The input file can be a network in tab delimited format. The network file
NAP accepts as input, an obligatory, tab-delimited file, containing all network connections. This file must contain headers, namely: 'Source' and 'Target'. A 2-column file represents the connections between the nodes and refers to an unweighted network, whereas a third column can be used for weights. Each network can be handled as directed or undirected.
Source Target Weight
A B 3
A C 3
A D 4
B C 1
C D 1
A E 4
A F 5
D D1 3
A1 B1 3
A1 C1 3
A1 D1 4
B1 C1 1
C1 D1 1
A1 E1 4
A1 F1 5
NAP comes with various network generation options. Users are able to generate:
A random scale-free network (Barabasi-Albert)
A completely random network without any special topology (Erdos-Renyi)
A random network with a small world topology (Watts-Strogatz)
A bipartite network
For any of the options, users can define the network sizeof by adjusting the number of nodes and choose whether it will be directed or undirected. Notably, users can upload or generate as many networks as they like. Every time a network is uploaded, a name must be given first. Download examples:1) Download Gavin_2002 network here 2) Download Gavin_2006 network here
Usage:Users can upload or generate as many networks as they like. Every time a network is uploaded, a name can be given first. Once a network file has been named and uploaded, it will appear as an option in any of the NAP’s dropdown selection lists. Users can remove indifferent networks at any time.
Table View:Users can select a network or an annotation file at a time and see its content as an interactive table. Notably, one can search by suffix in the table, using the Search field.Network 2D:This Tab offers a dynamic network visualization in its simplest form. Nodes are connected with edges and their coordinates are calculated using any of the offered layouts. The network is fully interactive as zooming, dragging and panning are allowed either by using the mouse or the navigation buttons.
In addition, nodes can be selected and dragged anywhere on the plane, whereas the first neighbors of any node can be highlighted upon selection. Finally, the network view is automatically updated when a different network is selected.Layouts:Currently, NAP hosts the following layouts:
Fruchterman-Reingold: It places nodes on the plane using the force-directed layout algorithm developed by Fruchterman and Reingold.
Random: This function places the vertices of the graph on a 2D plane uniformly using random coordinates.
Circle: It places vertices on a circle, ordered by their vertex ids.
Kamada-Kawai: This layout places the vertices on a 2D plane by simulating a physical model of springs.
Reingold-Tilford: This is a tree-like layout and is suitable for trees or graphs without many cycles.
LGL: A force directed layout suitable for larger graphs.
Grid: This layout places vertices on a rectangular 2D grid.
Sphere: This layout places vertices on a rectangular 3D-like sphere.
Bipartite graphs:In the case of bipartite graphs, users can export and subsequently visualize the two projection networks. Network 3D:NAP offers a fully interactive 3D network visualization using a force-directed layout. Users can zoom-in and out and interactively drag and drop any node or the whole network