RReportGenerator ReportGenerator : p : Automatic Automatic Reports - - PowerPoint PPT Presentation

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RReportGenerator ReportGenerator : p : Automatic Automatic Reports Reports p from Routine Statistical Analysis using R from Routine Statistical Analysis using R UseR! 2008, Dortmund, Aug 11-14 2008, Focus Session Reporting , , g ,

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SLIDE 1

RReportGenerator ReportGenerator :

: Automatic Automatic Reports Reports

p

p from Routine Statistical Analysis using R from Routine Statistical Analysis using R

UseR! 2008, Dortmund, Aug 11-14 2008, Focus Session “Reporting” , , g ,

p g

http://www-bio3d-igbmc.u-strasbg.fr/~wraff/

wolfgang.raffelsberger (at) igbmc.fr

Laboratoire de Bio-Informatique et Génomique Intégratives (LBGI)

IGBMC, Strasbourg

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SLIDE 2

Automatic Data Analysis Automatic Data Analysis

  • : Powerful Means for Statistical Analysis

☺ vast collection of additional modules (CRAN, Bioconductor) command-line structure : “inaccessible” for Biologists,… Our Motivation : Make R available in convenient way for Our Motivation : Make R available in convenient way for

automatic routine use

i hi l i t f (GUI)

via graphical user interface (GUI) allowing to access prewritten R-code creating reports in pdf-format

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SLIDE 3

RReportGenerator : Principle ReportGenerator : Principle

GUI managing tasks of :

g g

  • selecting the data to be treated,
  • calling command-line R,
  • passing Sweave code

( t i b b tit ti ifi t ) (customize by substituting specific terms)

  • file-name & location of report
  • Customizing options : preferred search paths, …
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SLIDE 4

Main Items

Analysis Scenario File :

  • Execution of R program : creating the .tex file ...
  • Scenario

1

www accessible collection of updated scenarios

RReportGenerator : statistical analysis with automatic reports Data Input File : Output Folder :

Browse … Browse …

> setwd("D:/tools1/RStatReportGenerator/v1.1/RRG_tmp") > Sweave("TCA_v1a.Rnw") Writing to file TCA_140307.tex Processing code chunks ... You can now run LaTeX on 'TCA-140307.tex'

  • Execution of pdfLaTeX program : creating the .pdf file ...
  • This is pdfeTeX, Version 3.141592-1.30.6-2.2 (MiKTeX 2.5) entering

extended mode (D:\tools1\RStatReportGenerator\v1.1\RRG_tmp\test1.tex LaTeX2e <2005/12/01> Babel <v3.8g> and hyphenation patterns for english, dumylang, nohyphenation, gerrman, ngerman, french, loaded …

Input Data

2

updated scenarios

D://projects D://projects/TCA_140307.txt C://ProgramFiles/RRG/scenarios/RRG_test1.Rnw

Infos Optional Items

Report File Name : Supplemental Data Input File : Supplemental Data Output File :

Browse … .pdf .dvi (+eps)

……………………………………………………………………… Execution finished: the following files have been created : ……………………………………………………………………… D://projects/TCA_140307.pdf D://projects/TCA_140307.txt _____________________________________

3

TCA_140307.pdf p j

Output

Generate Report Supplemental Data Output File : Reset

Keep the .tex file

D://projects/TCA_140307.txt

3b

Raffelsberger et al, Bioinformatics 2008

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SLIDE 5

Main Items

Analysis Scenario File :

  • Execution of R program : creating the .tex file ...
  • Scenario

1

www accessible collection of updated scenarios

RReportGenerator : statistical analysis with automatic reports Data Input File : Output Folder :

Browse … Browse …

> setwd("D:/tools1/RStatReportGenerator/v1.1/RRG_tmp") > Sweave("TCA_v1a.Rnw") Writing to file TCA_140307.tex Processing code chunks ... You can now run LaTeX on 'TCA-140307.tex'

  • Execution of pdfLaTeX program : creating the .pdf file ...
  • This is pdfeTeX, Version 3.141592-1.30.6-2.2 (MiKTeX 2.5) entering

extended mode (D:\tools1\RStatReportGenerator\v1.1\RRG_tmp\test1.tex LaTeX2e <2005/12/01> Babel <v3.8g> and hyphenation patterns for english, dumylang, nohyphenation, gerrman, ngerman, french, loaded …

