# Re: [igraph] motifs

```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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