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Looking at the code (with ??), J.eigenspaces() is equivalent to J.adjacency_matrix(vertices=list(J)).right_eigenspaces(), which uses another ordering of the vertices. Since the adjacency matrices are different (but similar), they produce the same eigenvalues, but different eigenspaces. You can use

sage: J.adjacency_matrix().is_similar(J.adjacency_matrix(vertices=list(J)), transformation=True)[1]

To get the change of basis between the two.

Looking at the code (with ??), J.eigenspaces() is equivalent to J.adjacency_matrix(vertices=list(J)).right_eigenspaces(), which uses another ordering of the vertices. Since the adjacency matrices are different (but similar), they produce the same eigenvalues, but different eigenspaces. You can use

sage: J.adjacency_matrix().is_similar(J.adjacency_matrix(vertices=list(J)), transformation=True)[1]

To get the change of basis between the two.

I've never worked with graph eigenspace before, is it supposed to be independent of the ordering ?