CORAL

An integrated suite of visualizations for comparing clusterings.

This tool is described in:

D. Filippova, A. Gadani, C. Kingsford. Coral: An integrated suite of visualizations for comparing clusterings. To appear: BMC Bioinformatics. 2012

Requirements

• Java 1.6 or newer

Download

From the bin folder:

• Windows: coral.zip. Run with java -jar coral.jar.
• MacOS: coral_mac.zip. Double-click on coral.app to run.
• Linux: coral.tar.gz. To run from command-line, use ./coral or java -jar coral.jar

TODO

• color scheme for matrix
• clusterings overview (density, mean size, # unique vert)
• dataModel to dispatch change events to listeners (containers)
• row reordering
• 2 clusterings comparison table
• slider to cut off J.score in module-module table
• clusterings comparison by metrics
• vertex table

• filter by the # of co-occurrences

• ladder component
• color ladder cells based on score
• add/remove clustering from the view

• small zoomable window on the matrix for navigation (lens w/ labels)
• network viz for the co-occured nodes
• labels on the matrix

• color legend for matrix

• save session/load old session

• matrix -> output for cytoscape (# cooccurences - weig, ts)
• bar chart w/ overview
• labels on the bar chart (overview panel)
• QUIT command not ending the process
• clicking on black area on the matrix - deselect the vertex pair
• style JaccardScore slider
• dockable windows for each panel

• data filtering panel - global filtering options on the whole dataset
• small multiples view for the slider above module table (row count 4 that table)
• filtering on table (search string)

• ladder doesn't show when you load it in some particular way

• selecting regions on the matrix to reorder it manually

• legend: forсe an update (waits for the 2nd coming of Christ)

• matrix dragging

• compute matrix reordering first; show matrix; then compute clustering comparison