Graphviz removes node from cluster

Question

I'm using dot to compile. So I have two nodes in cluster0 (MATH1036 and MATH1034). When I try to make an edge from MATH1034 to a node outside the cluster (n1), it freaks out and removes MATH1034 from cluster0.

digraph G {
    labelloc="t";
    label="";
    graph [splines=spline, nodesep=1]
  compound=true;

    subgraph cluster0{
        label="Math 1";
        MATH1034[label="MATH1034\nAlgebra"];
        MATH1036[label="MATH1036\nCalculus"];
        {rank=same;MATH1036->MATH1034;}
    }
    COMS1015[label="COMS1015\nBCO"];
    COMS1017[label="COMS1017\nALG"];
    COMS1016[label="COMS1016\nDCS"];
    COMS1018[label="COMS1018\nADS"];

    subgraph cluster1{
        label="Math 2";
        MATH2007[label="MATH2007\nMC"];
        MATH2018[label="MATH2018\nGT"];
        MATH2019[label="MATH2019\nLA"];
        STAT2XXX[label="STAT2XXX\nIntro to MS\nor\nSTAT1003\nStats 1"];
    }
    COMS2003[label="COMS2003\nAAA"];
    COMS2XXX[label="COMS2XXX\nMC"];
    COMS2002[label="COMS2002\nDBF"];
    COMS2001[label="COMS2001\nOS"];

    COMS3000[label="COMS3000\nAAI"];
    COMS3003[label="COMS3003\nFLA"];
    COMS3004[label="COMS3004\nAN"];
    COMS3002[label="COMS3002\nSE"];

    // This line will hide the formatting nodes.
    //node[shape=none,width=0,height=0, label=""];

    // THIS NEXT LINE CAUSES THE PROBLEM
    // If I remove MATH1034 from this line, things go normal.
    {rank=same;MATH1034->n1[ltail=cluster0,dir=none ]; n1->n2->n3->n4->n5[dir=none];}

    n1->COMS1015[style=dotted];
    n2->COMS1016[style=dotted];
    n4->COMS1017[style=dotted];
    n5->COMS1018[style=dotted];

    MATH1034 -> MATH2007[lhead=cluster1, ltail=cluster0];
    MATH2018 -> STAT2XXX[style=invis];
    MATH2007 -> MATH2019[style=invis];

    //edge[dir=none];
    n3->n6->n7[arrowhead=none];
    {rank=same; COMS1016->n6->COMS1017[style=invis];}
    {rank=same; COMS2001->n7[style=invis]; n7->COMS2003;}

    COMS1015 -> COMS2001;
    //{rank=same; COMS1017 -> p1 -> COMS1018;}
    //p1 -> COMS2003;
    //p1 -> COMS2XXX;
    COMS1017 -> COMS2XXX;
    COMS1017 -> COMS2001;
    COMS1017 -> COMS2003;

    COMS1018 -> COMS2003;
    COMS1018 -> COMS2XXX;
    COMS1018 -> COMS2002;

    COMS1016 -> COMS2003;
    COMS1016 -> COMS2001[weight=100,style=invis];

    MATH2007 -> COMS2001[ltail=cluster1,style=dotted]
    MATH2007 -> COMS2003[ltail=cluster1,style=dotted]


    {rank=same;COMS2XXX -> COMS2002[dir=back, style=dotted]}
    {rank=same;COMS2003 -> COMS2XXX[dir=back]}

subgraph cluster5{ 
    label="";
    {rank=same;COMS3004 -> COMS3003 -> COMS3000 ->  COMS3002[style=invis];}
}
    COMS2003 -> COMS3000[weight=1000];
    COMS1016 -> COMS3003;

    COMS2001 -> COMS3004[weight=1000];
    COMS2002 -> COMS3002[weight=1000];

    MATH2007 -> COMS3004[ltail=cluster1,lhead=cluster5];

}

The MATH modules should be next to each other and in a box.

Here is the very broken one:

Here is the correct layout, but without the edge between MATH1034 and n1:

Any help would really be appreciated I've looked everywhere and nothing seems to work.

Answer 1

The node Math1034 is in two different subgraphs which isn't allowed. dot actually emits the following warning:

Warning: MATH1034 was already in a rankset, deleted from cluster G

Warning: MATH1034 -> MATH2007: tail not inside tail cluster cluster0

Warning: MATH1034 -> n1: tail not inside tail cluster cluster0

---

The solution is to remove MATH1034 from the second cluster, and add the edge without constraining ranks:

{rank=same; n1[ltail=cluster0,dir=none ]; n1->n2->n3->n4->n5[dir=none];}
MATH1034 -> n1[constraint=false];