Category Archives: R

Simple R Debugging GUI for Bio7


For the next release of Bio7 I implemented a first simple debugging GUI (Graphical User Interface) for R scripts. For the debugging process a change from Rserve to an available Java R console connection in Bio7 is necessary (with Rserve alone a debugging interface wouldn’t be possible).
Both connections runs in the same process and all objects will be preserved if you switch from one connection to another (shutting down RServe or start R in the console).
Technically in the next version of Bio7 Rserve is started by default within a native Java R connection!

Still there is some work and testing to do but here is a short video about the new debugging interface:

Debugging With Bio7 and R

Bio7 R Documentation and Plot Examples


A very time expensive process is the documentation of software you created yourself. I was finally able to update and improve the documentation for Bio7 and the embedded R “Graphical User Interface”. For the documentation this time i used Lyx to export the LaTeX document as HTML with the available eLyXer export module.

The R Graphical User Interface is documented here:

The documentation to transfer images and image data from ImageJ to R and vice versa can be found in this section:

I hope that this documentation will make it easier to explore the Bio7 R functionalities beside the flash videos i created.

In addition i created a new video (the first time i used Screencast-O-Matic) which explains how you can easily create a R plot with Bio7 using ImageJ as the default plot device or different available devices (PDF, SVG):


R editor improvements for Bio7


For the next release of Bio7 based on Eclipse 4.4 an improvement of the R editor for a much better editing experience of R scripts will be available. The integrated editor itself is built bottom-up (based upon an Eclipse editor editor template) although there a great editor frameworks (DLTK) or frameworks to develop programming languages and domain specific languages (Xtext) for Eclipse available.

I decided to built the editor this way to avoid dependencies with Eclipse plugins adding unnecessary interfaces and complexities in a Rich Client Platform and because i wanted to understand the internals of the editor for manageable improvements of upcoming releases.

Until now i integrated a parser for R based on ANTLR, implemented error marking, code folding, a first simple version of “Quick Fixes” and an outline view for the R scripts.

This screenshot demonstrates:


Here a screenshot with error marking and a “Quick Fix”:


Beside other improvements coming from Eclipse (e.g. split editor capabilities) for the next release of Bio7 i hope that this new functionality will ease the development of R scripts inside of Bio7.







Bio7 1.7.1 MacOSX Released


Finally i released  Bio7 1.7.1 for MacOSX. This release is bundled with a Java Runtime Environment and the latest R version (3.0.2) for MacOSX. For the plot functionality eventually XQuartz has to be installed (if not already installed!).

Please note the installation requirements at the bottom of the page. Here are some screenshots for a first impression:

rmac2 rmac1 javamac imagejmac flowmac 3dmac
Installation Requirements:

  • MacOSX >=10.7.3 64-bit
  • Eventually XQuartz
  • Avoid blanks in the Bio7 installation path for the bundled JRE (Java Runtime Environment)

Eventually XQuartz has to be installed to use the default custom R plotting device of Bio7 on MacOSX. If you plot the first time with R and XQuartz is not available a dialog will inform you about the missing installation.


Simply unpack the in your preferred location. A double-click on the Bio7 file in the created Bio7 folder will start the application from the local bundled JRE.

If you would like to use Bio7 with your installed R application:

Please install the Rserve package. After the Bio7 start adjust the path to R in the Bio7 Preferences.
Preferences->Preferences Bio7
You can get the path from the R application with the command:
> R.home()
E.g. path to R: /Library/Frameworks/R.framework/Resources. Also adjust the path to the install location of the R packages:
Preferences->Preferences Bio7->Preferences Rserve
You can get the path from your R installation by evaluating the expression
in the R console. If an error is indicated in the Bio7 preferences please adjust wrong paths to the correct location or adjust them to a temporary available location else you can’t save the preferences.

New Features:

For an overview of the new Bio7 features in this release please read the following posts:

New in Bio7 1.7

New in Bio7 1.7.1

Bio7 1.7.1 can be downloaded here.

Bio7 1.7.1 for Linux Released


I released a new Linux version of Bio7 (64-bit only – see Screenshots below).
For an overview of the new features please read the release notes for Windows 1.7.0 and 1.7.1:

In addition some Linux specific improvements are embedded in this release.

Additional Linux features:

  • Rserve can be opened with a Gnome or xterm terminal
  • New silent Rserve connection (without the need to start xterm)
  • Improved Rserve shutdown
  • New option to open R  plots with Inkscape (*.svg, *.eps)
  • New option to open *.pdf files with a specific reader
  • Added a Linux pseudo terminal (using bash) in the Bio7 console




For an installation simply extract the Bio7 *.zip file at your preferred location.


To use R within Bio7 you have to install R and the package Rserve from within R.
The paths to R have to be adjusted in the following Bio7 R preferences:

Preferences->Preferences Bio7
Preferences->Preferences Rserve

The default path to R on Linux is:


Bio7 Linux 1.7.1 comes with a bundled Jre (1.7.40) so you don’t have to install the latest Java.
The default reserved memory space for Java on the Linux OS is 1024mb.

A more detailed instruction can be found in the Bio7 documentation:


Bio7 1.7.1 for Linux can be downloaded here!