Network Visualization

Network Visualization  Network Visualization

This page describes the different options to visualize networks with KNIME.

Nodes

The network plug-in provides the following nodes for visualizing networks.

Network Viewer  Network Viewer

The Network Viewer node provides a node view to interactive browse a given network within KNIME. It provides basic visualization and graph transformation options. The node provides also an image port that returns an image of the input network, which can be further used in KNIME e.g. embedded into a report.

Viz Output Connector  Viz Output Connector

The Viz Output Connector node allows to the send a network from KNIME to an external program e.g. network visualization program. The transferred graph contains all features and partition information of the network. However, it depends on the external program if all feature types and partition information are supported.

Viz Input Connector  Viz Input Connector

The Viz Input Connector node allows to receive a network from an external program e.g. network visualization program. The transferred graph contains all features and partition information if supported by the external program.

External Programs

The KNIME nodes for sending and receiving networks allow the seamless integration of external programs to analyze and visualize networks.

visone logo  visone

visone is a long-term research project, in which models and algorithms to integrate and advance the analysis and visualization of social networks are being developed. An important part of visone is the design and implementation of a software tool intended for research and teaching in social network analysis. It is specifically designed to allow experts and novices alike to apply innovative and advanced visual methods with ease and accuracy.
(Description copied from the visone homepage)

 

Installation

You can start visone without any installation using webstart including the KNIME extension. However it still needs to be activated. Do this by going to "extensions" tab in the visone option dialog (file->options...).

 

 

Usage

Activate the KNIME connection in the visone console dialog visone console icon in the KNIME tab. Networks received from KNIME are layouted and displayed immediately.

 

Tutorials and reference guides about visone are available on the visone manual page.

Cytoscape logo  Cytoscape

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration and visualization. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. Plugins may be developed by anyone using the Cytoscape open API based on Java™ technology and plugin community development is encouraged. Most of the plugins are freely available.
(Description copied from the Cytoscape homepage)

 

Installation

Cytoscape Plugin Manager Dialog

You have to download and install Cytoscape first. Notice that we currently only support Cytoscape 2.x. So the latest supported version is Cytoscape 2.8.3. Once you have Cytoscape installed you have to install the KNIME Connector plug-in, either by using the Cytoscape plugin manager, which is the preferred way, or by manually downloading the plug-in file.

To install the plug-in using the Cytoscape plugin manager start Cytoscape and open the plugin manager (Plugins->Manage Plugins). Search for "KNIME" in the "Manage Plugins" dialog. Select the KNIMEConnector plug-in in the "Network and Attribute I/O" section and click the "Install" button. Accept the licence agreement in the Plugin Licence Agreement dialog and close the "Manage Plugins" dialog by clicking the "Close" button. You should now see the KNIME Conncetor menu entry entry in the "Plugins" menu.

If you prefer to install the plug-in manually, download the plugin file to your hard disk. Open Cytoscape, go to the "Plugins" menu and select the "Install Plugin from File" option. Select the "KNIMEConnector.jar" file in the file selection dialog. You should now see the KNIME Conncetor menu entry entry in the "Plugins" menu.

 

Usage

Open the KNIME Connector panel via the KNIME Conncetor menu entry entry in the "Plugins" menu. The panel is displayed in the "Control Panel" which is displayed by default on the left side within Cytoscape. The connection to KNIME is activated automatically when you open the panel in order to exchange networks with KNIME. Networks received from KNIME will be layouted and displayed immediately.

 

In order to change the port Cytoscape should use to exchange networks with KNIME, click the "Change port button" and enter a new port according to the port you have entered in the configure dialog within KNIME. The standard port is 7777. If a port is already in use, an "Address already in use" exception is displayed in the KNIME Connector panel.

Quick start guides and user documents are available on the Cytoscape documentation page.