Hi Paul Thanks a lot for reply. I am able to run the code which was creating problem and is now working like charm. I am able to create my own layout now. Thanks for your prompt reply. The steps (general scheme) that you mentioned in your mail is of great help and most of the problem I was facing was because of that only. One very basic question. Is there any function to find maxx, maxy, minx and miny? (x and y coordinate of the four corners of the Cy screen) Thanks again Fahim On Sun, Feb 20, 2011 at 1:42 PM, Paul Shannon <pshannon@systemsbiology.org>wrote: > Hi Fahim, > > I reworked your second (and failing) example so that it works. I will > paste the code in below, along with a tiny example data file, so you can see > the kind of nodes and edges I was testing with. > > Please keep this general scheme in mind. RCytoscape expects to be used > primarily like this: > > 1) create the graph > 2) add all nodes and edges > 3) add all node and edge attributes > 4) cw = new.CytoscapeWindow ('your.window.title', graph=yourGraph) > 5) call 'displayGraph (cw) > 6) call 'layout (cw)' or > 7) do manual layout using setPosition > 8) apply visual mapping rules (e.g., setNodeColor, setEdgeLineStyleRule, > setEdgeTargetArrowRule, etc) > 9) redraw (cw) > > I see that RCytoscape does not always handle undirected graphs cleanly. > Nishant and I may need to talk a bit further, in order for me to understand > recent changes he has made to his graph classes. So this should get better > soon. In the meantime, I apologize, and recommend your stick with directed > graphs. > > Please let me know if this code works for you, and provides you the > foundation to do the analyses you have in mind. > > Cheers! > > - Paul > > > #------------------------------------------------------------------- ----------------------------------------------- > # my version of your second example, with quite a few modifications > filename = 'nodePairs.csv' # my guess at the kind of file you wish to > read, with node pairs implying edges > intxn = read.csv (filename, header=TRUE); # the edge list is represented > as node pair > > all.nodes = unique (c (intxn$from, intxn$to)) > g <- new ('graphNEL', edgemode='directed') # at present -- soon to be > remedied -- RCy handles directed graphs best > g <- graph::addNode (all.nodes, g) > for (i in 1:nrow (intxn)) { > from.node = intxn$from [i] > to.node = intxn$to [i] > printf (sprintf ('adding edge between %s and %s', from.node, to.node)) > g <- graph::addEdge (from.node, to.node, g) > } > > # create a CytoscapeConnection object for utility functions not > restricted to a particular window > # here we will check to see if a prior attempt at your window is still > hanging around, as > # will happen in debugging, and deleting it before creating a new one > > cy <- CytoscapeConnection () > > window.title <- 'intxOutFromSkin' > if (window.title %in% as.character (getWindowList (cy))) > destroyWindow (cy, window.title) > > cw <- new.CytoscapeWindow (window.title, graph=g) > displayGraph (cw) > redraw (cw) > > # now perform manual layout, by explicit calls to setPosition > # note that this particular layout obscures some of the edges > > node.count = length (all.nodes) > x.start = -150 > y.start = -50 > x.incr = 60 > y.incr = ceiling (120/node.count) > > x.locations = seq (from=x.start, by=x.incr, length.out=node.count) > y.locations = seq (from=y.start, by=y.incr, length.out=node.count) > setPosition (cw, all.nodes, x.locations, y.locations) > > # my sample data file, nodePairs.csv > from,to > A,B > A,C > D,E > F,A > > > > > On Feb 18, 2011, at 10:50 AM, Fahim M wrote: > > > 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 > > -- Fahim Mohammad Bioinforformatics Lab University of Louisville Louisville, KY, USA Ph: +1-502-409-1167 [[alternative HTML version deleted]]