Gaggle - R - String

[Cedric Ginestet]

Dear Gagglers,

I am new to Gaggle, but I must say that I am very impressed by the
setup so far, even though I haven't been able to do much. I am trying
to follow the R vignette described here (http://
gaggle.systemsbiology.net/R/vignettes/1/) in order to obtain a use
Gaggle, R and String in tandem.

I have installed R, bioconductor and the Gaggle R package using the
instructions given here:
http://gaggle.systemsbiology.net/docs/geese/r/install.php
so that if I do:
library(gaggle)
gaggleInit()
source("http://gaggle.systemsbiology.net/R/gaggleUtil.R")
I am able to open the Boss, by asking R to show it
(showGoose('boss')).

However, when I follow the steps in the vignette (http://
gaggle.systemsbiology.net/R/vignettes/1/):
# 1. Start the Gaggle Boss via Java Web Start. Wait for this to
appear on your screen before you proceed. Skip this step if you still
have a Boss running from part 1.
# 2. Start the STRING web intermediary goose.
# 3. Start R, and load the gaggle package. If R is already running,
skip this step.

Steps 1 and 2 work fine, and string appears in the Boss's panel.
However, if I simply follow step 3 loading the gaggle R package and
do
> setSpecies ('Homo sapiens')
Error in inherits(obj, "jobjRef") : object 'goose' not found

or if I do:
> gaggleInit()
initializing gaggle package 1.14.0 (2007-04)
Failed to connect to Gaggle Boss:
RemoteException occurred in server thread; nested exception is:
java.rmi.UnmarshalException: unrecognized method hash: method not
supported by remote object
Possible causes:
1) There is no Gaggle Boss running.
2) You are using an out-of-date Gaggle Boss.
3) Hang on a sec, a boss is probably autostarting now;
(Wait a few moments and give the showGoose('boss') command.)
name: R
RShellGoose: 2680

############################

I have tried loading R first and then String, but then I am told that
String 'cannot connect to Gaggle'.
What shall I do?

I am using:
Ubuntu 10.04 LTS - Lucid Lynx
Sun Java 6 Web Start (update 20)
R version 2.10.1 (2009-12-14)
gaggle.R $Revision: 3504 $ $Date: 2008-09-22 10:45:45 -0700 (Mon, 22
Sep 2008) $
(jvm version: 1.6.0_18)


Thank you very much for your help,

Cedric

[Lee Pang]

Hi Cedric,

This is an unfortunate case of us not cleaning up our website.

The STRING WBI you are using was developed using an older version of the Gaggle API (ca. 2005).  The current version of the API (2007-04) - which the R goose you installed is based from - is not backward compatible for a number of reasons.

So the easy solution to your problem - getting STRING data to R via Gaggle - would be to use the Firegoose Extension to Firefox:

http://gaggle.systemsbiology.net/docs/geese/firegoose/

which I believe has all the capabilities of the old STRING WBI goose and more.

Lee

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[Christopher Bare]

Hi Cedric,

Lee is correct. That RemoteException is due to mismatched versions of Gaggle. That vignette is out-dated, but you can do similar things using Firegoose. A similar R session (assuming Cytoscape and Firegoose are already started and connected) would look something like this:

> library (gaggle)

Loading required package: rJava

Loading required package: graph

Loading required package: RUnit

onLoad -- libname: /Library/Frameworks/R.framework/Resources/library pkgname: gaggle 

path to jar: /Library/Frameworks/R.framework/Resources/library/gaggle/jars/gaggleRShell.jar 

      script:  gaggle.R $Revision: 4478 $   $Date: 2010-06-30 14:23:20 -0700 (Wed, 30 Jun 2010) $ 

  os version:  Mac OS X 

 jvm version:  1.6.0_20 

> gaggleInit()

 initializing gaggle package 1.17.0 (2007-04)

        name:  R 

 RShellGoose:  2680 

ttl settings changed in goose

Connected to gaggle with goose name R

Use the disconnectFromGaggle() method to disconnect.

> g = randomEGraph (LETTERS [1:8], edges=10)

> setTargetGoose('Cytoscape v.2.6.1')

> broadcast(g)

> setTargetGoose('Firegoose')

> broadcast (c ("EDN3", "PBX2"))

[[ broadcast genes to STRING, expand network, broadcast network back to R ]]

network ready, node count 12, edges: 101

> pdx2.network <- getNetwork()

Warning in .local(from, to, graph) :

  The following edges already exist and will be replaced:

RET|EDN3

[[... lots of warnings snipped]]

> pdx2.network

A graphNEL graph with directed edges

Number of Nodes = 12 

Number of Edges = 40 

> nodes(pdx2.network)

 [1] "RET"   "EDN3"  "GDNF"  "EDN2"  "ECE1"  "EDNRB" "SOX10" "EDNRA" "EDN1"  "KEL"   "MITF"  "PBX2" 

Both STRING and Cytoscape support multiple edges between the same pair of nodes. Those warnings lead me to think that either the R graph package doesn't support that or maybe we're not calling it correctly. You can also broadcast a list of names.

The third step of that vignette, translating names, is no longer necessary as STRING switched to using more "biologist friendly" names.

Please let us know how Gaggle works for you and if we can help,

-Chris

On Wed, Oct 6, 2010 at 5:50 AM, Cedric Ginestet <c.gine...@googlemail.com> wrote:

Dear Gagglers,
...