User Manual
Contents
Overview
The Semantic Summary Cytoscape Plugin allows you to visualize a selected set of nodes in a network as a word tag cloud. It will operate on any Cytoscape network. The tag cloud can be built based up the words in the node ID's or the words appearing in any node attribute that is comprised of Strings, or a List of Strings. The size of the words appearing in the word tag cloud is representative of the word's importance for the node selection as a function of the number of times the word appears in the selected nodes and the entire network for the selected node attribute.
Installation
Quick Start Guide
Creating a Semantic Summary Word Cloud
After loading a Cytoscape network, and selecting the nodes of interest, there are 3 locations from which you can create a Semantic Summary Word Cloud.
- Right click on a node in the network and select "Create Cloud". This will create a Semantic Summary Word Cloud using all of the default parameters.
- Under the Plugins Menu, select Semantic Network Summary / Create Cloud. This will create a Semantic Summary Word Cloud using all of the default parameters.
- Under the Plugins Menu, select Semantic Network Summary / Settings. This will load the Semantic Summary Input Panel on the left side of the screen. At the bottom right corner of this panel is a button labeled "Create" that will also create a Semantic Summary Word Cloud.
You can use the parameter defaults for all of these methods for creating a Semantic Summary Word Cloud. For a more careful choice of the parameter settings, please go to the Full User Guide.
Exploring the Semantic Summary Word Cloud
- The "Network" tab in the "Control Panel" on the left lists all available networks in the current session and at the bottom has an overview of the current network which allows for easy navigation in a network, even a high zoom levels by dragging the blue rectangle (the current view) over the network.
- The "Semantic Summary" tab will be loaded into the "Control Panel" on the left whenever a Semantic Summary Word Cloud is first created, or the Semantic Network Summary / Settings option is selected from the Plugins Menu. This tab contains a list of all Word Clouds created for the currently selected Network as well as all of the parameters that can be set by a user.
- The "Semantic Summary Cloud" tab in the "Data Panel" on the bottom side of the window is where a Semantic Summary Word Cloud will be displayed.
Advanced Tips
- With large networks and low zoom-levels Cytoscape automatically reduces the details (such as hiding the node labels and not showing the node borders). To override this mechanism click on "View / Show Graphics Details"
- To see which nodes in the network contain a word in the tag cloud, click on the word in the tag cloud. If a Network View is available for the network from which the cloud was created, all nodes in the network that contain the specified word in the chosen attribute will be highlighted.