Hmmm - I think I am misunderstanding fundamentally what maximal.cliques() is doing - I assumed there should be no overlap but of course there will be as vertices can be shared amongst cliques! What I am trying to achieve is effectively clustering by pulling out complete subgraphs, but vertices should appear uniquely in the final set of clusters. Can you suggest a way of doing this?
One thought I had was to recursively calculate the largest.cliques(), delete the associated vertices, and continue until there are no vertices left. However, I am still stuck with the problem that largest.cliques() can return more than one clique (if vector lengths are equal) and these can contain overlapping vertices, so there still has to be a choice made of which vertices to use... On 18 November 2013 17:23, Gábor Csárdi <[email protected]> wrote: > On Mon, Nov 18, 2013 at 11:57 AM, Tony Larson <[email protected]> > wrote: > > OK, > > Here's a toy example (and on the latest igraph) - still not behaving as > > expected?? > > You need to set the random seed to make this example reproducible. > > >> mat <- matrix(sample(c(0,1), 100 * 100, replace = TRUE, prob = c(0.8, > >> 0.2)), 100, 100) > >> g <- graph.adjacency(mat, mode = "undirected", weighted = TRUE, diag = > >> FALSE) > >> mc <- maximal.cliques(g) > >> any(duplicated(unlist(mc))) > > No, this is not good, you just create a long vector from all clique > vertices, and there will be duplicates if there is overlap.... you > need to check whether one is a subset of any of the others. > > G. > > [...] > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > -- *************************************** Dr. Tony R. Larson CNAP Department of Biology, Area 7 University of York Wentworth Way Heslington York YO10 5DD UK Tel: +44(0)1904 328 826 (office) Tel: +44(0)7833 471 685 (mobile) Fax: +44(0)1904 328 762 E-mail: [email protected] *************************************** Times Higher Education University of the Year 2010 Disclaimer: This email and any attachment(s) are strictly confidential and contain information intended only for the use of the individual(s) named above. If you are not the intended recipients please delete this message from your system, do not use or disclose the information in any way and notify us by return e-mail.
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