Download
as PDF

Organic Layout

Organic is a multi-purpose layout style for undirected graphs. It produces clear representations of complex networks and is especially fit for application areas such as

- Bioinformatics
- Enterprise networking
- Knowledge representation
- Systems management
- WWW visualization

The Organic Layouter is based on the force directed layout paradigm. When laying out a graph nodes are considered to be physical objects with mutually repulsive forces, like protons or electrons. The connections between nodes also follow the physical analogy and are considered to be metal springs attached to pairs of nodes. These springs produce repulsive or attractive forces between their endpoints if they are too short or too long. The layouter simulates these physical forces and rearranges the positions of the nodes in such a way that the sum of the forces emitted by the nodes and the edges reaches a (local) minimum.

Resulting layouts often expose the inherent symmetric and clustered structure of a graph, a well-balanced distribution of nodes, and few edge crossings.

The layouter is well-suited for the visualization of highly connected backbone regions with attached peripheral ring or star structures. These structurally different regions of a network can be easily identified by looking at a drawing produced by this layouter.

Visual Tab

Scope

All
The whole graph will be laid out.
Mainly Selection
The selected nodes will be rearranged. The unselected nodes are only allowed to move to a certain degree.
Only Selection
Only the selected nodes will be rearranged.

Preferred Edge Length

Allows you to specify the preferred length of all edges. The layouter tries to arrange the nodes in such a way that the edges have the desired edge length. The edge length is measured from node border to node border.

Consider Node Labels

Determines whether node labels should be considered in the layout process.

Allow Overlapping Nodes

Whether or not nodes are allowed to overlap. If this feature is disabled, the Minimal Node Distance will be used to arrange the nodes in such a way, that the given distance will be obeyed.

Minimal Node Distance

The minimal node distance which will be used if Allow Overlapping Nodes is disabled.

Avoid Node/Edge Overlaps

Whether or not nodes are allowed to overlap with edges.

Compactness

Adjusting this value can lead to a variety of differing layouts. For small values the resulting layout will use a lot of space and nodes tend to be far away from each other. Values around 0.5 lead to evenly distributed nodes, whereas values near 1.0 produce highly compact layouts.

Use Natural Clustering

Places nodes of the same natural cluster closely together and avoids overlapping of the drawing areas of different groups. This setting does not create group nodes. More information on natural clusters can be found in the article on automatic grouping.

Natural Clustering Quality

Controls the weighting between the quality of the grouping and the calculating time when computing a natural clustering. More information on this setting can be found in the article on automatic grouping.

Restrictions

Output Area

The graph will be arranged to fit into a given area. Different types of areas can be specified.

Grouping

Group Layout Policy

Determines the basic policy for the layout process.

Layout Groups
Instructs the algorithm to layout groups and open folders as well as their contents in a global manner. All visible nodes' positions will be recalculated.
Fix Contents of Groups
The algorithm will keep the relative position of nodes inside of groups and performs the layout on the top level only.
Fix Bounds of Groups
The algorithm will keep both size and position of group nodes, but will rearrange all normal nodes of the graph.
Ignore Groups
This setting will make the algorithm ignore group nodes entirely. Nodes will be rearranged as if there were no group nodes. This may lead to overlapping group nodes.

Algorithm Tab

Quality / Time Ratio

This setting can be used to adjust the quality versus the running time of the layout algorithm. Small values lead to short running times, while greater values result in better quality. For large graph structures (hundreds and thousands of nodes) it is advisable to begin with smaller values and to gradually increase them.

Maximal Duration (sec)

Sets the maximal duration of the layout process in seconds. If this upper bound is hit during the layout process, the quality of the layout may not be optimal. In this case increasing this value increases the likeliness of an optimal layout.

Activate Deterministic Mode

Whether or not the layout process should be deterministic. In Deterministic mode the layouter produces identical results for identical input graphs and identical settings.