We admire the construction of this diagram. We note especially the dot language features used and the orderly construction in 25 editing steps.
digraph { rankdir=LR node [shape=box style=filled] edge [dir=none] subgraph cluster_G { subgraph cluster_A { label="Governance" node [width = 2.5, height = .5] Guardians [fillcolor=yellow] Research [fillcolor=green] Members [fillcolor=lightblue label="Member Ecosystem"] { rank=same Guardians Research Members } } subgraph cluster_P { URL="http://platform.earth" label="Platform" node [shape=square, width = .5, height = .5] { rank=same Accounting Deliberation Participation } Accounting [fillcolor=red, label=""] Deliberation [fillcolor=darkgreen, label=""] Participation [fillcolor=blue, label=""] } } Guardians -> Accounting Research -> Deliberation Members -> Participation Participation -> Deliberation -> Accounting }
digraph { rankdir=LR node [shape=box style=filled]
This much is routine
edge [dir=none]
Edges are directed thus considered in layout but not drawn with arrow heads.
subgraph cluster_G { subgraph cluster_A { ... } subgraph cluster_P { ... } }
The nested clusters organize nodes without regard for edges enumerated later.
URL="http://platform.earth" label="Platform"
Cluster properties similar to those of nodes.
node [width = 2.5, height = .5] node [shape=square, width = .5, height = .5]
Regular node shape and size specified and thus insured.
{ rank=same Guardians Research Members } { rank=same Accounting Deliberation Participation }
Brackets here create a subgraph but not a cluster. Rank choices are min, max, source, sink and same. graphviz 
One can learn something of drawing strategy by stepping through all 25 versions of this diagram captured in the journal and noting the incremental improvements.