= Semantic Network Summary Parameter Tutorial =
== Outline ==
This tutorial will guide a user through how to use and manipulate the parameters associated with the Semantic Network Summary plugin using the Cytoscape session file provided. See the Semantic Summary [[GSoC2010_UseExamples|Basic Tutorial]] for an introduction to using the Semantic Network Summary.

Pre-requisites -

 * Cytoscape >= 2.7.0 must be installed
 * The Semantic Network Summary plugin must be in the Cytoscape-v2.7.x/plugins folder
 * Download the test data

Go to this page to [[GSoC2010_SoftwareDownload|download the plugin and test data]]

== Instructions ==
=== Version 0.5 or newer ===
1. Open Cytoscape

2. Open the provided [[GSoC2010_SoftwareDownload|sample data file]] (File / Open / select the file AlzheimerEM.cys)

3. Be careful not to change the set of selected nodes for the network titled "EM1_Enrichment Map" as this will change the results that you will get.

'''The example network with the correct set of nodes selected:'''

''' {{attachment:Selected_Nodes.jpg}} '''

4. Create a cloud using the nodes already selected in the nodes already pre-selected in the network.  Change the node attribute used for the semantic analysis to EM1_GS_DESCR and update the cloud.  From here forth we will refer to this as the "Original Cloud".

'''Expected Original Cloud:'''

{{attachment:Original_Cloud.jpg}}

5. Expand the Advanced parameters section of the Input Panel.  Change the "Max Num of Words" from the default of 250 to 5 and create a new cloud.  This will cause only the top 5 most significant words to appear in your cloud.

 * Word significance is determined by the size of the word.  If you have cloud display style selected that includes clustering (which you do for this example) ties are broken using cluster membership.  Also, notice that clusters are organized by decreasing order of importance where importance is determined using both the number of words appearing in a cluster as well as their size.

'''Expected Result:'''

''' {{attachment:Max_Word_Cloud.jpg}} '''