Hi Tamas, Many thanks to your elegant answers. Allow me first to try them before I come out more feedback.
Appreciate, Phil ___________________________________________________________ Phil Hengjun Cui Drexel University | Electrical and Computer Engineering Philadelphia, USA ___________________________________________________________ On Thu, Aug 6, 2015 at 5:24 PM, Tamas Nepusz <[email protected]> wrote: > On 08/04, Phil Cui wrote: > > (1) it gives motifs including those are the same type as g1 and also > those are > > different types from g1 according to the result from > > isomorphism_class; > It could be the case that the issue is that you *expected* igraph to do > an induced subgraph isomorphism search. For instance, consider the > following > pattern graph: > > A --> B --> C > > and the following target graph in which the pattern is being searched: > > a --> b --> c --> a > > igraph will happily return the mapping A=a, B=b, C=c as well as A=b, B=c, > C=a > and A=c, B=a, C=b because the edges A --> B and B --> C can be mapped to > some > edges of the target graph and the subgraph isomorphism algorithm does not > aim > to map _nonexistent_ connections of the pattern graph to _nonexistent_ > connections of the target graph. If you want to ensure that missing > connections > between a pair of vertices in the pattern graph are mapped to missing > connections in the target graph, you need to use *induced* subgraph > isomorphism search. > > subgraph_isomorphisms() in the R interface of igraph actually uses one of > two > algorithms behind the scenes: VF2 or LAD. The LAD algorithm supports > induced > subgraph isomorphisms, while VF2 does not, so if you want to search for > induced subgraph isomorphisms, you need to call subgraph_isomorphisms with > method="lad" and induced=T. > > > (2) there are many duplicated combinations of nodes which relates to > > the same motif; > It can probably happen if the motif is isomorphic to itself -- in such > cases, > multiple mappings may exist between the pattern and the target graph such > that > the same nodes of the target graph are mappend to the pattern but in > different > order. > > > (3) the result provided is based on the vertex name, but I prefer vertex > id. > > I tried unlist to get the ids, however, that will combine all > > everything together. > Just erase the vertex names temporarily before performing the search and > add > them back later. (There could be a better solution for the problem in the > R interface but I'm not too familiar with R). > > All the best, > T. > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help >
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