All the sample files can be directly loaded into VisANT

Gene Ontology Networks, Visual Customization, Network of Complexes, Hierarchical Network,

More metagraph examples, Layout the huge network,

Load this network in VisANT

Download this network (VisML)

This file changed:

  • the line width of the edge by assign different weights.

  • add label to the edge.

  • add detailed annotation of the edge that will be part of quick tip when mouse-over the edge.

The complexes were determined by tandem affinity mass spectrometry and were colored to indicate subsequent functional assignments. The gray edges connect complexes that share protein components. The components of each complex are included in the model and are visible when the metanode representing the complex is expanded. As an example, the complex labeled as 175 is expanded so that its components, as well as the one being shared (shadowed) with complex 36, are visible.


Load this network in VisANT

Download this network (VisML)

Note: double-click on metanode to expand/contract

Note: Click the left image for full-size screenshot that is taken after the network is saved as SVG file.

The batch mode makes it possible for VisANT to handle the network with millions of nodes and edges. As a test, we layout the functional network downloaded from http://www.functionalnet.org/mousenet/ using spring-embedded relaxing method. This layout is carried out by the batch command: layout=spring_embedded_relaxing:###, where ### shall be replaced by any integer to indicate the number of iterations. The big network in general requires to bigger number of iteration. The effect of this number, as well as the startup position of nodes, are listed below. The number for each figure represents the iteration time while the * indicate that the network is first laid out using circle layout, i.e., if the * presents, the command is:

layout=scramble
layout=spring_embedded_relaxing:###

 

otherwise, the commands will be:

layout=circle
layout=spring_embedded_relaxing:###

 

The whole package (VisANT, data file, command file, the script to run the batch mode) can be downloaded here. Please reference here for more information regarding the batch mode.

Click the image below to get the full size view.

before layout, the nodes are randomly positioned.

iteration=150*

iteration=250

iteration=250*

iteration=350

iteration=450

iteration=550

iteration=650

iteration=750

iteration=1050

iteration==2050

iteration=3050