Some example networks like this:

enter image description here

  • $\begingroup$ Yes, but it will take some hacking with VertexShapeFunction and EdgeShapeFunction and some information encoding in the specification of the nodes. Do you have a full specification of node types and connection rules? $\endgroup$ – Sjoerd C. de Vries Apr 22 '15 at 22:52
  • $\begingroup$ @SjoerdC.deVries basically, each rectangle represents a molecule say a protein. The circles inside are reaction points. Green arrows means protein can switch between different states. The problem is green arrows is on rectangles and black line and the other two type arrows are between circles. $\endgroup$ – LifeWorks Apr 23 '15 at 0:15
  • $\begingroup$ That's all doable. My question was more about connection logic. Do red and blue always point to purple, and black to black? What kind of nodes are possible? 1, 2, 3 circles in a green box as shown or are there more possibilities? Black and purple always in an oval and blue in a square? Please be specific as it may determine what is possible and how it needs to be specified. Additionally, do you want to use graph algorithms further on or do you simply want a pretty picture? $\endgroup$ – Sjoerd C. de Vries Apr 23 '15 at 5:46
  • $\begingroup$ @SjoerdC.deVries red and blue always point to purple ones, but black lines can connect any circles. The top and bottom oval are fixed. In the middle there are only boxes with green or grey. Green on has a green switching arrows. Grey one doesn't. (Ideally, any two or more boxes can be stick to each other, but this might make it too difficult.) if graph algorithms can be applied will be much much greater (still, I think this makes it even harder). Thanks. $\endgroup$ – LifeWorks Apr 23 '15 at 7:29
  • $\begingroup$ @SjoerdC.deVries In the middle boxes, they one or more circles. The colour of circles can be black, red, blue, purple. $\endgroup$ – LifeWorks Apr 23 '15 at 7:40

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