I did not actually download your notebook. I just tested what happens with more than 999 vertices.
Now I tried your notebook and I believe there is (yet another!) bug in Mathematica's graph functionality. That is why you get the pink boxes. You should report this to Wolfram Support (please do).
VertexShapeFunction -> "Circle"
should be used in Graph
, as you have. This code works:
Graph[Range[1000], {}, VertexShapeFunction -> "Circle", VertexSize -> 1/2]
The default size seems to be too small for the vertices to be visible.
As a workaround for your case, you can use VertexShapeFunction -> (Disk[#1,#3]&)
.
This sort of styling will be much easier to do in the next version of the IGraph/M package, by chaining IGVertexMap
functions. I plan to release a preview version on the weekend that you can play with. Until then, here's a teaser:
