When biological networks are studied, it is common to look for clusters, i.e. sets of nodes that are highly inter-connected. To understand the *biological meaning* of a cluster, the user usually has to sift through many textual annotations that are associated with biological entities. The WordCloud Cytoscape plugin generates a visual summary of these annotations by displaying them as a "tag cloud", where more frequent words are displayed using a larger font size. Word co-occurrence in a phrase can be visualized by arranging words in clusters or as a network. These visualizations provide a concise visual summary of annotations which is helpful for network analysis and interpretation.
The WordCloud Plugin 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.