Graphviz: make invisible node take no space -


consider graph 

digraph "graph b9ca21a1-971e-400c-a7f4-cd650986476a" {     graph [ margin=10 ];     node [ shape=point ];      "invisible"  [         //height=0,         //width=0,         //margin=0,         //style=invis,         color="red"         ];      subgraph "cluster_1" {         "a";         "b";         "invisible";         "c";         "d";     }  }

resulting in

image1

i want red node invisible, taking no space, has remain there, such can used lhead/ltail other such miscellaneous things.

when uncommenting commented lines, result is

image2

as see, there still spatial artifact of node.

question: there way remove completely, without affecting other nodes' layout in graph?

you can use nodesep minimize node separation (min 0.02) , instead add invisible peripheries visible nodes in order accomplish approximately equal separation of them.

here's example of how transform approximation of first graph approximation of second:

<!doctype html>  <meta charset="utf-8">  <body>  <script src="//d3js.org/d3.v4.min.js"></script>  <script src="https://unpkg.com/viz.js@1.8.0/viz.js"></script>  <script src="https://unpkg.com/d3-graphviz@0.1.2/build/d3-graphviz.min.js"></script>  <div id="graph" style="text-align: center;"></div>  <script>    var dots = [      `  digraph "graph b9ca21a1-971e-400c-a7f4-cd650986476a" {      graph [ margin=10, nodesep=0 ];      node [ shape=point, peripheries=3, penwidth=0 ];        "invisible"  [          //height=0,          //width=0,          //margin=0,          //style=invis,          color="red"          ];        subgraph "cluster_1" {          "a";          "b";          "invisible";          "c";          "d";      }        "x" [color="blue"];      "x" -> "invisible" [headclip="false"]  }      `, `  digraph "graph b9ca21a1-971e-400c-a7f4-cd650986476a" {      graph [ margin=10, nodesep=0 ];      node [ shape=point, peripheries=3, penwidth=0 ];        "invisible"  [          peripheries=0,          height=0,          width=0,  //        margin=0,  //        style=invis,          color="red"          ];        subgraph "cluster_1" {          "a";          "b";          "invisible";          "c";          "d";      }        "x" [color="blue"];      "x" -> "invisible" [headclip="false"]  }      `  ];    var dotindex = 0;  var graphviz = d3.select("#graph").graphviz();    function render() {      var dot = dots[dotindex % dots.length];      var transition1 = d3.transition()          .delay(1000)          .duration(1000 + 4000 * dotindex);      graphviz          .tweenshapes(false)          .engine("dot")          .dot(dot)          .transition(transition1)          .render();      dotindex += 1;        transition1        .transition()          .duration(0)          .on('end', function () {              if (dotindex != dots.length) {                  render();              }          });  }    render();    </script>


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