Category Archives: R

Bio7 R Documentation and Plot Examples

18.07.2014

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:

http://bio7.org/documentation/Main.html#toc-Section-4.6

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

http://bio7.org/documentation/Main.html#toc-Subsection-4.3.3

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):

http://bio7.org/videos/RPlots.mp4

 

R editor improvements for Bio7

30.01.2014

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:

screenreditor1

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

screenreditor2

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

15.10.2013

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.

Installation:

Simply unpack the Bio7_1.7.1_Mac64.zip 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
>.libPaths()
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
http://bio7.org/?p=2049

New in Bio7 1.7.1
http://bio7.org/?p=2112

Download:
Bio7 1.7.1 can be downloaded here.

Bio7 1.7.1 for Linux Released

24.09.2013

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:

http://bio7.org/?p=2049
http://bio7.org/?p=2112

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

linux2

linux1

Installation

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

R

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:
/usr/lib/R

Java

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:

http://bio7.org/?page_id=10

Download

Bio7 1.7.1 for Linux can be downloaded here!

 

 

New Bio7 1.7.1 Release with Improved R Plot Image Display

05.09.2013

I released a new Windows version of Bio7. This release improves the general R plot functionality of Bio7. The default image plots are now displayed in a Image stack if more than one plot command is executed. In this way all plots are automatically openend and not only the last image plot. Multiple plots (e.g. an animation or simulation) can then be saved as an animated *.gif file (see example below) or an *.avi file, etc. with the available default ImageJ methods.

Furthermore i added some templates in the preferences to switch e.g. to a *.pdf (displaying multiple plots) or *.svg plot (displaying a single plot) which will be opened with the default registered software if available – for *.svg i recommend Inkscape).
For antialiased image plots i added an “Image Cairo” option.

 Click on the image below to open an overview video!

Plot

Animated *.gif exported with ImageJ

Changes:

  • Updated ImageJ to version 1.48b.
  • Improved the custom R plot display.
  • Synchronized the “Plot Data” actions  in the “R-Shell” view with the settings in the Bio7 Rserve preferences.
  • Added more R plot options (with templates) in the Bio7 Rserve preferences (see screenshot below).
  • Synchronized the “Plot Data” actions with the settings of the plot preferences.
  • Updated Rserve to version 1.7-3
  • Updated some useful links to R resources and documents (Menu Help->Bio7 Internet).

rserveplotpref

Bug Fixes:

  • Fixed a bug which occured when opening the 3d panels of Bio7 while a resized! ImageJ image was displayed.
  • Fixed a bug of the embedded ImageJ.

A Linux and Mac version is planned after the next Java Runtime release.

The new Bio7 release can be downloaded here!