Hi Tamas! Thank you very much for your reply. Actually, it makes sense to me on the use of connected subgraphs as motifs, in the sense that an isolated vertex doesn’t play a important role in the subgraph structure.

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On the other hand, motifs() returns a vector with the number of occurences of each motif in the graph ordered by their isomorphism class. How do I know which isomorphism class are present in my graph. I mean, a possible result of motifs(graph, size =3) could be something like this: > NA NA 32 18 For me, this means that there are 32 motifs of x-isomorphic class and other 18 motifs of y-isomorphic class. But, which classes? I’ve playing with something like this to explore how all possible isomorphic classes (n = 3) look like: iso <- vector(mode = "list", length = 3) iso.class <- 1:length(iso) for(i in 1:length(iso)){ iso[[i]] <- graph_from_isomorphism_class(3, i, directed = FALSE) iso[[i]]$name <- paste("Class", iso.class[i]) } par(mfrow = c(1,3)) for(i in 1:length(iso)){ plot(iso[[i]], layout = layout_in_circle(iso[[i]]), main = iso[[i]]$name) } But How do I know which of them are present in the original graph? Thank you very much! Manuel > El 14/10/2016, a las 02:31, Tamas Nepusz <nta...@rmki.kfki.hu> escribió: > > Hi! > > I haven't read the papers once again, but in my opinion a disconnected > motif doesn't really make sense. Consider a disconnected motif that > consists of a fully connected triangle and an additional isolated > vertex, and then take a graph that contains one triangle and one > million isolated vertices. Does that really mean that this "motif" > appears one million times in the graph? Is that a significant finding? > If I added an additional one million totally unrelated vertices to the > graph, does that make the motif appear twice as frequently? > > Anyway, if you want to search for disconnected patterns in a graph, > you can still use count_subgaph_isomorphisms() with method="lad" and > induced=TRUE; see: > > http://igraph.org/r/doc/count_subgraph_isomorphisms.html > > It will be much slower, though -- searching for connected motifs is > much easier if the average degree of a vertex is low. > > T. > > > On Fri, Oct 14, 2016 at 8:59 AM, Manuel Zetina-Rejon <mjzet...@gmail.com> > wrote: >> Hi Guys! >> >> This is probably a basic question, but I don’t find the clear criteria or >> reference, why in igraph help, you mention that unconnected subgraphs (of x >> isomorphic class) are not considered motifs? For that reason, motifs() is NA >> for unconnected subgraphs. It is also not clear if you mean strongly or >> weakly connected subgraphs >> >> According to Milo et al. (2002) and Shen-Orr et al. (2002) motifs are not >> necessarily connected, even in directed graphs. >> >> Thank you for your opinions >> >> >> Manuel >> _______________________________________________ >> igraph-help mailing list >> igraph-help@nongnu.org >> https://lists.nongnu.org/mailman/listinfo/igraph-help > > _______________________________________________ > igraph-help mailing list > igraph-help@nongnu.org > https://lists.nongnu.org/mailman/listinfo/igraph-help

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