Use this if you are using igraph from R
permute {igraph}  R Documentation 
Create a new graph, by permuting vertex ids.
permute(graph, permutation)
graph 
The input graph, it can directed or undirected. 
permutation 
A numeric vector giving the permutation to apply. The
first element is the new id of vertex 1, etc. Every number between one and

This function creates a new graph from the input graph by permuting its
vertices according to the specified mapping. Call this function with the
output of canonical_permutation
to create the canonical form
of a graph.
permute
keeps all graph, vertex and edge attributes of the graph.
A new graph object.
Gabor Csardi csardi.gabor@gmail.com
# Random permutation of a random graph
g < sample_gnm(20, 50)
g2 < permute(g, sample(vcount(g)))
graph.isomorphic(g, g2)
# Permutation keeps all attributes
g$name < "Random graph, Gnm, 20, 50"
V(g)$name < letters[1:vcount(g)]
E(g)$weight < sample(1:5, ecount(g), replace=TRUE)
g2 < permute(g, sample(vcount(g)))
graph.isomorphic(g, g2)
g2$name
V(g2)$name
E(g2)$weight
all(sort(E(g2)$weight) == sort(E(g)$weight))