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NetworkAnalyzer computes a comprehensive set of topological parameters for undirected and directed networks, including:

NetworkAnalyzer also constructs the intersection, union and difference of two networks. It supports the extraction of connected components as separate networks and the removal of self-loops.

Network Analysis

Analyze Network

To run NetworkAnalyzer, select Tools → NetworkAnalyzer → Network Analysis → Analyze Network.

NetworkAnalyzer.png

The NetworkAnalyzer will determine whether your network contains directed or undirected edges. At this point, you can choose to ignore edge direction information.

When results are calculated, they will appear in the Results Panel.

NetworkAnalyzerResults.png

The results have multiple tabs. Details on the network parameters can be found here.

You can also save the statistics for later use by using the Save Statistics button.

Analyze Subset of Nodes

An exhaustive topological analysis of very large networks can be a time consuming task. The computation of local parameters for the nodes is significantly faster than the computation of global (path-related) parameters. Examples of local parameters are node degree, neighborhood connectivity, topological and clustering coefficients. Betweenness and closeness centralities, as well as stress, are global parameters.

NetworkAnalyzer provides the Analyze Subset of Nodes option for computing local parameters for a subset of nodes. If one or more nodes in the network are selected before starting an analysis, only the sub-network induced by the selected nodes is analyzed. Moreover, only local parameters are computed. Shared neighbors distribution and shortest path lengths distribution, among others, are not displayed in the results.

Batch Analysis

The Batch Analysis option is used to perform topological analysis on all networks stored in specific directory, using all possible interpretations for every network. Batch analysis consists of three simple steps:

Load Network Statistics

Existing network statistics can be loaded from a file saved previously in NetworkAnalyzer.

Plot Parameters

The Plot Parameters dialog offers a possibility to plot two parameters against each other. The parameters to be plotted can be chosen from two drop-down menus. The Table Column 1 menu provides the values for the domain/category axis, and the Table Column 2 menu specifies the values for the range/value axis. The plot is updated each time a different parameter is selected in one of the menus.

Generate Style from Statistics

NetworkAnalyzer computed parameters can be visualized as node/edge size and color, if the Store node / edge parameters in node / edge table option in NetworkAnalyzer Settings is enabled. Parameters loaded from a .netstats file cannot be visualized because the network itself is not stored in the network statistics file. If, after performing topological analysis, the network is modified by introducing or removing nodes or edges, it is recommended (and sometimes required) to run NetworkAnalyzer again before visualizing any parameters.

The visualization is initiated by the Generate Style from Statistics... menu option. There are two ways of mapping computed parameters.

NetworkAnalyzer_VisualizeParameters.png

NetworkAnalyzer Settings

The following settings can be configured by the user:

Subnetwork Creation

NetworkAnalyzer allows for the creation of sub-networks of connected components. The user selects a number of connected components from a list and each selected components is visualized as a sub-network.

NetworkAnalyzer_ConnectedComponents.png

Cytoscape_3/UserManual/Network_Analyzer (last edited 2016-04-26 22:18:35 by TimHull)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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