R Snippet
RSnippet-Node extension for KNIME Workbench version 4.0.0.v201906200740 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
Output Ports
Best Friends (Incoming)
- R Snippet (8 %)
- CSV Reader (5 %)
- Column Filter (5 %) Streamable
- File Reader (4 %) Streamable
- Column Rename (4 %) Streamable
- CSV Writer (3 %) Streamable
- RowID (3 %) Streamable
- Table Creator (3 %)
- Database Reader (legacy) (2 %)
- Row Filter (2 %) Streamable
- R Snippet (2 %)
- Column Resorter (2 %) Streamable
- GroupBy (2 %)
- Joiner (2 %)
- Sorter (2 %)
- Group Loop Start (1 %)
- Concatenate (1 %) Streamable
String To Number(1 %) StreamableDeprecated- Row Sampling (1 %)
- Transpose (1 %)
- Rule-based Row Filter (1 %) Streamable
- R Source (Table) (1 %)
- Spark to Table (< 1 %)
- Example Data (< 1 %)
- Table Row to Variable (< 1 %)
- Chunk Loop Start (< 1 %)
- Column List Loop Start (< 1 %)
- Category To Number (< 1 %) Streamable
Number To String(< 1 %) Deprecated- Reference Column Filter (< 1 %) Streamable
- Reference Row Filter (< 1 %)
- Missing Value (< 1 %)
- Data Generator (< 1 %) Streamable
- Empty Table Creator (< 1 %)
- Math Formula (< 1 %) Streamable
XLS Reader(< 1 %) Deprecated- Excel Reader (XLS) (< 1 %) Streamable
- Star (< 1 %)
- BinningAnalysis (< 1 %)
- Normalize Plates (NPI) (< 1 %)
- Normalize Plates (POC) (< 1 %)
- Python Snippet (< 1 %)
- Convert to Table (< 1 %)
- R Snippet (< 1 %)
- R Snippet (2:1) (< 1 %)
- Fix Column Names (< 1 %)
- Octave Script (< 1 %)
- MolConverter (< 1 %) Streamable
- Download (< 1 %)
- URL to File Path (< 1 %) Streamable
- Table Column to Variable (< 1 %)
- Table Row To Variable Loop Start (< 1 %)
- ARFF Reader (< 1 %)
- Database Connection Table Reader (legacy) (< 1 %)
- Table Reader (< 1 %) Streamable
- Java Edit Variable (< 1 %)
- Feature Selection Loop End (< 1 %)
- Loop End (Column Append) (< 1 %)
- Loop End (< 1 %)
- Hierarchical Clustering (< 1 %)
- Scorer (< 1 %)
- SVM Predictor (< 1 %) Streamable
Tree Ensemble Predictor(< 1 %) StreamableDeprecated- Perl Scripting (< 1 %)
- Add Empty Rows (< 1 %)
- Concatenate (Optional in) (< 1 %) Streamable
Cell Splitter(< 1 %) Deprecated- Column Combiner (< 1 %) Streamable
- Insert Column Header (< 1 %)
- Column Merger (< 1 %) Streamable
- Column Rename (Regex) (< 1 %) Streamable
- Constant Value Column (< 1 %) Streamable
- Linear Correlation (< 1 %)
- Cross Joiner (< 1 %) Streamable
- Domain Calculator (< 1 %)
- Row Splitter (< 1 %) Streamable
- Normalizer (< 1 %)
- Partitioning (< 1 %)
- Round Double (< 1 %) Streamable
- Column Splitter (< 1 %) Streamable
- String Manipulation (< 1 %) Streamable
- String Replacer (< 1 %) Streamable
- Rule Engine (< 1 %) Streamable
- Single sample t-test (< 1 %)
- Statistics (< 1 %)
- Column Expressions (< 1 %) Streamable
Excel Reader (XLS)(< 1 %) StreamableDeprecated- Java IF (Table) (< 1 %)
Bag of Words Creator(< 1 %) Deprecated- Weka Predictor (3.7) (< 1 %)
- Column Filter (< 1 %)
- Value Filter (< 1 %)
- Integer Input (< 1 %)
