On Fri, Dec 12, 2008 at 2:10 AM, dinesh kumar <baru...@gmail.com> wrote: > Dear R users > > I have a similarity matrix 100X100. I used this matrix as adjacency matrix > to generate igraph graph object. Its a fully connected graph. The similarity > score is the weight of the edge. Now I want to remove all possible lowest > scores (edges) but I want to get back a fully connected graph (dont want any > isolated vertex).How can I do it?
Actually your matrix is only 87x87. If you mean that you want a graph with 87 vertices, and some edge weights being zero, then you can simply do (assuming there are no negative edge weights) G <- graph.adjacency(adjmat+1, mode="undirected", weighted=TRUE) E(G)$weight <- E(G)$weight - 1 If you mean that you want to remove isolate vertices after creating the graph, that would be: G <- graph.adjacency(adjmat, mode="undirected", weighted=TRUE) G <- remove.vertices(G, V(G)[ degree(G)==0 ]) (For your data nothing really happens, there are no isolate vertices.) > Also is there any possibility that I can remove the edges which dont pass a > threshold (below 70% similarity score). You can remove it initially, from the matrix: adjmat2 <- adjmat adjmat2[ adjmat2 < 0.7 ] <- 0 G <- graph.adjacency(adjmat2, mode="undirected", weighted=TRUE) or after, from the graph itself: G <- graph.adjacency(adjmat+1, mode="undirected", weighted=TRUE) E(G)$weight <- E(G)$weight - 1 G2 <- delete.edges(G, E(G)[ weight < 0.7 ]) Gabor ps. there is also an igraph mailing list, you can find it from the igraph homepage. Just in case I miss your messages here. > I attached the similarity matrix. > > I would appreciate the reply > > Thanks in advance > > Dinesh > > > > -- > Dinesh Kumar Barupal > Junior Specialist > Metabolomics Fiehn Lab > UCD Genome Center > 451 East Health Science Drive > GBSF Builidng > University of California > DAVIS > 95616 > http://fiehnlab.ucdavis.edu/staff/kumar > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- Gabor Csardi <gabor.csa...@unil.ch> UNIL DGM ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
