Hi Paul
Thanks a lot for ur help and sorry for being late since my system broke
after upgrading my system.

I managed to execute my example program as desired by following your
suggestion in the prev mail. However, my actual data it is still showing the
error.

#This is my example program which is working fine now
g <- new ('graphNEL', edgemode='directed')
nodesFr = c('A', 'B', 'C')
nodesTo =c('D', 'E', 'F')
nodesAll = union(nodesFr, nodesTo)
nElemFr = length(nodesFr)
nElemTo = length(nodesTo)

#add all the nodes to the graph
g <- graph::addNode(nodesAll, g)
#create cytoscape window
cw <- CytoscapeWindow ('smallExample', graph=g)
displayGraph (cw)

#calculate the location of 'From' nodes
locx= rep(400, nElemFr)
yPos = 100
incr = ceiling(600/nElemFr)
locy = c()
for(j in 1: nElemFr) {locy = c(locy, (yPos+j*incr))}
setPosition(cw, nodesFr , locx, locy)

#calculate the location of 'To' nodes
locx= rep(600, nElemTo)
yPos = 100
incr = ceiling(600/nElemTo)
locy = c()
for(j in 1: nElemTo) {locy = c(locy, (yPos+j*incr))}
setPosition(cw, nodesTo , locx, locy)

#add edge to the graph: Suppose the edges are: (A ->D , A -> E, B ->E, C->F,
C->E)
edgeList = rbind(c('A', 'D'),rbind(c('A','E'), rbind(c('B','E'),
rbind(c('C','F'), c('C', 'E')))))
for(j in 1: length(edgeList[,1]))
    {
    g = graph::addEdge(edgeList[j,1], edgeList[j,2], g)
    }

cw@graph = g
layout (cw, 'jgraph-spring')
displayGraph(cw)

#This works fine and show output as desired in cytoscape
#########################

#However, an  error is shown in the following code which is almost similar
to the example code above.

> g <- new ('graphNEL', edgemode='undirected')
> cw <- new.CytoscapeWindow ('intxOutFromSkin', graph=g)
> displayGraph (cw)
entering RCytoscape::displayGraph
RCytoscape::displayGraph, empty graph, returning
NULL
> intxn = read.csv(fileNames[i], header=TRUE);  # the edge list is
represented as node pair
> numEdge = length(intxn[,1])
> to = sort(unique(as.character(intxn[,'to']))) #find unique destination
nodes
> g <- graph::addNode(to, g) #add nodes to the graph
> nNodes = length(to)
> locx = rep(i*150, nNodes)
> yPos = 10
> incr = ceiling(600/nNodes)
> locy = c()
> for(j in 1: nElem) {locy = c(locy, (yPos+j*incr))}

> setPosition(cw, to , locx, locy)
Error in convertToR(xmlParse(node, asText = TRUE)) :
  faultCode: 1001 faultString: Node with id: 10108 could not be found.
>
I am not sure why this error is coming as '10108' is already a node in the
the graph (g)

> nodes(g)
  [1] "10108"  "102056" "106563" "106873" "107425" "107886" "113095" "11369"

  [9] "118326" "118596" "119236" "119823" "119827" "124746" "125026"
"125212"
 [17] "130086" "130658" "131786" "131860" "136566" "136742" "137170"
"137540"
 [..............



#######
SessionInfo()
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] hash_2.0.1        RCytoscape_1.1.32 XMLRPC_0.2-4      RBGL_1.26.0
[5] graph_1.28.0

loaded via a namespace (and not attached):
[1] RCurl_1.5-0  tools_2.12.1 XML_3.2-0
>


Thanks a lot for your reply.

--Fahim



On Mon, Feb 14, 2011 at 9:57 AM, Paul Shannon
<pshannon@systemsbiology.org>wrote:

> Hi Fahim,
>
> There is an easily resolved omission in the sample code you sent.
>
> Please note the the 3rd line below, 'displayGraph', which does not appear
> in your email.  This method transmits your graph from R to Cytoscape,
> creating a Cytoscape network.
>
>  cw <- CytoscapeWindow ('smallExample',
> graph=RCytoscape::makeSimpleGraph())
>   displayGraph (cw)      # this command sends your R graph to Cytoscape.  I
> believe you left this out...
>   layout (cw, 'jgraph-spring')
>  redraw (cw)
>   setPosition (cw, 'A', 50, 80)
>
> If you want to place 'A' directly between 'B' and 'C', try this:
>
>  pos.b <- getPosition (cw, 'B')[[1]]    # where is B?
>  pos.c <- getPosition (cw, 'C')[[1]]    # where is c?
>  new.x <- (pos.b$x + pos.c$x)/2         # calculate the x coordinate for A
>  new.y <- (pos.b$y + pos.c$y)/2         # and the y
>  setPosition (cw, 'A', new.x, new.y)    # place A mid-way between B and C
>
> Please try these steps, ensure that they work for you, then we can then
> look at the next spot where trouble arises for you.
>
> Also, please attach your sessionInfo.  It may be wise to update your code
> to the latest version of the package.
>
> Cheers!
>
> - Paul
>
> On Feb 14, 2011, at 5:25 AM, Martin Morgan wrote:
>
> > On 02/13/2011 11:28 AM, Fahim M wrote:
> >> Hi
> >> Can some one please point out where i am wrong.
> >>
> >> I am trying to position set of nodes column-wise in cytoscape using
> >> RCytoscape
> >> A----D
> >> B----E
> >> C----F
> >
> > Hi Fahim -- please ask questions about Bioconductor packages on the
> > Bioconductor mailing list
> >
> > http://bioconductor.org/help/mailing-list/
> >
> > and include packageMaintainer('RCytoscape') in the post.
> >
> > Martin
> >
> >>
> >> -------------------
> >>
> >> g <- new ('graphNEL', edgemode='undirected')
> >> cw <- CytoscapeWindow ('smallExample',
> graph=RCytoscape::makeSimpleGraph())
> >> layout (cw, 'jgraph-spring')
> >> redraw(cw)
> >>
> >> nodesFr = c('A', 'B', 'C')
> >> nodesTo =c('D', 'E', 'F')
> >> nodesAll = union(nodesFr, nodesTo)
> >>
> >> nElemFr = length(nodesFr)
> >> nElemTo = length(nodesTo)
> >>
> >> g <- graph::addNode(nodesAll, g)
> >>
> >> setPosition(cw, nodesFr , c(400, 400, 400), c(100, 200, 300))
> >> setPosition(cw, nodesTo , c(600, 600, 600), c(100, 200, 300))
> >> Error in convertToR(xmlParse(node, asText = TRUE)) :
> >>  faultCode: 0 faultString: Failed to invoke method setNodesPositions in
> >> class tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: null
> >>
> >> setPosition(cw, nodesTo , c(600, 600, 600), c(100, 200, 300))
> >> Error in convertToR(xmlParse(node, asText = TRUE)) :
> >>  faultCode: 1001 faultString: Node with id: D could not be found.
> >>
> >> Thanks
> >> --Fahim
> >>
> >>      [[alternative HTML version deleted]]
> >>
> >> ______________________________________________
> >> R-help@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> >
> > --
> > Computational Biology
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> >
> > Location: M1-B861
> > Telephone: 206 667-2793
>
>


-- 
Fahim Mohammad
Bioinforformatics Lab
University of Louisville
Louisville, KY, USA
Ph:  +1-502-409-1167

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