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Cytoscape how to

Cytoscape how to

by DAVIDE RUCCI -
Number of replies: 3

Is there any real tutorial online on how to export our data to Cytoscape? I read the documentation on cytoscape.org but it is very generic and not useful at all. All I have understood is that we can import .csv files that contain the structure of a graph, but no other info is provided. For example, I tried to create a .csv file containing a pair of numbers for each row that identifies an edge in the graph but it created, for example, the same node two times instead of adding an edge to the existing node.

So, has anyone tried Cytoscape and has some useful "how-to" for it?

Thank you.

In reply to DAVIDE RUCCI

Re: Cytoscape how to

by MARCO SPINOSA -

Did you set the source and the target when you imported the csv*? (clicking on the column name in the import dialog)

I use the same structure, and it works.

*Be sure to click on import network and not on import table

In reply to DAVIDE RUCCI

Re: Cytoscape how to

by ORLANDO LEOMBRUNI -

In general, Cytoscape supports these kinds of files:

http://manual.cytoscape.org/en/stable/Supported_Network_File_Formats.html

I successfully imported data into Cytoscape by storing it into a SIF (simple interaction file): for each edge, you have a row in the file that goes like

node1 edgetype node2

where edgetype can be anything in practice. My file looks like this:

0.0.0.220:1016 link 0.0.1.79:2711
and the result is the one in the image (partial view, since it's a huge graph with 500 nodes and 64000 edges).


                                    

                
                
                                                

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                                        In reply to DAVIDE RUCCI
                                        
Re: Cytoscape how to

                                        

                                            by ANDREA MICHIENZI - 
                        

                                

                            

                
                            

                                        

                                        

                
                                

                                    

                                        
Hi Davide,
I googled a little bit and found this link: http://manual.cytoscape.org/en/stable/Creating_Networks.html
Let me know if you need further help. Also consider using Cytoscape as a java (or python or whatever other supported language) library rather than a standalone software, if you want.