OK, Here's a toy example (and on the latest igraph) - still not behaving as expected??
> 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))) [1] TRUE > g <- simplify(g) > mc <- maximal.cliques(g) > any(duplicated(unlist(mc))) [1] TRUE > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] reshape_0.8.4 plyr_1.8 Matrix_1.0-12 lattice_0.20-15 [5] xcms_1.37.2 Biobase_2.20.1 BiocGenerics_0.6.0 mzR_1.6.1 [9] Rcpp_0.10.4 igraph_0.6.5-2 loaded via a namespace (and not attached): [1] codetools_0.2-8 grid_3.0.0 tcltk_3.0.0 tools_3.0.0 > On 18 November 2013 15:31, Gábor Csárdi <[email protected]> wrote: > Btw. you can also try to remove multiple and loop edges if you have > any. Just a guess, maybe they are not a problem, but it's worth > trying, just call simplify() on the graph. > > G. > > On Mon, Nov 18, 2013 at 10:27 AM, Tony Larson <[email protected]> > wrote: > > Will try and work up a toy example later this afternoon, as the graph I > am > > working on is too large to post (generated from a 4000 x 4000 adjacency > > matrix). > > > > Thanks > > Tony > > > > On 18 Nov 2013 15:06, "Gábor Csárdi" <[email protected]> wrote: > >> > >> Hi! > >> > >> On Mon, Nov 18, 2013 at 10:00 AM, Tony Larson <[email protected]> > >> wrote: > >> > Hi, > >> > I am using igraph 0.6.2 on R. > >> > >> That is 0.6-2, right? Note that there is a newer version. I can't > >> recall any changes in maximal cliques, though, so it won't fix your > >> issue, probably, but it fixes other issues. > >> > >> > When I use maximal.cliques() to get a list of > >> > complete subgraphs back, several have partly duplicated values, e.g > >> > > >> > [1] 1 2 3 4 5 > >> > [2] 1 2 3 4 5 7 8 > >> > [3] 1 2 3 4 5 6 > >> > > >> > If all vertices in each listing are completely connected, then why in > >> > the > >> > example above don't I get single list entry for indices 1:8? > >> > >> If you do, then this is a bug. Can you please show us an example that > >> reproduces it? Thanks. > >> > >> Gabor > >> > >> > Why do I get > >> > 3? How can I merge these into one list item? > >> > > >> > Thanks > >> > Tony > >> > > >> > > >> > _______________________________________________ > >> > igraph-help mailing list > >> > [email protected] > >> > https://lists.nongnu.org/mailman/listinfo/igraph-help > >> > > >> > >> _______________________________________________ > >> igraph-help mailing list > >> [email protected] > >> https://lists.nongnu.org/mailman/listinfo/igraph-help > > > > > > _______________________________________________ > > igraph-help mailing list > > [email protected] > > https://lists.nongnu.org/mailman/listinfo/igraph-help > > > > _______________________________________________ > 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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