search for: graphnel

Hello everyone, Im working with graphNEL object and want to extract all the nodes which have adjacent nodes with at least 20 nodes in between them. acc(graph, graphnodes) obviously provides a list for the accessable nodes of every node from a node and a number of the edges between them. Like this: $`hsa:8379` hsa:100131844 hsa:103...

...[ncmr0202][/gpfs1/home/shivali/gang/R-3.1.1/bin/package]> /gpfs1/home/shivali/gang/R-3.1.1/bin/R CMD INSTALL Matrix the package compiled successfully but while loading Matrix package the installation hanged up - in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL" in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL" Creating a generic function for 'format' from package 'base' in package '...

Full_Name: Christian Kuehnert Version: 2.7.1 OS: Windows XP Submission from: (NULL) (91.14.237.109) Hello, I've installed the package RBGL (and XML and Rgraphviz) and tried to follow the examples in the RBGL-manual http://bioconductor.org/packages/2.2/bioc/vignettes/RBGL/inst/doc/RBGL.pdf But when I try to plot the graph using e.g. plot(dijk) an error message occurs: "Error in

The package 'graph' defines classes graph and graphNEL (extending graph) and a union,graph,graph-method. These are all exported and fully documented. The package 'GSEABase' Imports: graph and importClassesFrom(graph, graphNEL). GSEABase defines methods on union for its own classes (not graph / graphNEL), and has exportMethods(union). union,gra...

...graph" in the BioConductor assortment and writing some functions based on its classes. My question is not specific to this package or BioConductor (I think), but it serves as a useful example. I recently wanted to look at the code for the function "edgeMatrix" for the class "graphNEL". Usually I would type > func.foo and the code for the function func for class foo would appear (where func and foo are edgeMatrix and graphNEL respectively). Similarly I would type > methods(func) to see for what classes the function func is defined. However, these do not work for...

Dear useRs I have uploaded a new package, gRain, for propability propagation in graphical independence networks; sometimes also called probabilistic expertsystems and Bayesian networks. Regards S?ren H?jsgaard _______________________________________________ R-packages mailing list R-packages at r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages

Dear useRs I have uploaded a new package, gRain, for propability propagation in graphical independence networks; sometimes also called probabilistic expertsystems and Bayesian networks. Regards S?ren H?jsgaard _______________________________________________ R-packages mailing list R-packages at r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages

...bugs and memory leaks were fixed, see the News section on the igraph homepage for details. NEW FEATURES IN THE 0.5.1 VERSION - DrL layout generator was added, see ?layout.drl. - Uniform sampling of graphs with a given degree sequence, see ?degree.sequence.game. - Conversion functions to/from graphNEL objects (graph package), see ?igraph.to.graphNEL and ?igraph.from.graphNEL. - Conversion functions to/from sparse matrices (Matrix package), see ?graph.adjacency and the 'sparse' argument of ?get.adjacency. - Creating graphs from adjacency lists, see ?graph.adjlist. - The function gra...

...bugs and memory leaks were fixed, see the News section on the igraph homepage for details. NEW FEATURES IN THE 0.5.1 VERSION - DrL layout generator was added, see ?layout.drl. - Uniform sampling of graphs with a given degree sequence, see ?degree.sequence.game. - Conversion functions to/from graphNEL objects (graph package), see ?igraph.to.graphNEL and ?igraph.from.graphNEL. - Conversion functions to/from sparse matrices (Matrix package), see ?graph.adjacency and the 'sparse' argument of ?get.adjacency. - Creating graphs from adjacency lists, see ?graph.adjlist. - The function gra...

...definition for ?numEdges? graph.wgtMatrix: no visible global function definition 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 fu...

The bulk is on my forums - the final post for today is: Results to date: A. It looks like I am going to need a newer compiler for C - xlc/xlC V11 apparently does not understand this code: "/data/prj/cran/R-3.2.3/src/main/memory.c", line 2149.31: 1506-046 (S) Syntax error. I will have to check if R-devel has different code before asking for assistence. +2139 #ifdef

...yNodes = c("s", "p", "q", "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,...

Hi, I have network data in the form of a couple of edgelists containing weights in the format "x,y,weight" whereby x represents row header and y represents column header. All edgelists are based on links among 634 nodes and I need to convert them into a 634*634 weighted matrix. I searched for online help using possible keywords I know, but I could not find a clue how to do this in

...edL <- vector("list", length=length(V)) names(edL) <- V for (i in 1:length(Eidx)){ tmp <- Eidx[[i]] print(tmp) edL[[tmp[1]]]$edges <- c(edL[[tmp[1]]]$edges, tmp[2]) edL[[tmp[2]]]$edges <- c(edL[[tmp[2]]]$edges, tmp[1]) } G <- new("graphNEL", nodes=V, edgeL=edL) nAttrs <- list() nAttrs$fillcolor <- c("red","red","blue","blue") names(nAttrs$fillcolor) <- V plot(G, "neato",nodeAttrs=nAttrs)

...ges: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Rgraphviz_1.21.7 graph_1.21.3 loaded via a namespace (and not attached): [1] cluster_1.11.12 tools_2.9.0 > I then define a graph using the following G = new("graphNEL", nodes = c("A","B","C")) plot(G) And RUI.exe crashes... Any help would be most appreciated. Thanks, Fraser

Hey, all. I'm looking for packages that are good at two things 1) Drawing directed graphs (i.e nodes and edges), both with single and double headed arrows, as well as allowing for differences in line width and solid versus dashed. Note: I've tried Rgraphviz here, but have run into some problems (which seem fixable and I may go with it in the end), and it doesn't satisfy need

...edL <- vector("list", length=length(V)) names(edL) <- V for (i in 1:length(Eidx)){ tmp <- Eidx[[i]] print(tmp) edL[[tmp[1]]]$edges <- c(edL[[tmp[1]]]$edges, tmp[2]) edL[[tmp[2]]]$edges <- c(edL[[tmp[2]]]$edges, tmp[1]) } G <- new("graphNEL", nodes=V, edgeL=edL) nAttrs <- list() nAttrs$fillcolor <- c("red","red","blue","blue") names(nAttrs$fillcolor) <- V eAttrs <- list(color = c("A~B" = "green", "B~C" = "green", "C~D&quo...

Hi all! I¹m just implementing the Ullmann¹s algorithm for searching subgraph isomorphisms in graphNEL objects. The algorithm is running with smaller graphs, but when I¹m calling it i get an R error message saying that functions are nested too deeply in source code. I found out that the problem is in the so called refinement procedure of the algorithm which consists of 10 different functions, return...

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: