RWrapper Class Reference

R-Wrapper Class. More...

#include <OpenMS/SYSTEM/RWrapper.h>

Static Public Member Functions
static String	findScript (const String &script_file, bool verbose=true)
	Look for an R script in the share/OpenMS/SCRIPT folder. More...
static bool	findR (const QString &executable=QString("Rscript"), bool verbose=true)
	Check for presence of 'Rscript'. More...
static bool	runScript (const String &script_file, const QStringList &cmd_args, const QString &executable=QString("Rscript"), bool find_R=false, bool verbose=true)
	Run an R script with certain arguments on the command line. More...

Detailed Description

R-Wrapper Class.

Call R scripts from OpenMS, mainly to produce plots.

Member Function Documentation

findR()

static bool findR ( const QString &  executable = QString("Rscript"), bool  verbose = true  )

static

Check for presence of 'Rscript'.

Parameters

executable	Name of the R interpreter
verbose	Print failure information?

Returns

Success status

findScript()

static String findScript ( const String &  script_file, bool  verbose = true  )

static

Look for an R script in the share/OpenMS/SCRIPT folder.

The script filename can be an absolute filename (in which case the filename is returned unchanged), or a relative filename or just a filename. In the latter cases, the script will be searched in the OpenMS 'SCRIPTS' path (share/OpenMS/SCRIPTS) and the full filename will be returned.

An exception will be thrown if the file cannot be found.

Parameters

script_file	Name of the R script
verbose	Print error message to OPENMS_LOG_ERROR upon FileNotFound

Returns

Full filename with absolute path

Exceptions

Exception::FileNotFound

runScript()

static bool runScript ( const String &  script_file, const QStringList &  cmd_args, const QString &  executable = QString("Rscript"), bool  find_R = false, bool  verbose = true  )

static

Run an R script with certain arguments on the command line.

The following checks are done before running the script: 1) [optional] 'Rscript' executable is searched (see findR() – set find_R to true) 2) The script_file is searched in 'OpenMS/share/SCRIPTS' (see findScript()). 3) The script is run as $ Rscript <path/to/script> <arg1> <arg2> ...

If any of the above steps fail, an error message is printed and false is returned.

The 'cmd_args' are passed via commandline and should be read by the R script using R' commandArgs() function. Usually, the args are input and output filenames.

Parameters

script_file	Filename of the R script
cmd_args	Command line arguments to the script
executable	Name of the R interpreter
find_R	Run findR()? May be skipped if runScript() is run repeatedly
verbose	Print status information; also passed internally to findR() and findScript().

Returns

Success status