similar to: graph or svn

Hello I am a relatively new user of R and am struggling to use the 'network' package. I have a correlation matrix (produced using 'cor'), and want to draw a network where each item showing correlation above a threshold (say 0.5) is joined by a green line, and each item showing correlation below a threshold (say -0.5) is joined by a red line. Does anyone have any hints of how to

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

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

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

I am using 'igraph' package to make some graphs of 'gene-gene interaction'. I can get a data.frame which has three columns. gene1 gene2 pvalue AGT MLR 1.2e-04 MLR 11BHSD1 1.71e-05 IFG2 11BHSD2 2.2e-07 . . . . . . . . . AGTR1 NPPA

Dear R users, I am trying to draw a network using igraph package. I intend to place the hub nodes (the ones with the relatively more connection with other nodes) in the center of the graph. Also, the graph need to be in the fashion that the higher the correlation between two nodes is , the closer the two nodes will be. Is there any layout that can help or any other way to do this? Thanks in

Hi R users, I am using built-in functions in igraph package to draw networks . I need to compare several network with exactly the same structure but with edge hightlighted differently. I am wondering if there is a way to save the layout so that every graph will look the same as each other except for the colors of edges. Or is there any parameter I can set for this purpose?? Thanks in advance,

I'm new to R and igraph and I was wondering if anybody can help me with the following. I want to find the edge weight between two vertices in a graph. My graph structure is defined by the normal ego (node1), alter (node2) and the weight of the edge between them. I know that I can get the weight for each of the edges in the list of edges that originate from node number 5 using

I am getting some unexpected results from some functions of igraph and it is possible that I am misinterpreting the vertex numbers. Eg., the max betweenness measure seems to be from a vertex that is not connected to a single other vertex. Below if my code snippet: require(igraph) my.graph <- graph.adjacency(adjmatrix = my.adj.matrix, mode=c("undirected")) most.between.vert <-

Hello R experts, I went through R mailing,Nabble R.I could not find solution.Can someone help me. I have undirected Graph. Here is an example of spreadsheet I have( Unique 3559 Nodes) snippet of 4 rows. Node1 Node2 Weights 1 2 5 2 3 30 2 4 30 1 4 5 3 4 30 1 3 2 I created a program reading the csv and created a Adjacency matrix.From the adjacency matrix I created graph.I am not sure the

**Hi, I wanted to create a network of drugs that are being studied together. So, I created a file as a graph. But plot of my network is not corect! It looks like to me that something else is lying behind this network links created. Could someone help me with this? Thanx! a<-read.graph(file=file.choose(), format="edgelist") plot.igraph(a) File (number present ID of drug): 15 2 10

Hello, I am working with graph and adjacency matrix, the package 'graph' seems to be appropriate for this. An example in the package > mat <- rbind(c(0, 0, 1, 1), + c(0, 0, 1, 1), + c(1, 1, 0, 1), + c(1, 1, 1, 0)) > rownames(mat) <- colnames(mat) <- letters[1:4] > graph1 <- new("graphAM", adjMat=mat) > graph1 A

Hi all, I'm very new to R and read a few tutorials, however I'm having difficulty trying to figure out how to plot a minimum spanning tree. I have a csv file that contains an n-by-n matrix of distances between strains of bacteria called matrix.csv. Looks like: id,strain1, strain2,strain3 strain1,0,.2,.8 strain2,.3,0,.7 strain3,.4,.6,0 I've been messing around with some information

Hi, I have a data set consisting of the x and y coordinate locations of 1600 points. I would like to generate a graph using the functions in igraph. However the graph making functions in igraph requires the data to be in the form of an adjacency matrix. I'd like some advice on how to convert my point pattern to an adjacency matrix or functions out there that would do it directly. I've

Estimados, estoy ?jugando? con unos datos clínicos donde realizo un análisis de redes, utilicé igraph como nerwork, pero finalmente uso igraph (creo que tiene más opciónes). Son algo de 200 nodos y algo más de 2000 relaciones. Puedo graficarlos. Los datos están de la siguiente forma, por ejemplo, individuo, patología, (las dos primeras columnas son la relación), luego un fármaco, el grupo

Dear all, I'm having some problems getting my recursive function to work. At first I though that maybe my data was too big and I increase option(expressions=50000). Then I thought that I would try it on some smaller data. Still not working. :( I would have thought there should be a function for this already, so any suggestions are welcomed for other methods. I did try igraph but couldn't

I've been using sna to work with some networks, and am trying to visualize them easily. My networks are hierarchical (food webs). All of the layout engines I've tried with gplot don't seem to plot hierarchical networks, as one would using dot from graphviz. While I could do all of this by outputting to dotfiles and running it through graphviz, the graphics I get from R are much

Estimados Copio un mensaje de error que da igraph, es más fácil verlo que explicarlo. > fastgreedy.community(udatos) Error in .Call("R_igraph_community_fastgreedy", graph, as.logical(merges), : At fast_community.c:553 : fast-greedy community finding works only on graphs without multiple edges, Invalid value > cluster_louvain(udatos) IGRAPH clustering multi level, groups: 7,

Hi, I am plotting a graph with kamada.kawai layout. But I am getting direction arrows in the graphs. Please let me know how to avoid this. g <- watts.strogatz.game(1, 2000, 5, 0.4) comps <- clusters(g)$membership colbar <- rainbow(max(comps)+1) V(g)$color <- colbar[comps+1] png(filename) plot(g, layout=layout.kamada.kawai, vertex.size=2, vertex.label=NA) dev.off() Please find

Hi R-users, I'm using igraph for an undirected graph. i used clusters() igraph function to know the component size(subgraphs) as shown bellow: c <-clusters(g)    # component sizes size <- sort(c$csize, decreasing=TRUE) cat("Top 20 cluster of the graph","\n") for (i in 1:20) {   cat(i,"  size:",size[i] ,"\n") } Can anyone help how to extract the