a simple question

[Ernesto Diaz-Flores]

Hi everyone,

 a very very basic question: how do I open a Cytoscape network (let's call it "test.Cys") that i have on my desktop from R?

thanks

Ernesto

[Dexter Pratt]

Hi Ernesto,

.cys files are snapshots of your Cytoscape session, not a single network. They are only intended to be opened by the Cytoscape application.

There are two convenient ways to work with a Cytoscape network in R:  via NDEx (ndexbio.org), the Cytoscape system for storing, sharing, publishing, and using networks and via the RCy3 package that accesses the Cytoscape application via its automation interface (https://github.com/cytoscape/cytoscape-automation/wiki).

Via NDEx, 

1. go to the NDEx website (ndexbio.org) and create an account (using the Login/Register button in the top right corner), 
2. then upload the network you want to work with to your account (https://apps.cytoscape.org/apps/cyndex2. This app is pre-loaded in Cytoscape, you don't need to install anything)
3. access it via the R package. see: 
   1. the R section in https://home.ndexbio.org/readme-developers-best-practices/ndexr 
   2. or go to. https://www.bioconductor.org/packages/release/bioc/html/ndexr.html

Via RCy3, 

• see this getting started tutorial. https://cytoscape.org/cytoscape-tutorials/presentations/modules/prep-advanced-automation/index.html#/
• You open your .cys file containing the network in Cytoscape and then access the running Cytoscape from your R script via the RCy3 package.

Have fun,

Dexter

[Ernesto Diaz-Flores]

Dexter,

 this is great info, thanks a lot for the details and i will be following the tutorial using RCy3 as i have that already installed and fits what i want to do. If i encounter a problem that i cannot figure out i will get back but hopefully i will be able to do the analysis i want without problems.

thanks again

Ernesto 

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[Ernesto Diaz-Flores]

Hi again,

 I followed the tutorial of using RCy3 to manage Cytoscape from R but it end by saving the .cys file. Now, how do you access it again from RCy3?  I assume openSession(file.location = ) but for file location, what is the way you set the path? or you have to put the name of the file?

thanks

Ernesto

[Alex Pico]

File paths for read and write functions in RCy3 will default to the working directory you have set in R/RStudio. You can optionally specify a full path.  So, if you only provide a filename when you save a CYS, then it should be saved to your current working directory. You should be able to just specify the filename in openSession and it will look for the file in your current working directory.

If this doesn’t work, please file a bug with steps to reproduce it.

https://github.com/cytoscape/RCy3/issues

Thanks!

 - Alex

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