HTTPS SSH

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

More recent "bleeding edge" releases, as well as older stable versions, are available at the 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

[Coming soon]

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