The network navigator

The network navigator applet is developed to make it easier to explore the hierarchical and modular structure often found in real-world network data.

When you load your weighted or unweighted, directed or undirected network, the network navigator clusters the network based on the map equation and generates a hierarchical map for you to explore (see the bftree format).

References

• Multilevel compression of random walks on networks reveals hierarchical organization in large integrated systems (Martin Rosvall and Carl T. Bergstrom)
• The map equation (Martin Rosvall, Daniel Axelsson, and Carl T. Bergstrom)
• Community detection and visualization of networks with the map equation framework (Ludvig Bohlin, Daniel Edler, Andrea Lancichinetti, and Martin Rosvall)

File formats

Network data with the formats below can be loaded into the Network Navigator:

Pajek (.net) format

Structure your network into Pajek's .net format. Here is an example network with three nodes and four directed and weighted links:

*Vertices 6
1 "Node 1" 1.0
2 "Node 2" 1.0 
3 "Node 3" 1.0 
4 "Node 4" 1.0 
5 "Node 5" 1.0 
6 "Node 6" 1.0
*Arcs 8
1 2 2.0
2 3 2.0
3 1 2.0
1 4 1.0
4 5 2.0
5 6 2.0
6 4 2.0
4 1 1.0

Pajek uses "Edges" for undirected links and "Arcs" for directed links. We accept both "Edges" and "Arcs" and the choice of load button determines whether the algorithm treats the network as undirected or directed. Directed links have the form "from to weight". That is, the first link in the list above goes from node 1 to node 2 and has weight 1.9. The link weight is optional and the default value is 1 (we aggregate the weights of links defined more than once). Node weights are optional and sets the relative proportion to which each node receives teleporting random walkers in the directed version of the code. Default value is 1.

Link list (.txt) format

A .txt file is assumed to contain a simple list of all links in the network, implicitly defining the nodes:

#source target weight.
1 2 1.0
1 3 0.4
1 5 3.2
2 3 0.8
2 4 2.1
3 4 1.0

The above network will thus consist of 5 nodes and 6 links.

Streamable binary flow tree (.bftree) format

To be able to start navigate the network as soon as the hierarchical structure has been calculated and loaded into the network navigator, we use a customized streamable format that includes the tree structure in a breath first order, including the flow links of each sub-network. That way, only a small part of the file has to be loaded to start visualize the result, and the deeper structures can be loaded on demand.

The .bftree file is generated by Infomap, which is also compiled into the Network Navigator. As the Flash-version of Infomap runs slower, the stand-alone version is better suited for large networks.

Instructions

Using only the Network Navigator

1. Click on the button Load network and browse your network file matching the file formats.

2. Choose between Undirected/Directed links and Multilevel/Two-level clustering.

3. If you loaded a link list, you have to check Zero-based numbering if the node numbers in the file starts from 0, otherwise they are assumed to start from 1.

4. Click on Calculate clusters.

5. The Infomap algorithm will start to cluster your network and print its progress in the Network loader module. When it is finished, the Network loader module will automatically close and you can start navigate your network from the Finder or from the Network view. If Infomap exited with error, please check the error message in the Network loader module.

Using stand-alone Infomap + Network Navigator

1. Run Infomap on the network with the --bftree flag (see code).

2. Click Load map in the Network Navigator and browse your .bftree file from the Infomap run.

3. The Network loader module will automatically close and the Finder and Network view will open with the top level data visible more or less immediately.

Navigating

• Use the keyboard arrows → ↓ ← ↑ to navigate in the Finder.

• Use click and alt + click to navigate down and up respectively in the Network view.

• Use the search field in the Finder to directly navigate to nodes anywhere in the tree.

• The module names are generated automatically from its biggest children, adding a new dot for each level.

Customizing the network

• Click the button to the top right in the Network view module to toggle the control panel.

• Filter the number of nodes by setting the link limit.

• Change the size and color scales in the corresponding tab.

Explaining the graphics

• The horizontal bars to the left of the node names in the Finder shows the amount of flow captured by that node, as a fraction of the whole network (the color) and as a fraction of its parent node (the size). The size is scaled logarithmically so that for each halvation the flow is reduced by a factor ten. Thus, the two vertical lines within the bar measures, from left to right, 1% and 10% of its parents flow.

• The numbers after the modules in the Finder shows the maximum depth under that node in the tree. It is also encoded in the color of the arrow.

• Every module represents a cluster of nodes and the links between the modules represent the flow between the modules. The size of a module is proportional to the average time a random walker spends on nodes in the module and the width of a link is proportional to the per step probability that a random walker moves between the modules: