 years ago by Maria0

I am not familiar with that plugin, but cytoscape is capable of importing extremely simple interaction data. If you reformat your data output to what I described above (two columns denoting interactions, optional edge attributes), that might help you get around this difficulty

ADD REPLYlink written 5.5 years ago by Natasha Latysheva50
gravatar for sugus
3.0 years ago by
China Pharmaceutical University
sugus40 wrote:

Hi man, you have no need to setup any plugin to finish what you want because you can just click File and choose Network and import your edge data. Than you can chose the from-node and the target-node.That's it,you can work out your network. And i am interested in how you construct your bayesian network,can you share me more details about the R code for i can just construct a co-expression network but no regulatory network. So thank you if you can share with me.

ADD COMMENTlink written 3.0 years ago by sugus40
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