How to createGroups from R command line

[Mehdi]

Hello --

Probably pretty naive question, new to RCy3! I am confused how to identify certain nodes in a network in order to put them into a group.

I understand the usage for createGroup is:

createGroup(group.name, nodes = NULL, nodes.by.col = "SUID",
network = NULL, base.url = .defaultBaseUrl)

Lets say I have three nodes named "AKT1", "AKT2", and "AKT3" that I want to group into "AKT".

I tried:

createGroup("AKT", nodes = c("AKT1","AKT2","AKT3"))

Doesn't work. I'm guessing I have a lack of understanding for how to identify and select nodes in a network. Any help would be greatly appreciated!

-M

[Alex Pico]

HI M,

The group functions are only supported in Cytoscape 3.7+. You should be seeing a message explaining this when you attempt the functions in 3.6.1, for example. Version 3.7 will be out in early Fall. You can get a pre-beta, dev version at code.cytoscape.org.

 - Alex

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[Alex Pico]

Oops, never mind my previous response. I was thinking of other functions I recently added :)

Group functions work fine in 3.6.1.  The default value for “nodes.by.col” is SUID. This is for more reliable referencing across functions. However, you can use node names (like in your example), but you have to specify nodes.by.col = “name”

Hope this helps!

 - Alex

[Mehdi]

Thanks for your prompt response! Ok, so I'm performing:

> createGroup("AKT", nodes.by.col = c("AKT1","AKT2"))

Which gives the output:

group 

14340 

So, it seems to have run but I don't see the grouping in Cytoscape. I must be missing something. Also, I'm not sure how to get SUIDs for a given node...

Thanks,

Mehdi

On Thursday, August 16, 2018 at 6:37:54 PM UTC-7, Alex Pico wrote:

Oops, never mind my previous response. I was thinking of other functions I recently added :)

Group functions work fine in 3.6.1.  The default value for “nodes.by.col” is SUID. This is for more reliable referencing across functions. However, you can use node names (like in your example), but you have to specify nodes.by.col = “name”

Hope this helps!

 - Alex

On Aug 16, 2018, at 6:32 PM, Alex Pico <alex...@gladstone.ucsf.edu> wrote:

HI M,

The group functions are only supported in Cytoscape 3.7+. You should be seeing a message explaining this when you attempt the functions in 3.6.1, for example. Version 3.7 will be out in early Fall. You can get a pre-beta, dev version at code.cytoscape.org.

 - Alex

On Aug 16, 2018, at 5:56 PM, Mehdi <mehdibo...@gmail.com> wrote:

Hello --

Probably pretty naive question, new to RCy3! I am confused how to identify certain nodes in a network in order to put them into a group.

I understand the usage for createGroup is:

createGroup(group.name, nodes = NULL, nodes.by.col = "SUID",
     network = NULL, base.url = .defaultBaseUrl)

Lets say I have three nodes named "AKT1", "AKT2", and "AKT3" that I want to group into "AKT".

I tried:

createGroup("AKT", nodes = c("AKT1","AKT2","AKT3"))

Doesn't work. I'm guessing I have a lack of understanding for how to identify and select nodes in a network. Any help would be greatly appreciated!

-M

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[Mehdi]

Oh I got it! I needed to do this:

createGroup("AKT", nodes = c("AKT1","AKT2"), nodes.by.col="name")

.. as name is the name of the column containing the names of each of my nodes. That makes sense now. Ok thanks!