R Debugging GUI Improvements for Bio7


In my last post i presented the first version of a debugging GUI for R in Bio7 which is just a visual wrapper for the default R debugging functions. In the meantime i added some new methods and also improved the visualization. For the upcoming Bio7 release i have to make some cleanups but however here is a short video showing some basic functionalities of the GUI.

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 GUI Building Options


I recently integrated JDT as the default Java framework of Bio7 to edit Java for the next release. Just out of curiosity i tried to install the GUI development tool WindowsBuilder for Eclipse from the default update site to see if it works with Bio7 and JDT. The first tests were promising and i could easily built up custom GUI’s, compile and load them dynamically into a running Bio7 instance. Beside the upcoming integrated JavaFX SceneBuilder for the next release the possibility to use the powerful WB would be great to create custom Bio7 views’s rapidly.

Below you can see a screenshot:




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):


New Look And Feel


I was very unhappy with the default look and feel of my Rich Client Platform based on Eclipse 4.4 so i decided to work on a new custom CSS with gradients for Bio7. The nearly finished CSS (tested on Windows) is displayed below which corrects not only colours but also the different toolbar settings (background of the main toolbar and height of the view toolbars) to display e.g. the floating toolbar actions correctly without hiding other window elements.

2014-06-23 17_33_39-Bio7

2014-06-23 17_42_14-Bio7

There are still some minor bugs to correct. E.g. the Maximize, Minimize icons have to be resized to display the toolbar colour correctly.

In addition i was able to correct the alignment of the different Bio7 editor actions and i could even improve the integration of the JDT actions and hide unnecessary GUI elements for Bio7 (menu and toolbar – see screenshot below).

2014-06-23 18_18_04-Bio7