Input Data

2

updated scenarios

D://projects D://projects/TCA_140307.txt C://ProgramFiles/RRG/scenarios/RRG_test1.Rnw

Infos Optional Items

Report File Name : Supplemental Data Input File : Supplemental Data Output File :

Browse … .pdf .dvi (+eps)

……………………………………………………………………… Execution finished: the following files have been created : ……………………………………………………………………… D://projects/TCA_140307.pdf D://projects/TCA_140307.txt _____________________________________

3

TCA_140307.pdf p j

Output

Generate Report Supplemental Data Output File : Reset

Keep the .tex file

D://projects/TCA_140307.txt

3b 4

Sweave &

L T X

E

A data for export

temporary report (.tex)

4

final final .pdf report

Raffelsberger et al, Bioinformatics 2008

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SLIDE 6

Sample Code : Sample Code : Sweave Sweave

%@RRG_INFO

% Read a tab-delimited file & draw a scatter plot.

%@RRG INFO END @ _ _

\documentclass[a4paper]{article} \title{Minimal test scenario for RReportGenerator} \usepackage{a4wide,Sweave} \begin{document} \begin{document} \maketitle The file selected as 'Data Input File' is read : <<chunk_read, echo=FALSE, print=TRUE>>= mydata <- read.table("<DATA_IN_FILE>") t.test(mydata[,1],mydata[,2],paired=TRUE) @ <<chunk plot1, echo=FALSE, fig=TRUE>>= _p , , g plot(mydata[,2]~mydata[,1]) @ % If a name for 'Supplemental Data Output File' was given … <<chunk save echo=F print=F results=hide>>= <<chunk_save, echo=F, print=F, results=hide>>= write.table(summary(mydata), "<DATA_OUT_FILE>", row.names=F) @ \end{document}

Raffelsberger et al, Bioinformatics 2008

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SLIDE 7

Applications Applications

Automatic analyses for routine applications in Automatic analyses for routine applications in

  • Transcriptomics : Quality control, data normalization
  • Comparative Genomics Hybridization (CGH)

Counseling to amplified/lost regions

  • Transfected cell array (TCA) :

Graphical and statistical summary Graphical and statistical summary

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SLIDE 8

Examples : Transcription Profiling Examples : Transcription Profiling

(Affymetrix CQ)

1 5

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SLIDE 9

Examples : Transcription Profiling Examples : Transcription Profiling

(Affymetrix QC)

6 10

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SLIDE 10

Availability Availability

Windows & Linux versions

i ith i t ll l d b i t f l i i

htt // bi 3d i b t b f / ff

coming with installer, user-manual and basic set of analysis scenarios under free GNU public license at :

http://www-bio3d-igbmc.u-strasbg.fr/~wraff

RReportGenerator Version 1.3.3

  • Paper Format : Automatic switch between US and A4 paper format
  • Windows : Customize memory allocation of R
  • Updated Analysis Scenarios

More information : RReportGenerator : Automatic reports from routine statistical analysis using R.

  • Updated Analysis Scenarios

epo tGe e ato uto at c epo ts

  • ut e stat st ca a a ys s us g

Raffelsberger W, Krause Y, Mouliner L, Kieffer D, Morand AL, Brino L, Poch O Bioinformatics 2008, 24(2):276-278 Or : http://alnitak.u-strasbg.fr/wikili/index.php/RReportGenerator_English

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SLIDE 11

Acknowledgments Acknowledgments

2006

LBGI LBGI

Yannick Krause Luc Moulinier David Kieffer Guillaume Berthommier Odile Rousselet Bela Tiwari

all users of RReportGenerator for feed-back !

Odile Rousselet all LBGI members

Olivier Poch

INSERM U682 f f

CEBGS - IGBMC TCA-Platform

AL Morand, L Brino

Hôpital Hautepierre, CGE

Institut de la Vision (INSERM U592) CHU Bordeaux University of Zurich

IGBMC Microarray Platform Plate-forme Bioinformatique de Strasbourg

  • Collaborations :

University of Zurich University College London CRP Santé Luxembourg Trinity College Dublin Lund University

Département de Pathologie Moléculaire