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.net network file (see File formats for details) into the map generator by clicking on the button
Load network and chose between undirected and directed network. For very large networks, the load and clustering time can be long in the Flash-based Map Generator. If you are encountering problems, you can run the clustering code offline and load the
.map file into the applet (see .map files under File formats for details).
If you just want to try out the map generator, we have provided a few sample networks. The weighted undirected network is the largest connected component of a coauthorship network compiled (for details of how weights are assigned, see M. E. J. Newman, Phys. Rev. E 64, 016132 (2001)) from two network reviews and one community detection review:
M. E. J. Newman, SIAM Review 45, 167-256 (2003);
S. Boccaletti et al., Physics Reports 424, 175-308 (2006);
S. Fortunato, Physics Reports 486, 75-174 (2010), and can be downloaded in
.net format here.
The networks of science come from Thomson-Reuters’ Journal Citation Reports 2004. Our data tally on a journal-by-journal basis the citations from articles published in a given year to articles published in the previous five years, and self-citations are excluded. See Eigenfactor.org for more information about ranking of scientific knowledge.
Cluster the network based on the map equation or alternatively provide a clustering in Pajek's
The algorithm tries to minimize the description length of a random walker's movement on the network and reveals important aspects of network structure with respect to the dynamics on the network. (More information in the Map demo.)
The map generator displays the network as a map. 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:
Customize the map by changing the position of the modules automatically (see "Placement tools" in the control panel) or manually, by changing the names of the modules (double click on a module to see the nodes within the module), by changing the color of modules and links (see
Color and size tools in the control panel), by moving the labels, etc. All adjustments can also be applied only to selected modules (
shift-click selects a single module and
shift-drag selcts multiple modules).
Save the customized map in scalable vector graphics as a
.map file for later access in the Map Generator (see
Network input/output in the control panel).
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.
Structure your clustering file in Pajek's
.clu format, which is just a list of module assignments:
*Vertices 6 2 2 2 1 1 1
For very large networks, the load and clustering time can be long in the Flash-based Map Generator. To overcome this problem, the clustering algorithm can be run offline with the code provided here. The code outputs a file with extension
# modules: 2 # modulelinks: 2 # nodes: 6 # links: 8 # codelength: 2.51912 *Directed *Modules 2 1 "Node 1,..." 0.5 0.0697722 2 "Node 4,..." 0.5 0.0697722 *Nodes 6 1:1 "Node 1" 0.209317 1:2 "Node 3" 0.147071 1:3 "Node 2" 0.143613 2:1 "Node 4" 0.209317 2:2 "Node 6" 0.147071 2:3 "Node 5" 0.143613 *Links 2 1 2 0.0697722 2 1 0.0697722
This file format only contains the necessary information to generate a map. The names under *Modules are derived from the node with the highest PageRank within the module. The values 0.5 and 0.0697722 represent, respectively, the aggregated PageRank of all nodes within the module and the per step exit flow from the module. The nodes are listed with their module assignments together with their PageRanks. Finally, all links between the modules are listed in order from high flow to low flow.
We have developed the Flash applet above to make it easier for you to simplify and summarize important structural changes in your networks with alluvial diagrams (we recommend that you use the latest version of FlashPlayer). Load multiple networks with coinciding node names and partition them one by one with the map generator (see left column). If you want to perform a significance analysis to separate real change from mere noise, instead download and run conf-infomap on your networks and load the generated
.smap files. The alluvial diagram highlights organizational changes with streamlines between your networks.
Follow the instructions for the map generator to load a first network. To include significance information about the network clusters, download and run conf-infomap on each network and load the
.smap files instead of your networks. You can load multiple
.smap files at once if you first first archive them in a Zip file and then load the single Zip file. Networks will be displayed in lexicographic order. For example, a Zip archive with files network-1.map, network-2.map, etc., will be displayed in numerical order.
Add network above the control panel to load additional networks. You can rearrange the order of loaded networks. Simply click a network thumbnail above the control panel and drag it to its preferred position.
The alluvial diagram is displayed to the right of the control panel. If you need more room, you can collapse the map by clicking the collapse button in the upper left corner of the map. It is easy to rearrange the modules and the streamlines, just click and drag to the new position. Highlighted nodes in a module can be rearranged if you keep the mouse button pressed for two seconds. The modules are first named by the most important node in the module (highest PageRank), but all names can be selected and changed appropriately. To change the layout of the diagram, use the size controls under
Alluvial diagram in the control panel.
To remove, highlight, or explore a module, just click the module and select one of the options under
Alluvial diagram in the control panel. A double-click takes you directly to the
Module explorer. Drag and select multiple modules to perform actions to multiple modules at the same time.
Module explorer, you can select and highlight individual or groups of nodes. The left column corresponds to the selected module(s) and the right column corresponds to the module assignment in the network marked in the drop-down list. Grayed out names belong to modules that are not included in the diagram. To include such a module, just double-click the grayed-out module name. A dash
- means that the node does not exist in the network.
FULLSCREEN in the upper right corner you can use your entire screen. For security reasons, Flash does not allow for inputs from the keyboard in fullscreen mode and you cannot edit any text. Pressing
ESC takes you back to normal mode.
To separate change from mere noise, we have provided code that automatically generates, clusters, and performs statistical significance analysis on bootstrap networks. The code outputs a file with extension
# modules: 2 # modulelinks: 2 # nodes: 6 # links: 8 # codelength: 2.51912 *Directed *Modules 2 1 "Node 1,..." 0.5 0.0697722 2 "Node 4,..." 0.5 0.0697722 *Insignificants 1 2>1 *Nodes 6 1:1 "Node 1" 0.209317 1:2 "Node 3" 0.147071 1;3 "Node 2" 0.143613 2:1 "Node 4" 0.209317 2:2 "Node 6" 0.147071 2;3 "Node 5" 0.143613 *Links 2 1 2 0.0697722 2 1 0.0697722
This file contains the necessary information to generate a significance map in the alluvial generator. Compared to the
.map file described to the left, this file also contains information about which modules that are not significantly standalone and which modules they most often are clustered together with. The notation
*Insignificants 1 in the example field above means that the significant nodes in module 2 more often than the confidence level are clustered together with the significant nodes in module 1. In the module assignments, we use colons to denote significantly clustered nodes and semicolons to denote insignificantly clustered nodes. For example, the colon in
1:1 "Node 1" 0.209317 means that the node belongs to the largest, measured by flow, set of nodes that are clustered together in at least a fraction, given by the confidence level, of bootstrap networks.