similar to: Finding a path using the Graph package

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

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

Good morning, I'm trying to draw a graph, and I'm using the following code. test.matrix<-read.table("~/Desktop/Results/testgephi.csv", header = T, sep=",") colnames(test.matrix) <- gsub("X", "", colnames(test.matrix)) #drop first column drops <- c("") test.matrix<-test.matrix[,!(names(test.matrix) %in% drops)] test.matrix

Hello, First the version info: platform powerpc-apple-darwin8.6.0 arch powerpc os darwin8.6.0 system powerpc, darwin8.6.0 status major 2 minor 3.1 year 2006 month 06 day 01 svn rev 38247 language R version.string Version 2.3.1 (2006-06-01) I have encountered some unusual behavior when trying to

This is a rather interesting, but I don't think it is a bug - it is just things that "you are not supposed to do"... you are assuming a certain evaluation order of the 4 "$" operators in " D$ABC[D$M] = D$V[D$M] " as in: temp1 <- D$M # 2nd and 4th temp2 <- D$V[temp1] # 3rd D$ABC[temp1] = temp2 # 1st What R did was this:

Hello, I'm running an algorithm for graph structural cohesion that requires a depth-first search of subgraphs of a rather large network. The algorithm will necessarily be redundant in the subgraphs it recurses to, so to speed up the process I implemented a check at each subgraph to see if it's been searched already. This algorithm is very slow, and takes days to complete on a

Hi All, After a lengthy battle just to get the package installed, I am not able to actually use Rgraphviz to generate any plots. I tried just using the sample code in the documentation (http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/rgraphviz/) and I get the following: *> > library(Rgraphviz) > test.matrix<-matrix(rep(c(0,1,0,0), 9), ncol=6, nrow=6) >

Dear all, Are there any functions in R to reverse the order of the string. smth like reverse("abc") to get "cba"? Thanks a lot. [[alternative HTML version deleted]]

Greetings all, I have two sets of data that I would like to investigate. The first is gene/genome related data given different 'cell-states'. The second set of data is relates the genes to a biological pathway. /(I think in pictures so here goes.)/ *dataframe1* gene, cell-state1, cell-state2 gene1, x1, y1 gene2, x2, y2 gene.x, ..., ... *dataframe2* pathway1, gene-x1, gene-x2, ...

Dear R-users, I'm finding for a R-package concerning graphs. Is there some kind of that package? I've a set of correlation coeffients between several variable and I wish to built a graph to link variables correlated. Many thanks. Best, Vito ===== Diventare costruttori di soluzioni "The business of the statistician is to catalyze the scientific learning process." George

Dear R Users, I am looking clique a graph technique, to identify the values from the dataset. I tried with help.search("graph") it show's the graphics related stuff Is there any package that i can use to find Clique in a dataset? Thanks in Advance JJ -- Lecturer J. Joshua Thomas KDU College Penang Campus Research Student, University Sains Malaysia [[alternative

I'm putting together an R package. I would like to show example code in the vignette, where example data files (included in the package) are used to generate an (example) output file. I read about using example data in Hadley Wickham's post ( http://r-pkgs.had.co.nz/data.html), and believe I should keep my example data as raw data, as it must be parsed to generate the output. So, I

hello, can i authenticate samba to pam and then ldap? thank you. --David Weise OIT Rider University "The real race is not on the hot, paved road, the torturous off-road course or the smooth-surface velodrome. It is in the electrochemical pathways of your mind."--Alexi Grewal

Hi, I have a CSV file where each row has at least 20 columns and some rows have up to 30 columns of data. When I use the command, Pathways<-read.table('MetaCycSample3.csv',sep=',',header=FALSE,quote='"') anything past the 21st column gets kicked down to a new row. How can I fix this? Thanks, -Nina

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 am trying to construct a social network from a data frame with rows acra numa acrb numb year expab eabo impab iabo 10 USA 2 CAN 20 1957 4017.000 0.0 3187.000 0.0 91 USA 2 CUB 40 1957 628.000 0.0 526.000 0.0 144 USA 2 HAI 41 1957 25.000 0.0 20.000 0.0 and so on. I want the network to have directed edges from node acra to node

Dear R users, I am sorry to disturb you! But I really need your help for the usage of sigPathwy. Actually, I want a sliding window analysis for possible chromosome expression pattern mining. My research microorganism is a plant pathogen, Gibberella zeae, and I first used SAS to divide locus number with 10, 20, 30, or 40 on the fungal chromosome according to their location. I really

I would like to apply network measures (such as betweenness centrality, upper boundedness, etc.) to a weighted graph with non-integer weights, defined by a euclidean distance matrix. The package sna provides the measures that I want to use, but seems only to operate on binary graphs. I have read work by Mark Newman (http://aps.arxiv.org/abs/cond-mat/0407503/), who suggests that a weighted graph

Dear all, I would like to ask your advice about a suitable computer for the following usage. I (am starting to) work with moderately big data in R: - cca 2 - 20 million rows * 100 - 1000 columns (market basket data) - mainly clustering, classification trees, association analysis (e.g. libraries rpart, cba, proxy, party) Can you recommend a sufficient computer for this volume? I am routinely

Hello, Is there a convenient way to import RDF/OWL data into R? I'm interested in importing BioPAX/SBPAX data into R to make them available for a wider audience. One exciting application would be to use pathway data to explain differential microarray measurements by identifying upstream nodes that are likely involved in causing the differences. This could also be used to validate