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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 into a figure.

treeview_screenshot.png

DOWNLOAD

Downloads page

INSTALL & RUN

Requirements

Windows

  1. Download the msi package from the download page
  2. Double-click the downloaded msi package.
  3. Follow the on-screen instructions in the TreeView3 Setup Wizard.
    • Click Next.
    • Click the checkbox to accept the license agreement.
    • Click Next.
    • If desired, change the install location & click Next.
    • Click Install.
    • Click Yes to allow installation of the app from an unknown publisher (bitbucket.org).
    • Click Finish.
  4. Click the start menu in the lower left-hand corner
  5. Scroll down until you see TreeView3
  6. Click TreeView3
  7. If you have used a previous version of TreeView3: Select File->Preferences->Reset Preferences & click reset. You will have to restart TreeView3 afterwards.

OPTIONAL: If you would like to edit the default amount of memory to assign to TreeView3, refer to the instructions here.

Mac

  1. Download the dmg package from the download page
  2. Double-click the downloaded dmg package.
  3. Drag TreeView3.app to your Applications folder.
  4. Double-click TreeView3
  5. Security steps (if necessary)
    • If you are prompted to confirm open of an app downloaded from the internet, click "Open".
    • If your security preferences prevent you from opening TreeView3, dismiss the warning, then right-(or control-)click the TreeView3 app and click "Open".
  6. If you have used a previous version of TreeView3: Select File->Preferences->Reset Preferences & click reset. You will have to restart TreeView3 afterwards.

OPTIONAL: If you would like to edit the default amount of memory to assign to TreeView3, refer to the instructions here.

Linux (Debian)

  1. Download the deb package from the download page
  2. Open a terminal.
  3. cd to the location of the deb package.
  4. Run the following commands.
    • sudo apt install ./treeview3*.deb
    • treeview3
  5. If you have used a previous version of TreeView3: Select File->Preferences->Reset Preferences & click reset. You will have to restart TreeView3 afterwards.

OPTIONAL: If you would like to edit the default amount of memory to assign to TreeView3, refer to the instructions here.

Note, the ./ in front of the deb package (or rather, the path to the package) is essential. Otherwise, the installation will fail. Alternatively, you can run sudo apt install ./treeview3*.deb.

Linux (Redhat)

  1. Download the rpm package from the download page
  2. Open a terminal.
  3. cd to the location of the rpm package.
  4. Run the following commands.
    • sudo rpm -ivh treeview3*.rpm
    • treeview3
  5. If you have used a previous version of TreeView3: Select File->Preferences->Reset Preferences & click reset. You will have to restart TreeView3 afterwards.

OPTIONAL: If you would like to edit the default amount of memory to assign to TreeView3, refer to the instructions here.

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.

In the Beta 1 Release

  • Added: Label export capabilities
  • Added: Simplified installation for specific operating systems
  • Fixed: File open bug
  • Added: Data ticker improvements: visible data average & column/row hover averages
  • Added: New label settings to control how live labels are displayed
  • Fixed: "As seen on screen" export bug
  • Added: Performance enhancements
  • Other minor updates and bug fixes

In the Alpha 3 Release

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

DOCUMENTATION

TreeView3 is designed to be intuitive and easy to use. If anything is unclear, contact us at treeview@princeton.edu.

HOW TO CITE

The manuscript describing Treeview 3.0 is currently in preparation. In the meantime, please use the following reference:

Keil C, Leach RW, Faizaan SM, Bezawada S, Parsons L, Baryshnikova A. (2016). Treeview 3.0 (beta 1) - Visualization and analysis of large data matrices [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1303402

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.