[kepler-users] Kepler and R (bioinformatics)

[Dan Higgins]

Hi Bruno,

    I am the person who wrote the existing version of the RExpression 
actor in Kepler, so I can probably supply some answers for your 
questions ;-)

   There are a number of limitations in the current implementation on 
using multiple R actors in Kepler. First of all, each R actor runs in a 
seperate process. In other words, R is started up, the commands in the 
actor R-script execute, and R then shuts down. If you create an output 
port that has the same name as an R variable, the R variables value is 
'translated' to a Kepler variable (with limits discussed below) and sent 
through the port to any connected actor.

   This output of values limited to a few simple R data structures due 
to problems of converting arbitrary R classes to some equivalent in 
Kepler. Strings, numbers, arrays, matrices, and dataframes can be 
output, but arbitrary classes cannot. If you check out the nightly build 
zip file of Kepler (which is a build of the latest version), you will 
see under a workflow called $Kepler/demos/R/ReadTable.xml that demos 
passing a dataframe from one R actor to another.

    As I said, by default one R actor does not inherit the workspace of 
another. However, there is a parameter of the RExpression actor called 
'save or Not' that has the default value of '--no-save'. This can be 
changed to '--save'. Doing so saves the R workspace. Another actor can 
be connected to this first actor and the script of the second actor set 
to load the saved workspace. Thus one can pass a complete R workspace 
from one RExpression actor to another. A series of 4 R actors use this 
technique in the example workflow "$Kepler/demos/R/BEAM_$_1.xml". In 
this approach, data is NOT passed through the ports; instead, an output 
port just passes a 'trigger' to the input port of the next RExpression 
actor and this trigger controls the sequencing of how the actors fire. 
Some people have complained that this technique 'subverts' the basic 
Kepler concept of passing all data through the ports. It also does 
create some potential problems with workflows where actors are not 
configured to fire sequentially. Nevertheless, it does allow modularized 
R scripts to be used in a sequential manner.

    Hopefully these comments will be useful. Let me know if you have 
additional questions.

Dan Higgins
NCEAS/Ecoinformatics


------------------------

Bruno Yoshimura wrote:
> I am writing a paper about Visual Programming for bioinformatics and 
> it would be wonderful if I found somebody who knows how to use R with 
> Kepler. The main objective of this study is to decide whether or not 
> it is worth to use Kepler in this area.
>
> More specifically, I would like to know the challenges and problems in 
> using R inside Kepler. I had some problems trying to run some R 
> Expressions, and I could not find a solution. The problem is the 
> following: When I try to link two "R Expressions" ("a" and "b"), the R 
> Expression "b" does not inherit  the classes and imports  of the R 
> Expression "a" (using the ports).
>
> It is possible to link two or more R Expressions? How should I do it?
> It is possible to send a entire Class using ports?
>
> Thanks,
> Bruno
> ------------------------------------------------------------------------
>
> _______________________________________________
> Kepler-users mailing list
> Kepler-users at ecoinformatics.org
> http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/kepler-users
>   


-- 
*******************************************************************
Dan Higgins                                  higgins at nceas.ucsb.edu
http://www.nceas.ucsb.edu/    Ph: 805-893-5127
National Center for Ecological Analysis and Synthesis (NCEAS) Marine Science Building - Room 3405
Santa Barbara, CA 93195
*******************************************************************

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