Are "Reversible" and "Weighted" arrows mutually exclusive?

[man-shu]

I was trying to add the fluxes to the reactions by adding the "solution" dictionary to the "flux_dict" parameter. I did get the weighted links, but lost all the reversible links (with arrows on both sides). The cobrapy model and the .json file for the representation still have the "reversibility" property as "true", though. So, is there any workaround?

[pstjohn]

The way the code's currently written it would be mutually exclusive. Otherwise it would be tough to indicate which way the flux was flowing if you had arrowheads in both directions. I think some papers use different sized arrowheads to indicate direction and reversibility, which is something I could look into.

If you knew a bit of javascript, you're welcome to send in a PR :)
the relevant code would be here

d3flux/d3flux/templates/d3flux.js

Lines 481 to 503 in 24430e9

	svg.append("defs").selectAll("marker")
	.data(reactions)
	.enter()
	.append("marker")
	.attr("id", function (d) { return "{{ figure_id }}" + d.id + "_rev"; })
	.attr("viewBox", "0 0 10 10")
	.attr("refX", 9)
	.attr("refY", 5)
	.attr("markerUnits", "userSpaceOnUse")
	.attr("markerWidth", "7pt")
	.attr("markerHeight", "7pt")
	.attr("orient", "auto")
	.attr("class", function (d) {
	var labels = "startmarker"
	if ('flux' in d.notes.map_info) {
	if (d.notes.map_info.flux == 0) {
	labels = labels.concat(" inactive");
	}
	}
	return labels;
	})
	.append("path")
	.attr("d", "M 10,10 0,5 10,0 Z");

dummy arrowheads get added everywhere, and then I selectively show them based on some logic here

d3flux/d3flux/templates/d3flux.js

Lines 203 to 206 in 24430e9

	function plot_reverse_arrowhead(rxn) {
	return (((Math.abs(rxn.notes.map_info.flux) < 1E-8) || isNaN(rxn.notes.map_info.flux))
	&& rxn.notes.map_info.reversibility);
	}

You'd probably need to code in some logic about scaling the reverse arrowheads to be some fraction of the forward direction's size? That would involve changing how the markers are scaled, since I do them all at once here. Not sure why I don't just scale them in the code above when they're created...

d3flux/d3flux/templates/d3flux.js

Lines 792 to 796 in 24430e9

	svg.selectAll("marker")
	.attr("markerWidth", markerscale)
	.attr("markerHeight", markerscale)
	.select("path")
	.attr("fill", get_flux_stroke);