[BioC] RCytoscape on Windows

[Paul Shannon]

Hi Mark,

Bioconductor graphs (graphNEL, graphAM, …) have to be either directed or undirected: no hybrid graphs are possible.  If I understand your question, this can be worked around quite easily, both in a graphNEL object and in its display in RCytoscape.   See the sample code below.  

The current design of graphNELs includes a penalty for undirected graphs:  every edge is stored twice.  Until we fix that, RCytoscape does best with directed graphs only.

Let me know if this helps.

 - Paul


library(RCytoscape)
g <- graphNEL(edgemode="directed")
g <- initNodeAttribute(g, "label", "char", "unspecified")
g <- initEdgeAttribute(g, "edgeType", "char", "unspecified")
g <- addNode(c("A","B"), g)
  # comment this next line to see one-way regulation between B and A
  # leave it live to see reciprocal regulation
  # edge target rules, below, display differently in the two cases
g <- addEdge("A", "B", g)
edgeData(g, "A", "B", "edgeType") <- "regulation"
nodeData(g, nodes(g), "label") <- nodes(g)

  # now add a regulatory relation between B and A
  # check first to see if A already regulates B
if("B" %in% edges(g)$A) {
  edgeData(g, "A", "B", "edgeType") <- "reciprocal regulation"
} else {
  g <- addEdge("B", "A", g)
  edgeData(g, "B", "A", "edgeType") <- "regulation"
}

cw <- new.CytoscapeWindow("demo", g, overwriteWindow=TRUE)
displayGraph(cw)
layoutNetwork(cw, "jgraph-spring")
setNodeLabelRule(cw, "label")
setEdgeTargetArrowRule(cw, "edgeType", c("regulation", "reciprocal regulation"), c("Arrow", "Arrow"))
setEdgeSourceArrowRule(cw, "edgeType", c("regulation", "reciprocal regulation"), c("No Arrow", "Arrow"))
redraw(cw)

On Dec 5, 2012, at 11:30 PM, Mark Christiansen wrote:

> Hi Paul,
> 
> I have been using your examples in the RCytoscape package to build up a gene network.   I am using the commands:
> 
> g=new ("graphNEL", edgemode="directed")
> ...
> g=addEdge(from,to,g) 
> 
> This works well to construct a network, but I can't tell that the edges are directed.  Is there a flag I am missing (maybe I should use addCyEdge?)  
> 
> Also, I would like to be able to check to see if there is an edge going in the other direction (via g=addEdge(to,from,g) and then change the edge to be bidirectional.  
> 
> Is it possible to check if an edge exists and if so, to change its directionality?
> 
> Thank you for your help,
> 
> Mark 
> 
> 
> On Mon, Nov 19, 2012 at 10:42 AM, Paul Shannon <pshannon at fhcrc.org> wrote:
> Hi Mark,
> 
> The remote communication protocol for Cytoscape3 has not yet been documented, but we know that they will no longer support XMLRPC.  This means that RCytoscape support for Cytoscape 3 has to wait until the protocol and the 'commands' API are both well-defined.  Jan Bot, who wrote CytoscapeRPC, suggests that this is a big job and won't happen for a while.
> 
> Until then, maybe you can get by with the venerable Cytoscape 2.8.3?
> 
>  - Paul
> 
> On Nov 19, 2012, at 10:37 AM, Mark Christiansen wrote:
> 
> > Hi Paul,
> >
> > It seems the same Plug-In Manager to install CytoscapeRPC is not available on Cytoscape v3.  Has this been replaced by the Apps Manager?  If I try to import the CytoscapeRPC.jar file as an App in v3, I get the following error:
> >
> >         org.cytoscape.app.internal.exception.AppParsingException: Jar is missing value for entry Cytoscape-App in its manifest file
> >
> > Thank you for your suggestions,
> >
> > Mark Christiansen
> >
> >
> >
> > On Sun, Nov 18, 2012 at 9:06 PM, Mark Christiansen <mwchristiansen at gmail.com> wrote:
> > Hi Paul,
> >
> > Thank you for your response.  I was trying to install XML-RPC manually from source and ran into some difficulty.  I just tried installing CytoscapeRPC via the Cytoscape plug-in manager and it worked like a charm.
> >
> > Thanks again!
> >
> > -Mark
> >
> >
> > On Sun, Nov 18, 2012 at 8:21 PM, Paul Shannon <pshannon at fhcrc.org> wrote:
> > Hi Mark,
> >
> > The RCytoscape package should install fine on Windows.  XML-RPC and its prerequisite XML work on Windows.   Maven is not needed, not unless you are building Cytoscape from scratch, and not necessariliy even then.   The installation instructions avaialable at http://rcytoscape.systemsbiology.net should get you going.
> >
> > If not, could you give us the results of sessionInfo ()?    Be forewarned:  our next repsonse will likely encourage you to upgrade R and R packages to the latest version.
> >
> >   - Paul
> >
> > On Nov 18, 2012, at 5:40 PM, Mark Christiansen wrote:
> >
> > > Greetings Paul,
> > >
> > > I was wondering if you have had success setting up RCytoscape on Windows.  I believe most of the software dependencies (XML-RPC, Maven, etc.) were designed to run on Linux or Mac, but I could be wrong.
> > >
> > > Thank you for your help.
> > >
> > > Best regards,
> > >
> > > Mark Christiansen
> >
> >
> >
> >
> > --
> > -Mark
> >
> >
> >
> > --
> > -Mark
> 
> 
> 
> 
> -- 
> -Mark