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TREEVIEW 3.0

TreeView is an open-source Java app for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it (or parts of it) into a figure.

treeview_screenshot.png

DOWNLOAD

Alpha 3 (current release) - released on July 5, 2016

Older versions: Treeview Wiki page.

INSTALL & RUN

Requirements

  • Java 7 or higher - visit http://java.com/en/download/installed.jsp to verify your current Java version.
  • If you tested an older version of Treeview 3.0, we recommend that you reset your preferences before you upgrade to the latest version (File > Preferences > Reset Preferences).

Windows

Place the downloaded JAR file anywhere on your computer and run it by double-clicking on the icon.

Mac

Place the downloaded JAR file anywhere on your computer.

First time: right-click on the icon and choose Open with > Jar Launcher.app.

Every time after that: double-click on the icon.

WHAT'S NEW

In Treeview 3.0

  • We have completely re-designed the interface to include one main data panel, with zooming, scrolling and searching options.
  • We have made clustering an integral part of TreeView (no need for Cluster 3.0).
  • We have added more flexible color settings (multiple colors, varying ranges) and label settings.
  • We have eliminated some of the features that we considered obsolete or in need of a major re-work.
  • We have improved image export.

Since Alpha 2

  • New window layout that optimizes screen space
  • Improved navigation:
    • whizzing labels and trees
    • double-click to zoom
  • New data export:
    • copy labels to clipboard
    • export matrix view to PDF, SVG, PNG, JPG and PPM
  • Improved search
  • Improved color selection and editing
  • Other minor updates and bug fixes

DOCUMENTATION

See our wiki.

HOW TO CITE

The manuscript describing Treeview 3.0 is currently in preparation. In the meantime, if you have used the latest pre-release version of the software (alpha 3) and wish to cite the source, please use the following reference:

Keil C, Leach RW, Faizaan SM, Bezawada S, Parsons L, Baryshnikova A. (2016). Treeview 3.0 (alpha 3) - Visualization and analysis of large data matrices [Data set]. Zenodo. http://doi.org/10.5281/zenodo.160573

To cite older alpha versions of Treeview 3.0, contact us at treeview@princeton.edu.

DEVELOPERS

TreeView was first developed by Michael Eisen in 1998 (Treeview 1.0) and updated a few years later by Alok Saldanha (Treeview 2.0). The development team for Treeview 3.0 includes:

  • Chris Keil - University of Hamburg
  • Robert Leach - Princeton University
  • Srikanth Bezawada
  • Faizaan Shaik
  • Lance Parsons - Princeton University
  • Anastasia Baryshnikova - Princeton University - http://www.baryshnikova-lab.org

FEEDBACK

If you are interested in providing feedback, you can watch this repository, create new issues or contact us at treeview@princeton.edu.

Also, you can subscribe to the (very low-traffic) Treeview users' mailing list at http://eepurl.com/A2Xzf. You will receive an email when new software versions are available.

LICENSE

Treeview 3.0 is released under the MIT license, which can be found here.

DEPENDENCIES