How to plot Motifs in igraph?

Question

I use igraph package to get motifs in Protein-Protein interaction network, It has a vector output, But I need plot or draw of motifs, figure of motifs.

code in R:

 motifs(graph_object, size = 3)

output:

1 NA NA 5 3

How to I get plot of motifs in R and igraph? Here have we four motifs?

Note: This question is different from How to mine for motifs in R with iGraph

Possible duplicate of [How to mine for motifs in R with iGraph](http://stackoverflow.com/questions/12374534/how-to-mine-for-motifs-in-r-with-igraph) — Tad Dallas, Jun 29 '16 at 06:56
The four motifs on three nodes are the empty graph, one edge, a 2-star, and a triangle. The first two motifs are not fully connected so the counts returned are NAs. Are you asking how to plot the 2-stars and triangles with node labels? — Ryan Haunfelder, Jul 01 '16 at 14:46

score 1 · Accepted Answer · answered Jul 04 '16 at 22:42

Construct the motif that you want to search for as a "template graph" (for instance, create a triangle graph), then use subgraph_isomorphisms to find all the mappings from the vertices of the template graph from the vertices of your protein-protein interaction network, and induced_subgraph combined with lapply to transform the list of mappings into the actual motifs. Example:

> pattern <- graph.full(3)
> my.graph <- grg.game(100, 0.2)        # just an example graph, use yours
> iso <- subgraph_isomorphisms(pattern, my.graph)      # takes a while
> motifs <- lapply(iso, function (x) { induced_subgraph(my.graph, x) })

motifs will then be a list of graphs, and you can plot them one by one using plot().

Thank you. It is that thing I need. – Saeed Rahmani Jul 05 '16 at 06:13 — Saeed Rahmani, Jul 05 '16 at 06:13

How to plot Motifs in igraph?

1 Answers1