[igraph] using colors when counting isomorphisms (also indexing)

[Jason Cory Brunson]

The use of colors with the graph-isomorphism functions seems inconsistent and 
problematic. I am sorry if this is old news; i do not see this topic in the 
help archives.

My understanding is that when both graphs have specified vertex colors (for 
instance), the isomorphisms tallied are restricted only by having each vertex 
map to a vertex of the same color. Hence, this makes sense:

g1 <- graph.ring(4)
g2 <- graph.ring(4)
V(g1)$color <- rep(1, length = vcount(g1))
V(g2)$color <- rep(2, length = vcount(g2))
graph.count.isomorphisms.vf2(g1, g2)
[1] 0
graph.count.isomorphisms.vf2(g1, g2, vertex.color1 = NULL, vertex.color2 = NULL)
[2] 8

However, this example (simplified from those in the documentation) is 
problematic:

V(g1)$color <- rep(1:2, length = vcount(g1))
V(g2)$color <- rep(1:2, length = vcount(g2))
graph.count.isomorphisms.vf2(g1, g2)
[1] 2

It seems to me that there should be four isomorphisms: two mapping node 1 to 
node 1 and two mapping node 1 to node 3.

Any help reconciling this issue would be greatly appreciated!

Also, the indices of the vertices returned by graph.get.isomorphisms are 1 less 
than they should be (possibly a relic of previous versions when graphs begin 
with vertex 0?):

graph.get.isomorphisms.vf2(g1, g2)
[[1]]
[1] 0 1 2 3

[[2]]
[1] 2 1 0 3

Cory Brunson