| OpenMS 2.5.0

Static Public Member Functions | List of all members
RWrapper Class Reference
System

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

  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
  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