How are the different pathway layout options calculated and what do they represent?

Pathway Studio comes equipped with multiple layout options: (Cellular) Localization, DirectForce, Hierarchical and Symmetrical. Select Layout on the pathway pane tool bar to see the menu.

Symmetrical Layout- The twopi algorithm chooses one entity at the center and puts at the origin. The remaining entities are placed on a sequence of concentric circles centered about the central entity, each a fixed radial distance from the previous circle. All entities with a distance 1 from the center are placed on the first circle; all entities with a distance of 1 from an entity on the first circle are placed on the second circle.  The process is repeated until all entities in the pathway are represented in circles.

Hierarchical Layout uses the dot algorithm and draws a graph in four main phases. The layout procedure used by dot relies on the graph being acyclic. Thus, the first step is to break any cycles, which occur, in the input graph by reversing the internal direction of certain cyclic edges. The next step assigns entities to discrete ranks or levels. In a top to bottom drawing, ranks determine Y coordinates. Edges that span more than one rank are broken into chains of virtual entities and unit length edges. The third step orders entities within ranks to avoid crossings. The fourth step sets X coordinates of entities to keep edges short, and the final step routes edge spines. 

Direct Force Layout – the neato algorithm considers links and relations as a spring and entities as poles with the same charge that are repulsed from one another.  The spring power can be regulated independently for every relation type. By default, the spring power of the binding relation is higher than for others, causing entities that bind each other to be closer on the graph, compared with other relations. The repulsion force between the entities is regulated by Polarization in the Start Layout dialog box. 

Dynamic Layout is the old Pathway Studio algorithm. It is essentially modified Direct Force algorithm that now can arrange entities by their localization in a cell.  A localization of an entity can be set by the right click menu Localization in Pathway.

The Layout by Localization places entities in relation to cellular components (extracellular, membrane, cytoplasm, golgi, nuclease, mitochondria, cholorplast).  The localization is determined by Gene Ontology assignment.  Note: an entity may have two or more Gene Ontology localization terms associated with it.  In this case, Pathway Studio will choose only one of the localization terms to use in the pathway display.