search for: reingold

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

...without node overlaps. But even with a not-so-big number of nodes (50) plotted graph has almost all nodes overlapped by neighbors vertices. The problem gets even worst if I increase vertex size. # R code require(igraph) NumOfNodes <- 10 g <- barabasi.game(NumOfNodes) g$layout <- layout.reingold.tilford(g) plot(g) NumOfNodes <- 50 g <- barabasi.game(NumOfNodes) g$layout <- layout.reingold.tilford(g) plot(g) Actually I'm using GraphViz which has an option to avoid overlaps but I can't find something similar in igraph documentation. Can someone point me to the rigth dire...

Hello all, I'm having a spot of trouble. I have made a very nice distance matrix from some comparison calculations. However, the matrix is 3096 x 3096, so it's relatively large. Currently I'm using the svn package as it seems to work for my data. The graph package errors and says the "adjacency matrix must be symmetric for undirected graphs". I though 3096 x 3096 was

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

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 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,

...racter) and I can handle it and display it fine within R using > package igraph. However, when I try to plot this network, node names > do not display in the plot. I am trying to produce a visualization of > the character network, like this: > >> plot(g, layout=layout.fruchterman.reingold, vertex.color="black", vertex.size=2.0, edge.color="gray70", vertex.label=V(g)$name, edge.arrow.size=0.3) > > where g is a an igraph network: > >> g > Vertices: 199 > Edges: 123 > Directed: TRUE > Edges: > > [0] '?' -> '?'...

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

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

...# Now make graphs and plot them: gg=graph.adjacency(wadj,mode="max") V(gg)$name = 1:50 V(gg)$label = V(gg)$name E(gg)$weight = count.multiple(gg) gg = simplify(gg) wt = 2*E(gg)$weight*E(gg)$weight par(mar=c(0, 0, 0, 0)) #c(bottom, left, top, right) l=layout.fruchterman.reingold(gg,coolexp=10) plot.igraph(gg, layout=l, vertex.color=gray(0.8), edge.width=wt, vertex.label.color='black', edge.color=gray(0.2), vertex.label.cex=1.5, vertex.size=12) ____________________________________________________________________ Thanks in ad...

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

...ated with the vertices/edges of the graph, or the graph itself. The attributes can be arbitrary R objects. - graph visualization using regular R devices, interactive visualization using Tcl/Tk, 3D visualization using RGL. - graph layout generators, the standard Kamada-Kawai and Fruchterman-Reingold algorithms are included, plus many more. - Functions for graph and subgraph isomorphism, the BLISS and the VF2 algorithms are included. - Functions for maximal network flows, minimal cuts, vertex and edge connectivity. - igraph can read and write many popular file formats used for storin...

...ated with the vertices/edges of the graph, or the graph itself. The attributes can be arbitrary R objects. - graph visualization using regular R devices, interactive visualization using Tcl/Tk, 3D visualization using RGL. - graph layout generators, the standard Kamada-Kawai and Fruchterman-Reingold algorithms are included, plus many more. - Functions for graph and subgraph isomorphism, the BLISS and the VF2 algorithms are included. - Functions for maximal network flows, minimal cuts, vertex and edge connectivity. - igraph can read and write many popular file formats used for storin...

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

**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

...ociated with the vertices/edges of the graph, or the graph itself. The attributes can be arbitrary R objects. - graph visualization using regular R devices, interactive visualization using Tcl/Tk, 3D visualization using RGL. - graph layout generators, the standard Kamada-Kawai and Fruchterman-Reingold algorithms are included, plus many more. - Functions for graph and subgraph isomorphism, the BLISS and the VF2 algorithms are included. - Functions for maximal network flows, minimal cuts, vertex and edge connectivity. - igraph can read and write many popular file formats used for storing gra...

...ociated with the vertices/edges of the graph, or the graph itself. The attributes can be arbitrary R objects. - graph visualization using regular R devices, interactive visualization using Tcl/Tk, 3D visualization using RGL. - graph layout generators, the standard Kamada-Kawai and Fruchterman-Reingold algorithms are included, plus many more. - Functions for graph and subgraph isomorphism, the BLISS and the VF2 algorithms are included. - Functions for maximal network flows, minimal cuts, vertex and edge connectivity. - igraph can read and write many popular file formats used for storing gra...

...er than what I had. Hrm. I don't know much about the algorithm graphviz uses for dot. Do you have a reference on hand? If it's simple, I'd be willing to take a whack at it. G?bor Cs?rdi-2 wrote: > > Jarrett, > > the 'igraph' package has a layout called layout.reingold.tilford that > is designed for trees, there is a slight chance that it is good enough > for you. > > Best, > Gabor > > On Wed, Apr 29, 2009 at 10:11 PM, jebyrnes <byrnes at msi.ucsb.edu> wrote: >> >> I've been using sna to work with some networks, and am...

Estimados compañeros estoy con un trabajo sobre redes pathfinder y quería saber si conocéis alguna librería o función para dada la matriz de proximidades sacar la matriz de la red pathfinder. Un cordial saludo y un mejor año 2013. Juan -- ========================================================= Juan Antonio Gil Pascual Prof. Titular de Metodología Cuantitatíva correo: jgil en edu.uned.es