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R Snippet

RSnippet-Node extension for KNIME Workbench version 4.0.0.v202009100739 by Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

This node executes a snippet/script using an R server (Rserve). The script for R can be selected from a snippet template repository. RGG (R GUI Generator) is used to configure the R code using a graphical user interface in a way that the user does not need to know scripting in R. URL of the template file can be set in KNIME->Preferences->KNIME->R-Scripting
The input data table is sent to R as a data frame named 'kIn'. The output data table is pulled from R. It has to be an R data frame named 'rOut'.

Script Editor:
Copy, cut or paste and R code to the editor and/or select the columns from your data table. If a template is loaded used the GUI to adapt the script to the input data.

Templates:
Select a snippet template from the template repository (double-click or "Use this template") to use that script and see the GUI. The description explains what a snippet does. Then configure the GUI according to your input data.

IMPORTANT :
This node is using R as back end, make sure that Rserve is running somewhere, and KNIME is accordingly configured (KNIME->Preferences->KNIME->R-Scripting). Scripting integration Wiki (R server)

Options

Open external: If checked, R will be opened externally, the KNIME input will be loaded as data frame and the script will be available at the clipboard.
Scipt Editor/Unlink from Template: Gives access to the R script after adaptation by the GUI.
Scipt Editor/Edit Template: Gives access to the RGG script.
Templates/Refresh: Loads again the template file.
Templates/Gallery: Generate a temporary webpage shown in a browser which gives an overview about all available templates.
Templates/Description,Source: Description explains what this snippet does. Source displays the RGG script.
Templates/Use this template: Click to load the GUI (or double-click onto the template)
Chunk size to push incoming data: Number of columns to push as one data chunk to R. The default (-1) leads to data transfer without splitting the data in chunks.
Chunk size to pull result data: Number of rows to push as one data chunk to R. The default (-1) leads to data transfer without splitting the data in chunks.

Input Ports

: A data table

Output Ports

: The data table that the snippet returns

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Installation

To use this node in KNIME, install KNIME R Scripting extension from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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