General preferences are organized into three categories: How the species are laid out in the diagram, how the reaction connections are assembled in the diagram, and how the compositions of associated bar charts are organized.

This group of controls alters the layout and dimensions of the Reaction Path Diagram. Controls are available for setting the layout manager, the zoom, font size, and borders on species.

The layout manager dictates the method used to determine the position of the species in the Reaction Path Diagram. This fundamental layout technique alters the format of the display, and can either improve or hamper the visualization of reaction paths, depending on the chemistry and results of the model. There are two options for layout handling, either the Tree Method or the Hierarchical Method.

The Tree layout uses a generated ancestor tree to determine the primary layout of the diagram panel. Each child is determined by a positive ROP leading from a chosen species to another species. The layout of the panel is chosen so that the progeny that can be reached by one species is maximized. In the ancestor tree layout, all depleting pathways exit from the bottom of a species, and all formation pathways enter at the top of a species.

GraphViz [1] is open-source graph visualization software. The program used by the Reaction Path Diagram for this type of layout is Dot. The Dot executable makes hierarchical, or layered drawings of directed graphs. The layout algorithm aims edges in the same direction (top to bottom, or left to right) and then attempts to avoid edge crossings and reduce edge length. GraphViz is open source, CPL-licensed software. It may be redistributed, without cost, and in other software distributions, as long as the license terms are met. The Reaction Path Analyzer assumes that the Dot executable is accessible on the path. If that is not the case, then add the GraphViz bin directory to your path environment variable.

The zoom level will change the relative sizing of all components in the Reaction Path Diagram.

Changing font size will alter the size of font for labels displayed in the Reaction Path Diagram.

This option will put boxes around the species in the Reaction Path Diagram.

There are several settings to modify how the reactions connecting species are displayed within a reaction path diagram. These controls modify the reaction line thickness, whether or not joints are added in a line, line labels, and the maximum magnitude of the displayed line.

Changing from Absolute ROP to Relative ROP will alter the relative sizing of the connecting pathways between species. The relative size of each arrow will be normalized by the sum of all ROPs exiting a source species. The Constant ROP line thickness will leave all lines at a constant thickness independent of their magnitude.

Selecting Straight lines will make all reaction pathways connecting species into single lines within the Reaction Path Diagram, making direct connections between the source and destination species. The (default) Jointed Line option causes lines to be wrap around the species and avoid overlap. This option applies to both the Tree and GraphViz layouts.

The labels on reaction lines can be composed of either the absolute magnitude of the rates in a connection or a relative magnitude of the rates. Additionally, the label can include information about side species associated with a reaction pathway. The concept of a side species is explained in Side Species Preferences. These labels appear with mouse hovering, mouse selection, or can be turned on for all reaction connections.

Composition controls set the data limitations of bar charts. The maximum species and maximum reactions set the number of entries in sensitivity, rate of production, or composition bar charts. Log scale will scale the bars on the Composition Bar Chart on the Control Panel using a logarithmic, rather than linear, scale. For this option, the minimum composition value is represented by a zero-length bar.