This fixed my problem of events being processed by the Cytoscape.js visualization even though I had a modal dialog box opened but I'm sure there is a better way and that I'm missing something.
//Hide the cytoscape.js visualization
NodeRightClickPopUp.prototype.hideVisualization = function(){
$("#visualization").hide();
};
//Show the cytoscape visualization and pan by 0,0 so the visualization is actually visible
NodeRightClickPopUp.prototype.showVisualization = function(){
$("#visualization").show();
var cy = $("#visualization").cytoscape("get");
cy.panBy({x:0, y:0});
};
R.