WordCloud Parameter Tutorial


This tutorial will guide a user through how to use and manipulate the parameters associated with the WordCloud app using the Cytoscape session file provided. See the WordCloud Basic Tutorial for an introduction to using the basic functionality of the WordCloud plugin.

Pre-requisites -

Go to this page to download the plugin and test data


WordCloud Version 3.0.1 or newer

1. Open Cytoscape

2. Open the provided 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:


4. In the main menu select Apps > WordCloud > Show WordCloud - this will bring up the WordCloud Input and Display panels.

5. Under "Current Values" in the Input panel change the selected attributes to just EM1_GS_DESCR. This will change what node attribute are used when performing the semantic analysis and creating the cloud. A WordCloud is automatically created in the WordCloud display panel.

Expected Original Cloud:


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

Expected Result:


7. Set Max Num of Words back to 250.

8. Change the Word Aggregation Cutoff from 1 to 50.

Expected Result:


9. Set Word Aggregation Cutoff back to 1.

10. Previously, the size of words in the word tag cloud was based entirely on the selected nodes. The Normalization slider allows the size of words to be calculated also using the make-up of the entire network. Try dragging the slider bar all the way from 0.0 to 1.0 and watch how the word tag cloud changes in real time.

Expected Result with Network Normalization = 1.0:


11. Set Normalization back to 0.0

12. In the Cloud Style combo box select Clustered-Boxes as the Cloud Style.

Expected Result:


13. In the Cloud Style combo box select No-Clustering as the Cloud Style.

Expected Result:


14. Set the Cloud Style back to Clustered-Standard.

15. Click the Excluded Words button, a dialog will pop-up. Add the word "cancer" to be excluded (hit the add button after typing the word) then click ok.

Expected Result:


16. Open the Excluded Words dialog again. Click on the word "cancer" then click Remove.

17. Under the section with the heading --Flagged Words-- select the word "kegg". Hit the Remove button and then click ok.

Expected Result:


18. Click the Delimeters button, a dialog will appear.. Under the section with the heading --Common Delimiter-- select the "space" option. Hit the Remove button then click Ok.

Expected Result:


19. Add the space character back to be used for tokenization.

20. Click the Enable Stemming checkbox.

Expected Result:


Software/WordCloudPlugin/ParameterTutorial (last edited 2015-04-17 19:32:40 by MikeKucera)

MoinMoin Appliance - Powered by TurnKey Linux