similar to: Questons about 'igraph' package

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-help, I create a graph of my baysian network. I use the package igraph. The names of vertex are within the circle, I would leave them outside the circle? > E(g)$color <- "black" > tkplot(g, ,vertex.label=names,layout=layout.kamada.kawai, edge.color=E(g)$color) Best Regards [[alternative HTML version deleted]]

I have a number of (directed) graphs based on social groups, where the members have expresed likes and dislikes in respect to the other members. tkgraph makes it simple to draw the graphs in a very pleasing way, but I would like to differentiate between positive and negative relations in the graph by having the edges for the negative relations dashed and the positive ones continuous. Is

Hello R users, I'm trying to extract random samples from a big array I have. I have a data frame of over 40k lines and would like to produce around 50 random sample of around 200 lines each from this array. this is the matrix ID xxx_1c xxx__2c xxx__3c xxx__4c xxx__5T xxx__6T xxx__7T xxx__8T yyy_1c yyy_1c _2c 1 A_512 2.150295 2.681759 2.177138 2.142790 2.115344 2.013047

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

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

igraph is a package for graphs/networks. It has a C core and uses a simple and fast graph representation allowing millions of vertices and edges. LINKS Release notes for the 0.5.2 version: http://igraph.sourceforge.net/relnotes-0.5.2.html Release notes for the 0.5.1 version: http://igraph.sourceforge.net/relnotes-0.5.1.html Complete list of changes: http://igraph.sourceforge.net/news.html The

igraph is a package for graphs/networks. It has a C core and uses a simple and fast graph representation allowing millions of vertices and edges. LINKS Release notes for the 0.5.2 version: http://igraph.sourceforge.net/relnotes-0.5.2.html Release notes for the 0.5.1 version: http://igraph.sourceforge.net/relnotes-0.5.1.html Complete list of changes: http://igraph.sourceforge.net/news.html The

Dear All: I tried to use heatmap.2 to generate hierarchical clustering using the following command: heatmap.2(datamatrix, scale="row", trace="none", col=greenred(256), labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE) datamatrix is subset of a RMA normalized data subset by a genelist. The problem is a lot of times, the z-score in key are from, like -5 to 15 or

Dear sir/madam, I have been using R for a while now for microarray analysis, and I would like to make a "master" data frame in which I can combine information from many different sources. The basic list a genelist with 25.000 probes, then I would like to have a subcompartment with the statistical information, a subcompartment with more extensive information regarding each gene, and then

Dear r-helpers, I wonder if you can figure out why the following is working: ******************************************************************** > sessionInfo() Version 2.3.1 (2006-06-01) powerpc-apple-darwin8.6.0 attached base packages: [1] "tcltk" "methods" "stats" "graphics" "grDevices" "utils"

Hallo, > fit12<-lmFit(qrg[,1:2]) > t12<-toptable(fit12,adjust="fdr",number=25,genelist=qrg$genes[,1]) > t12 ID logFC t P.Value adj.P.Val B 522 PLAU_OP -6.836144 -8.420414 5.589416e-05 0.01212520 2.054965 1555 CD44_WIZ -6.569622 -8.227938 6.510169e-05 0.01212520 1.944046 Can anyone tell me what the difference is between P.Value

I am having trouble converting the output from Sweave into a valid PDF file. I have created a simple .Rnw file which will become a full vignette at some point, but during the intermediate testing, I got errors from texi2dvi. This is what I have done. 0) Using a Windows Xp system 1) Created a file called GeneSpring.Rnw 2) Convert this to Tex using Sweave("GeneSpring.Rnw") from within R

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, 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

I am having trouble plotting one of my graphs (think graph theory graph with edges and vertices, not scatterplots or histograms). For some pairs of vertices, I want multiple edges to be visible in my graph. As an example of this, in my script below, I want two edges to be visible from vertex 1 and vertex 9 (among some others) yet when I plot it, only one edge is visible.

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

I realize that matrix indexing has been addressed in various flavors, but I''m stumped and didn''t find anything in the archives. It''s not clear if it is an igraph issue or a more general problem. Thanks in advance for your patience. I am using igraph to read a gml file (http://www-personal.umich.edu/~mejn/netdata/football.zip ). The gml file contains vertex attributes

Dear R users, I'am using marray and Limma packages to analyze genepix output. 1) how can I filter bad spots from my data (data contains 3 types of bad spots). my experiment contains 12 samples and the bad spot are not associated to the same probes 2) how can I remove control probes from my data ? I'm sorry, i'm new with R and I can't find answer in packages doc. best regards,

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,