The hierarchic layout algorithm tries to arrange the compounds in a fashion that the irreversible reactions point in one direction. This type of visuallization is especially usefull for metabolic pathways, in which the reactions occur only in one direction. The algorithm partitions the compounds into layers and than arranges the compounds in the layers, such that the number of crossings between different reactions is low. The hierarchic layout algorithm usually produces few crossings and no overlaps. However, if the data is not directed, the reasulting layout may be not satisfactory and a force-directed layout may be more appropiate. The hierarchic layout algorithm is located in the package yWays.autolayout.hierarchic.
The hierarchic layout algorithm provides currently the following options: minimal node distance, minimal layer distance and drawing style. These options are discussed in the following sections.
This option defines the minimal distance between two consecutive layers. Increasing this value leads to placements which need more space, but choosing this value two small sometimes results in a crowded layout. Usually a value between 20 and 50 is best.
This options defines the minimal distance between two compounds in the same layer. Increasing this value leads to placements which need more space, but choosing this value two small sometimes results in a crowded layout. Usually a value between 20 and 50 is best.
The drawing style denotes how the reactions are drawn.
In the curved drawing style, the reactions are drawn, such that the diagram uses as few space as possible. This results normaly in a considerable amount of bends.
In the linear segment drawing style, each line, i.e. the skeleton and the connection lines of an reaction, has at most 2 bends. This resulting placements have few bends, but are usualy not very compact.