User Manual

Overview

The Semantic Network 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 both the number of times the word appears in the selected nodes and the entire network for the selected node attribute. There are also options for viewing a clustered version of the word tag cloud.

Installation

The Semantic Network Summary Plugin requires Cytoscape Version 2.7.x. If you don't have Cytoscape or have an older Version (2.6 or older), please download the latest Release from http://www.cytoscape.org/ and install it on your computer.

• Download the Semantic Network Summary Plugin FILL THIS IN WHEN I KNOW and manually place the file 'SemanticSummary.jar' in the 'Cytoscape/plugins' folder.

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.

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Full User Guide

Tips on Parameter Choice

Attribute Choice

You can choose which Cytoscape attribute to build your word cloud from in the Semantic Analysis section of the Input panel. Your options include the node ID (the default option) and all currently available attributes of the type String or List. Notice, that for an attribute of type List, only those entries that are String will be used to build the word cloud. When changing the attribute that a cloud is built from, a user must hit the "Update" button to see the updated results for the current cloud.

Network Normalization

The size of any word in a tag cloud is a reflection of how often that word appears in the selected nodes of the network, normalized over how often that word appears in the entire network. The Network Normalization parameter determines how much weight to give the word counts over the entire network when determining word size.

• A value of 0 for the Network Normalization parameters makes it so that the size of a word in the tag cloud is directly proportional to the number of times that the word appears in just the selected nodes. In this situation, word counts over the entire network are given a weight of 0 with respect to the word counts in the selected nodes.
• A value of 1 makes it so that the size of a word in the tag cloud is directly proportional to the ratio of the number of times that the word appears in the selected nodes to the number of times that the word appears in the entire network. In this situation, word counts over the entire network are given a weight of 1 with respect to the counts in the selected nodes.

Word Aggregation Cutoff

This parameter is only in use when a Cloud Layout Style that includes clustering is selected.

The Input Panel

FINAL SCREEN SHOT WILL GO HERE!

1. Cloud List - A list of all clouds that exist for the current network. If no network is currently selected, then this section will display "No Network Loaded". A cloud can be renamed by selecting the cloud in the list, right clicking on the mouse and selecting "Edit Cloud Name".

2. Semantic Analysis - Allows the user to specify which attribute to use when building the word cloud.

3. Display Settings - User can specify the maximum number of words to display in the word cloud, as well as the Network Weight Factor.

4. Word Exclusion List - User can add or remove words to be ignored when building the word cloud.

5. Actions - The user has three choices: Delete (deletes the currently selected cloud, Update (takes in all parameters, the set of currently selected nodes, and all nodes in the network and builds an updated word cloud), and Create (takes in all parameters, the set of currently selected nodes, and all nodes in the network and builds a new word cloud).

The Cloud Display Panel

• Appears in the bottom (south) panel.
• Is refreshed every time a cloud is selected from the input panel, a network is brought into focus, a cloud is created, updated or deleted.
• If a network view is available for the current network, clicking on a word in the currently displaying word cloud will highlight all nodes in the network that currently contain that word in the attribute that the word cloud was created using.

Default and Valid Parameter Values

Network Weight Factor:

• Default Network Weight Factor used when calculated word size
• Default Value: 1

• Valid Values: >=0.0, <=1.0

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