I need to draw a map of the core metabolism of E.coli. Associated with each reaction in the map I have a number that indicates the flux through this reaction. I want the map to reflect these fluxes through the color of each reaction in the map.

I have tried using tools like Mathematica and Cytoscape, but it is very hard to get a nice layout of the metabolic network. I have seen maps of E.coli metabolism which look very nice on paper. What I need is a map like these, but where I can define the colors of the reactions.

For example, see the image below for an example. Forget about the yellow bounding boxes delimiting compartments. I can spare those.

     ![enter image description here](https://i.stack.imgur.com/vAGU2.jpg)