Mathematica can do layered graph drawing with LayeredGraphPlot or GraphLayout -> "LayeredEmbedding". Is it possible to specify which node goes on which layer instead of letting the system figure this out? Determining the precise location on the layer would be left to the layout algorithm.
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VertexCoordinateRules, e.g. setting the x value of nodes toAutomaticand specify ayvalue. However, this does not work with all layout methods. Another question asking from my point of view the same is https://mathematica.stackexchange.com/questions/46018/plotting-network-with-layeredgraphplot-with-specific-order. – Hotschke Sep 27 '18 at 12:37