Create Dendrogram with JTreeView
When gene lists get longer than about 5000 genes, displaying clusters becomes slow in MAGIC Tool. One way to handle this is to export a cluster computed by MAGIC Tool for viewing in other software. We export files that are readable by the open source software Java TreeView. Only files created using the hierarchical clustering method currently work with Java TreeView. When you click the Export button in the JTreeView Export Information dialog, the files required to visualize the cluster in JTreeView are created, JTreeView is automatically launched, the files are loaded, and a dendrogram displayed. You can also visualize the data in the files in a karyoscope which can help detect aneuploidy; to do so reopen the file in JTreeView (click File * Open..., then choose the file you just exported and click Open), then choose "Karyoscope" from the Analysis menu.
For more information about Java TreeView, visit http://jtreeview.sourceforge.net.