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.
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
- 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).
Place the downloaded JAR file anywhere on your computer and run it by double-clicking on the icon.
Place the downloaded JAR file anywhere on your computer.
First time: right-click on the icon and choose
Open with >
Every time after that: double-click on the icon.
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
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 firstname.lastname@example.org.
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
If you are interested in providing feedback, you can watch this repository, create new issues or contact us at email@example.com.
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.
Treeview 3.0 is released under the MIT license, which can be found here.
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