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.

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
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>> igraph-help@nongnu.org
>> https://lists.nongnu.org/mailman/listinfo/igraph-help
> 
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