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KNIME UGM 2015
Antje Janosch – Technology Development Studio MPI-CBG Dresden
Scripting IntegrationWorkshop
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History
Antje Janosch, MPI-CBG, Dresden, Germany
2009 2015?R-Scripting, Python Scripting,
Matlab Scripting2010?
2013 / 2014
R integration vs. R integration
• Better editor (undo, redo)• Better attribute name insertion• Preserve column names• UI templates + centralized user template repositories• Dynamic repainting of plots• OpenInR nodes for rapid prototyping• (Support for ggplot2 and lattice plots)• Faster table conversion (~2x)• Flow-variable support in scripts• Generic nodes to process arbitrary R data structures
Antje Janosch, MPI-CBG, Dresden, Germany 4
General Features
• Server/Client based solution• Parallel execution• Centralized setup
• Remote template repositories• Template configuration via “KNIME-like” GUI
• Deployment of KNIME-nodes with scripting behind
Antje Janosch, MPI-CBG, Dresden, Germany 5
Short news
R• ROW-ID support (one direction KNIME > R)• Improved error messages (syntax errors, other errors)• generic R-port summary
Python• Support of pandas data frame
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Client-(server) model
Antje Janosch, MPI-CBG, Dresden, Germany
RServe
remote or local
Matlab-Server
local
remote or local
local
Pyth
on-
Serv
er
remote or local
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Getting started (Client)
• Install Scripting plugins from “Trusted Community Contributions” update site (KNIME >= 2.10 recommended)
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Preferences
Antje Janosch, MPI-CBG, Dresden, Germany 9
Node Types
• Plot• Snippet• OpenIn…• Generic nodes (R)
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Plot / Snippet – Script editor tab
Plot / Snippet – Template tab
Template Repository
Template Description / Source
Script editor tab – template view
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RGG interface of the selected template
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Script editor tab – template view
modify template (dev)
RGG (XML)
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Tips and Tricks for Editing (R)
• Mouse click = ”Column name” • Alt + Mouse click = kIn$”Column name”• Ctrl + Mouse click = Displays possible domain values of the
column and offers to insert a selection (comma separated• Press Apple/Windows key and select multiple = as soon as
you release the key, the selected column names will be inserted “column 1”,”column 2”,...
• FLOWVAR(currentColumnName) placeholder to enable the use of flow variables
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Plot – Output Options tab
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Template repositories
Template.txt################################################### name: A very cool method# author: Antje Janosch# category: KNIME-UGM/# preview: niceImage.png (optional)
This is my template description.######
R/Python/Matlab code Optionally emmbedded in RGG
################################################### name: Another very cool method# author: Antje Janosch...
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RGG
• R GUI Generator
• Additional element<panellistbox label="Label" items="item1,item2,item3" span="full"/>
http://rgg.r-forge.r-project.org/RGG: a general GUI Framework for R scripts.BMC Bioinformatics. 2009 Mar 2 ;10:74. doi: 10.1186/1471-2105-10-74.
<rgg>some interface elements definitions<![CDATA[R-script]]> </rgg>
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RGG
• Placeholders$$$NUM_ATTRIBUTES$$$ - for all numeric columns$$$STR_ATTRIBUTES$$$ - for all string columns$$$ALL_ATTRIBUTES$$$ - for all columns
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Demos (R)
1. I want to use templates
2. I want to write my own R-scripts
3. I want to create knimeR-workflows (generic nodes)
4. I want to create templates
5. I want to create a KNIME node with R behind
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Outlook
• Support of row IDs for all integrations and in both directions
• Console output view for R nodes• Keep offline copy of template files• Push KNIME color, size, shape descriptors• Support of domain values• …
