= Control Cytoscape from R Console =

== Introduction ==
[[https://wiki.nbic.nl/index.php/CytoscapeRPC|CytoscapeRPC]] is a plugin for Cytoscape to use Cytoscape as a RPC server.  You can call Cytoscape functions from variety of languages including Perl, Python, Ruby, and R.  In this tutorial, you learn how to use Cytoscape from R console.

== Setup ==
You need to install the following plugins/packages.

=== Cytoscape Plugin ===
Just copy the following jar files to Cytoscape plugin directory.
 * [[https://wiki.nbic.nl/index.php/CytoscapeRPC|CytoscapeRPC Plugin 0.95 or later]]. 
 * [[http://www.ecoficial.com/apachemirror/ws/xmlrpc/|Apache XML RPC library]]
    * Required files are in '''lib''' directory: xmlrpc-common-3.1.3.jar, xmlrpc-server-3.1.3.jar, ws-commons-util-1.0.2.jar

=== R Packages ===
 * XML-RPC package [[attachment:XMLRPC_0.2-mod.zip]] (Bug fix version by Paul Shannon.   BSD License)
 * [[http://igraph.sourceforge.net/|igraph]] graph utility package

== Tutorial ==
=== Start Cytoscape RPC ===
 1. Start Cytoscape.  If you want to see the all messages (including Exceptions from CytoscapeRPC plugin), start Cytoscape from command line (by executing '''''cytoscape.sh''''' or '''''cytoscape.bat''''')
 1. Select '''''Plugins-->CytoscapeRPC-->Activate RPC'''''
 1. Modify port number if necessary.  Default port is 9000.

=== Start R ===
 1. Start R console
 1. Load required libraries
  {{{
> library(igraph)
> library(XMLRPC)
}}}
 1. Test RPC Plugin.
  {{{
> testResponse = xml.rpc('http://localhost:9000', 'Cytoscape.test')
> testResponse
[1] "It works!"
}}}

=== Create Network with igraph and Visualize It in Cytoscape ===
 1. Create an empty network.
  {{{
> networkID = xml.rpc('http://localhost:9000', 'Cytoscape.createNetwork', 'R-Cytoscape Test')
> networkID
[1] "2"
> networkTitle = xml.rpc('http://localhost:9000', 'Cytoscape.getNetworkTitle', networkID)
> networkTitle
[1] "R-Cytoscape Test"
}}}
 1. Generate a scale-free graph according to the Barabasi-Albert model
  {{{
> g1 <- barabasi.game(200)
> g1
Vertices: 200 
Edges: 199 
Directed: TRUE 
Edges:
                
[0]     1 ->   0
[1]     2 ->   0
[2]     3 ->   1
.
.
.
}}}
 1. Create Cytoscape network from the generated graph
  {{{
> edgelist1 <- get.edgelist(g1)
> edgelist1
       [,1] [,2]
  [1,]    1    0
  [2,]    2    0
  [3,]    3    1
.
.
.
> edgeIDs <- xml.rpc('http://localhost:9000', 'Cytoscape.createEdgesFromVector', edgelist1[,1], edgelist1[,2])
}}}
 1. In the Cytoscape window, you can see one red node.  Actually, it's a graph with 200 nodes without any visual properties.  After applying layout and vizmap, you can see something like this:


  {{attachment:igraph1.png}}

(to be continued...)