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ModuleGraph - Documentation



Creating a ModuleGraph Network

After the module data are loaded (see 'Module Data' section), there are two possibilities to create a ModuleGraph network:

Both options will apply the default ModuleGraph visual style to the network, described in the Visual Style section below.

Visual Style

For a newly created network ModuleGraph will automatically use a force-directed layout. The parameters of that layout are chosen to arrange the network such that modules are close to their constituents. By default, ModuleGraph will show the different entities and relationships in a network as follows:

Entity / Relationship



  • Modules
A module is an aggregation of multiple elements. For instance a protein complex in a protein network. Quadratic green nodes
  • Elements
An element can (but does not have to) be part of a module. For instance a protein in a protein network. Round blue nodes
  • Inter element
There exists some relationship between two elements. For instance a regulatory relationship between two genes in a gene regulatory network. Thin blue edges
  • Overlap
Two modules have some elements in common. For instance, two protein complexes (can) have the same attachment. Thick green edges
  • Belongs to
An element can belong to a module. Thin black edges