search for: edgemod

...gt; colnames(test.matrix)<-c("a", "b", "c", "d", "e", "f") > test.matrix a b c d e f a 0 0 0 0 0 0 b 1 0 1 0 1 0 c 0 0 0 0 0 0 d 0 1 0 1 0 1 e 0 0 0 0 0 0 f 1 0 1 0 1 0 > am.graph<-new("graphAM", adjMat=test.matrix, edgemode="directed") > am.graph A graphAM graph with directed edges Number of Nodes = 6 Number of Edges = 9 > plot(am.graph, attrs = list(node = list(fillcolor = "lightblue"), + edge = list(arrowsize=0.5))) There were 18 warnings (use warnings() t...

...top to increase every time it's run. I traced the increase in memory usage to layoutGraph() and wrote the following short function that reproduces the problem: foo <- function () { library(Rgraphviz) set.seed(123) V <- letters[1:26] M <- 1:2 g1 <- randomGraph(V, M, 0.5) edgemode(g1) <- "directed" x <- layoutGraph(g1,name="foo",layoutType="twopi", recipEdges="distinct") } I expected that any memory allocated by this function would be freed when it returns, but that's not the case. Is there something that I need to be doi...

...uot;, "r") > myEdges = list( s = list(edges = c("p", "q")), p = list(edges = c("p", "q")), q = list(edges = c("p", "r")), r = list(edges = c("s"))) > g = new("graphNEL", nodes = myNodes, edgeL = myEdges, edgemode = "directed") > plot(g) but how about weights? Thanx. [[alternative HTML version deleted]]

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 ------------------- 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) nEl...

...s(test.matrix) <- gsub("X", "", colnames(test.matrix)) #drop first column drops <- c("") test.matrix<-test.matrix[,!(names(test.matrix) %in% drops)] test.matrix test.matrix<-data.matrix(test.matrix) am.graph<-new("graphAM", adjMat=test.matrix, edgemode="directed") am.graph plot(am.graph, attrs = list(node = list(fillcolor = "lightblue"),edge = list(arrowsize=0.5))) The file testgephi.csv is following. "","1","2","3","4","5" "1",393,55,66,44,88 "2&quo...

...for ?nodes? graph.wgtMatrix: no visible global function definition for ?edgeDataDefaults? graph.wgtMatrix: no visible global function definition for ?edgeData? Tsp2grNEL: no visible global function definition for ?ftM2graphNEL? coerce,graphAM-sparseMatrix: no visible global function definition for ?edgemode? coerce,graphNEL-TsparseMatrix: no visible global function definition for ?nodes? coerce,graphNEL-TsparseMatrix: no visible global function definition for ?edgemode? coerce,graphNEL-TsparseMatrix: no visible global function definition for ?edgeWeights? Logic,ltCMatrix-ltCMatrix: no visible global...

HI friends, I have very lengthy graph data in edge list format. I want to convert it into node list format. example: EDGE LIST FORMAT 1 2 1 3 1 4 1 5 2 3 2 4 3 2 4 1 4 3 4 5 5 2 5 4 ITS NODE LIST FORMAT SHOULD BE LIKE: 1 2 3 4 5 2 3 4 3 2 4 1 3 5 2 4 Kindly suggest me which package in R provides the support to do my task. Thank u friends in advance. -- View this message in context:

Hello there, I am using the igraph package to build graphs from my data. If I plot a graph though, it's not easy for me to see what's going on. Does anybody know how to rearrange a graph to get a plot without too many crossing lines? Maybe other packages? Thanks a lot in advance for any pointers, -- D --------------------------------- [[alternative

Hello, I apologise if someone has already answered this but I searched and googled but didn't find anything. I have a matrix which gives me the similarity of each item to each other. I would like to turn this matrix into something like what they have in the graph package with the nodes and edges. http://cran.r-project.org/doc/packages/graph.pdf . However I cannot find a method to

...DE LIST FORMAT SHOULD BE LIKE: > 1 2 3 4 5 > 2 3 4 > 3 2 > 4 1 3 > 5 2 4 > > Kindly suggest me which package in R provides the support to do my task. How long the list of egdes is? For not too large lists, consider also library(graph) G <- new("graphNEL", edgemode="directed") G <- addNode(as.character(1:5), G) edges <- read.table(file=stdin(), colClasses="character") 1 2 1 3 1 4 1 5 2 3 2 4 3 2 4 1 4 3 4 5 5 2 5 4 G <- addEdge(from=edges[, 1], to=edges[, 2], G) edgeL(G) $`1` $`1`$edges [1] 2 3 4 5 $`2`...