I have a fairly sparse adjacency matrix for which I can draw the graph. Right now, two nodes $i$ and $j$ are connected, or not ($w_{ij} \in \{0,1\}$). However, I have come up with a way to define new connections between previously unconnected vertices, and assign some value $0\le w_{ij}\le 1$ to these new edges. I want the resulting graph to be drawn with these new edges taken into account as far as the layout is concerned (i.e. the spring-electrical-embedding algorithm should include these edges). I do not, however, want these edges to be drawn visually.

The only solution I can come up with myself is to calculate the node-coordinates first, then cross-reference them with the adjacency-matrix and only draw the vertices in some sort of scatterplot. This seems a little inefficient and overcomplicated though... Any shortcuts?

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4 Answers 4


If somehow you don't like @belisarius's answer (it is very neat, there's no reason not to use it!), you can also get the vertex coordinates from the complete graph and force them on the original graph.

Stealing some of his answer's definitions:

g = AdjacencyGraph@Ceiling@newAdjM
PropertyValue[{g, #}, VertexCoordinates] & /@ VertexList[g]
AdjacencyGraph[adjM, VertexCoordinates -> %];
GraphicsRow[{%, g}]

  • 1
    $\begingroup$ Your code doesn't work on my V9. Are you using v10? $\endgroup$ Commented Dec 11, 2014 at 17:16
  • $\begingroup$ Yup! 10.0 for Mac OS X x86 (64-bit) But you're right! There was a Ceiling missing! $\endgroup$
    – Aisamu
    Commented Dec 11, 2014 at 17:17
  • 1
    $\begingroup$ GraphEmbedding[g] might be better to compute coordinates. $\endgroup$
    – halmir
    Commented Dec 11, 2014 at 17:20
  • $\begingroup$ @Aisamu Thanks! I accepted this answer, because it was the first one I could understand at a glance. Man, I hate Mathematica syntax... $\endgroup$
    – JorenHeit
    Commented Dec 11, 2014 at 20:34

You could use HighlightGraph:

m = {{0, 0.5, 1}, {1, 0, 0}, {0.1, 1, 0}};

g = WeightedAdjacencyGraph[m];

   Style[e_ /; (PropertyValue[{g, e}, EdgeWeight] < 1), 

enter image description here

  • $\begingroup$ That's a neat one $\endgroup$ Commented Dec 11, 2014 at 17:18

Another way is use AdjacencyGraph with the full graph and setting the EdgeStyle so that edges smaller than 1 are not visible:

paint[adj_?MatrixQ, style_] := AdjacencyGraph[
  EdgeStyle -> (DirectedEdge @@ # -> style & /@ Position[adj, _?(0 < # < 1 &)])]

and then you can go with

adjMat = RandomInteger[{0, 1}, {10, 10}] /. 
  {0 :> If[RandomChoice[{True, False}], RandomReal[], 0]};
Manipulate[paint[adjMat, {Opacity[v], Gray}],
 {{v, 1}, 0, 1}

Mathematica graphics

  • $\begingroup$ In v9 AdjacencyGraph[] fails with non integer values on the matrix :( $\endgroup$ Commented Dec 11, 2014 at 17:21
  • $\begingroup$ @belisarius That's why I use Ceiling. Doesn't the above code work for you?? Because I tested it on V9. $\endgroup$
    – halirutan
    Commented Dec 11, 2014 at 17:22
  • $\begingroup$ Sorry, my comment was a side-note, not a complain. Bad wording. $\endgroup$ Commented Dec 11, 2014 at 17:24

(* set up the before/after adjecency matrix *)
adjM = RandomInteger[{0, 1}, {5, 5}];
twoEdges = Position[adjM, 0][[1 ;; 2]];
newAdjM = ReplacePart[adjM, Thread[Rule[twoEdges, 1/2]]];

(* function to build the new graph*)
f[aM_, col_] := Module[{edgs},
  edgs = DirectedEdge @@@  Position[newAdjM, Except[_Integer], {2}, Heads -> False];
  WeightedAdjacencyGraph[aM /. 0 -> Infinity,  EdgeStyle -> Thread[edgs -> col]]]

GraphicsRow[{AdjacencyGraph@adjM, f[newAdjM, Red], f[newAdjM, Transparent]}] // Framed

Mathematica graphics


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