WordCloud Plugin Download Page
The WordCloud App is a Cytoscape App that generates a word tag cloud from a user-defined node selection, summarizing an attribute of choice. For instance, if selected nodes are proteins, and the string attribute "full protein name" is selected, every string will be broken down into words, which will be plotted on a panel with size proportional to their frequency.
It is also possible to use the plugin to cluster words that appear together in the selected nodes. For instance, if node A has name attribute "Origin Recognition Complex 1" and node B has name attribute "Origin Recognition Complex 2", then the words "Origin", "Recognition" and "Complex" will be clustered together, following the order in which they appear. The plugin operates on any network and on any selected attributes, although it has been specifically designed for string attributes such as gene names or gene ontology annotations.
Current Version (3.0)
Install directly from the Cytoscape App Store
App Jar file available on GitHub
SemanticNetworkSummary_v0.5.zip (The name of the plugin was previously SemanticNetworkSummary)
Sample Data Download
- gene/protein interaction networks
DNA Replication yeast: ReplDNA_v04.cys
gene-set networks (see Enrichment map)
Gene-sets enriched in Alzheimer: AlzheimerEM.cys
Step by step tutorials that include expected output for one of the sample data download Cytoscape sessions provided above.
Guided Basic Tutorial on the basic functioning of the WordCloud plugin.
Advanced Parameter Tutorial on using all of the parameters available for the WordCloud plugin.