- Image Properties (< 1 %) Streamable
Python Script (1⇒1)(< 1 %) Deprecated- Python Source (< 1 %)
- R to Table (< 1 %)
- String to Date&Time (< 1 %) Streamable
- Extract Date&Time Fields (< 1 %) Streamable
- Moving Aggregation (< 1 %)
- Show all 100 recommendations
Best Friends (Outgoing)
- R Snippet (11 %)
- Joiner (8 %)
- R Plot (7 %)
- Open in R (4 %)
- R Snippet (4 %)
- R Snippet (2:1) (3 %)
- Column Filter (3 %) Streamable
- GroupBy (3 %)
- CSV Writer (2 %) Streamable
- Loop End (2 %)
- Table to Spark (2 %)
- String Manipulation (2 %) Streamable
- Rule-based Row Filter (2 %) Streamable
- Interactive Table (local) (2 %)
- Convert to R (1 %)
- Recursive Loop Start (2 ports) (1 %)
- Concatenate (1 %) Streamable
- Constant Value Column (1 %) Streamable
- Row Filter (1 %) Streamable
- Partitioning (1 %)
- Statistics (1 %)
Strings To Document(1 %) StreamableDeprecated- Hive Loader (< 1 %)
- Table to Spark (< 1 %)
- Python Snippet (< 1 %)
- Python Plot (< 1 %)
- R Plot (< 1 %)
- R Snippet (2:1) (< 1 %)
- Octave Script (< 1 %)
- MyManipulator (< 1 %)
- Variable to Table Column (< 1 %) Streamable
- Table Row To Variable Loop Start (< 1 %)
- Database Writer (legacy) (< 1 %) Streamable
- Table Writer (< 1 %)
- Loop End (Column Append) (< 1 %)
- Counting Loop Start (< 1 %)
- Chunk Loop Start (< 1 %)
- PNN Predictor (< 1 %) Streamable
PCA Apply(< 1 %) Deprecated- Number To Category (Apply) (< 1 %)
String To Number(< 1 %) StreamableDeprecated- String To SVG (< 1 %)
- Column Appender (< 1 %) Streamable
- Lag Column (< 1 %) Streamable
- Column Resorter (< 1 %) Streamable
- One to Many (< 1 %)
- Linear Correlation (< 1 %)
- Cross Joiner (< 1 %) Streamable
- HiLite Row Splitter (< 1 %)
- Missing Value Column Filter (< 1 %)
- Nominal Value Row Filter (< 1 %) Streamable
- Normalizer (Apply) (< 1 %) Streamable
- Pivoting (< 1 %)
- Missing Value (< 1 %)
- Column Rename (< 1 %) Streamable
- RowID (< 1 %) Streamable
- String Replace (Dictionary) (< 1 %) Streamable
- Transpose (< 1 %)
- Unpivoting (< 1 %)
- Value Counter (< 1 %)
- Rule Engine (< 1 %) Streamable
- Data Explorer (< 1 %)
- End IF (< 1 %)
- Send Email (< 1 %)
- Box Plot (local) (< 1 %)
- Scatter Plot (local) (< 1 %)
- Color Manager (< 1 %)
- Random Boolean Assigner (< 1 %)
- Numeric Distances (< 1 %)
- Math Formula (< 1 %) Streamable
XLS Writer(< 1 %) Deprecated- Excel Sheet Appender (XLS) (< 1 %)
- Excel Writer (XLS) (< 1 %)
- Send to Tableau Server (< 1 %)
- MultilayerPerceptron (3.7) (< 1 %)
- SimpleCart (3.7) (< 1 %)
- Distance Matrix to Network (< 1 %)
- Add Table To R (< 1 %)
- R View (Table) (< 1 %)
- Table to R (< 1 %)
- Table Difference Checker (< 1 %)
- String to Date&Time (< 1 %) Streamable
- String to Date/Time (legacy) (< 1 %) Streamable
- Show all 83 recommendations
Workflows
hitIdentification- normalization
- 08_Regularized_Logistic_Regression
- 08_Regularized_Logistic_Regression
Installation
To use this node in KNIME, install RSnippet-Node extension for KNIME Workbench from the following update site: