The document outlines how to develop graphical user interfaces (GUIs) for R. It discusses motivations for building R GUIs and provides examples of existing R GUI projects like IsoGeneGUI and neaGUI that were developed using tcl/tk. It also describes how to build independent and embedded R GUIs, with steps for creating main windows, dialog boxes, and buttons. Plugins like RcmdrPlugin.biclustGUI that extend the R Commander interface are presented as a way to embed additional statistical analyses into an existing GUI framework.

1. Developing R Graphical User Interfaces
Setia Pramana
Medical Epidemiology and Biostatistics Department
Karolinska Institutet, Stockholm, Sweden

2. Outlines
• Motivations
• R GUI
• IsoGeneGUI
• neaGUI
• How to develop an R GUI?
• Independent GUI
• Embedded GUI (RcmdrPlugin.BiclustGUI)
• Summary
4/2/2013 2

3. R Pros and Con
 Free open source and widely used.
 Can be integrated with other languages
(C/C++, Java).
 R can interact with many data sources and
other statistical packages (SAS, Stata, SPSS,
and Minitab).
 For the high performance computing task 
multiple cores, either on a single machine or
across a network.
4/2/2013 3

4. R: A Command line interface (CLI)
 Users type commands to perform a statistical
analysis.
 Is preferred for advanced users  allows
direct control, more accurate, flexible and the
analysis is reproducible.
4/2/2013 4

5. R: A Command line interface (CLI)
 Requires good knowledge of the language 
difficult for beginners or less frequent users.
 R provides tools for building GUIs  RGUI
4/2/2013 5

6. Graphical User Interface (GUI)
 A tool to provide an event-driven user
interface.
 An extra layer between the user and the
program
 Based on menus, dialog boxes, icons and
controls.
 Window, icon, menu, and pointing device
(WIMP) paradigm
4/2/2013 6

7. R GUI Projects
 Integrated development environment
(IDE)/Script Editors aimed to provide feature-
rich environments to edit R scripts and code:
Rstudio (www.rstudio.com), and architect
(www.Openanalytics.eu)
 Web based application: the Rweb (Banfield,
1999), R.Net (www.u.arizona.edu/~ryckman/Net.php), or
gWidgetsWWW (Verzani, 2012).
4/2/2013 7

8. R GUI Projects
 Python: OpenMeta-Analyst (Wallace et al, 2012)
 Java: JGR (Java GUI for R), Deducer (Fellows,
2012), and Glotaran (Snellenburg, 2012).
 Php: R-php (http://dssm.unipa.it/R-php/)
 Other extensions connect R to graphical
toolboxes for developing menus and dialog
boxes: Tcltk, Gtk.
 Today, we focus on Tcltk
4/2/2013 8

9. R GUI Tcl/Tk
 Most commonly used: easy, no additional
software needed and ready to be used in R
(tcltk package)
 R-Tcl/Tk interface from the tcltk package
(Dalgaard, 2001 and Welch, 2000).
 The tcltk package allows the use of the Tk
(toolkit) graphical user interface elements
within R by embedding Tk commands into the
R language.
4/2/2013 9

10. R GUI Tcl/Tk
 R GUIs developed by using tcl/tk or RGtk:
• LimmaGUI (Wettenhall and Smyth, 2004),
• LMMNorm (Haldermans, 2010),
• IsoGeneGUI (Pramana et al. , 2010, 2012)
• NeaGUI (Pramana et.al, 2013)
• Rcommander (Fox, 2005)
• RcmdrPlugin.biclustGUI (Pramana, 2011)
4/2/2013 10

11. R GUI Tcl/Tk
 R GUIs developed by using tcl/tk or RGtk: Independent
GUI
• LimmaGUI (Wettenhall and Smyth, 2004),
• LMMNorm (Haldermans, 2010),
• IsoGeneGUI (Pramana et al. , 2010, 2012)
• NeaGUI (Pramana et.al, 2013)
• Rcommander (Fox, 2005)
• RcmdrPlugin.biclustGUI (Pramana, 2011)
4/2/2013 11

12. R GUI Tcl/Tk
 R GUIs developed by using tcl/tk or RGtk:
• LimmaGUI (Wettenhall and Smyth, 2004),
• LMMNorm (Haldermans, 2010),
• IsoGeneGUI (Pramana et al. , 2010, 2011)
• NeaGUI (Pramana et.al, 2013)
Embeded GUI
• Rcommander (Fox, 2005)
• RcmdrPlugin.biclustGUI (Pramana, 2011)
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13. IsoGeneGUI
 To perform dose response microarray
analysis in early drug development.
 Identify genes with a monotonic trend in the
expression levels with respect to the
increasing doses
 CLI based: IsoGene package (Pramana,2010)
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14. IsoGeneGUI
Main window of IsoGeneGUI
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15. IsoGeneGUI: Isotonic Regression Plot
Command line:
IsoPlot(dose, express , type="ordinal", add.curve=TRUE)
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16. IsoGeneGUI: Isotonic Regression Plot
Command line:
IsoPlot(dose, express , type="ordinal", add.curve=TRUE)
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17. IsoGeneGUI: Significant Analysis Microarray
qqstat <- Isoqqstat(x, y, fudge="pooled",
niter=50)
allfdr <- Isoallfdr(qqstat, , stat = "E2")
IsoSAMPlot(qqstat, allfdr, FDR = 0.1,
stat = "E2")
SAM.Res <- IsoTestSAM(x, y,
fudge="pooled", niter=50,
FDR=0.05, stat="E2")
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18. IsoGeneGUI: Significant Analysis Microarray
qqstat <- Isoqqstat(x, y, fudge="pooled",
niter=50)
allfdr <- Isoallfdr(qqstat, , stat = "E2")
IsoSAMPlot(qqstat, allfdr, FDR = 0.1,
stat = "E2")
SAM.Res <- IsoTestSAM(x, y,
fudge="pooled", niter=50,
FDR=0.05, stat="E2")
4/2/2013 18

19. IsoGeneGUI Manual Guide
 IsoGeneGUI
help: htlm
4/2/2013 19

20. IsoGeneGUI Manual Guide
 IsoGeneGUI
help: htlm
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21. IsoGeneGUI Manual Guide
 IsoGeneGUI
help: htlm
 Vignette:
http://www.bioconductor.org/packages/2.11/bioc/vignettes/IsoGe
neGUI/inst/doc/IsoGeneGUI.pdf
 Users’ manual:
http://www.ibiostat.be/software/IsoGeneGUI/files/IsoGeneGUI%
20users'%20manual.pdf
4/2/2013 21

22. neaGUI
 To help interpretation of
differentially expressed (DE)
genes in context of
biological processes,
pathways and networks.
 Perform network enrichment
analysis.
 Input: DE genes
 Output: enriched pathways
statistics based on gene
interaction networks.
4/2/2013 22

23. neaGUI Output
4/2/2013 23

24. neaGUI Output
4/2/2013 24

25. RGUI, How to Build One?
 Choose one of RGUI categories, and tools to be used
(tcltk, java, etc.) which suit with the package
purpose.
 Make sketches of the window box and consider:
• Input
• Options
• Output
 Can all functions be run in a single window (e.g.
neaGUI)? Or a main window with menu
(IsoGeneGUI) and separate dialog boxes are
needed? 4/2/2013 25

26. Create Main Window
tt <- tktoplevel()
tkwm.title(tt,"My New GUI")
topMenu <- tkmenu(tt)
tkconfigure (tt,menu=topMenu)
fileMenu <- tkmenu(topMenu,tearoff=FALSE)
openMenu <- tkmenu(topMenu,tearoff=FALSE)
tkadd(openMenu,"command",label="xls file",
command= getXls)
tkadd(openMenu,"command",label="text file”)
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27. Create Main Window
tt <- tktoplevel()
tkwm.title(tt,"My New GUI")
topMenu <- tkmenu(tt)
tkconfigure (tt,menu=topMenu)
fileMenu <- tkmenu(topMenu,tearoff=FALSE)
openMenu <- tkmenu(topMenu,tearoff=FALSE)
tkadd(openMenu,"command",label="xls file",
command= getXls)
tkadd(openMenu,"command",label="text file”) () {
getXls <- function
fileName <- tclvalue(tkgetOpenFile(filetypes=
gettext(' {"Excel Files" {".xls"}} {"All Files"
{"*"}}')))
data <- get( fileName) }
4/2/2013 27

28. Create Main Window
tt <- tktoplevel()
tkwm.title(tt,"My New GUI")
topMenu <- tkmenu(tt)
tkconfigure (tt,menu=topMenu)
fileMenu <- tkmenu(topMenu,tearoff=FALSE)
openMenu <- tkmenu(topMenu,tearoff=FALSE)
tkadd(openMenu,"command",label="xls file",
command= getXls)
tkadd(openMenu,"command",label="text file")
tkadd(fileMenu,"cascade",label="Open data",
menu=openMenu)
tkadd(fileMenu,"cascade",label="Edit data")
tkadd(fileMenu,"command",label="Quit",command=function() tkdestroy(tt))
tkadd(topMenu,"cascade",label="File",menu=fileMenu)
tkadd(topMenu,"cascade",label="Help")
tkfocus(tt)
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29. Create a Dialog Box
 Create the window
require(tcltk)
tt<-tktoplevel()
tkwm.title(tt,"Input Window")
 Edit Box
Name <- tclVar("")
entry.Name <-tkentry(tt,width="20",
textvariable=Name)
tkgrid(tklabel(tt,text="Name:"), entry.Name)
4/2/2013 29

30. Create a Dialog Box
 Radio button
rb1 <- tkradiobutton(tt)
rb2 <- tkradiobutton(tt)
rbValue <- tclVar("Male")
tkconfigure(rb1,variable=rbValue,
value="Male")
tkconfigure(rb2,variable=rbValue,
value="Female")
tkgrid(tklabel(tt,text="Sex:"))
tkgrid(tklabel(tt,text="Male"),rb1)
tkgrid(tklabel(tt,text="Female"),rb2)
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31. Create a Dialog Box
 List box with scroll bar
scr <- tkscrollbar(tt, repeatinterval=5,
command=function(...) tkyview(tl,...))
tl<-tklistbox(tt,height=4,selectmode="single",
background="white")
tkgrid(tklabel(tt,text="City:"), tl, scr)
city <- c("Brussels","Jakarta", "London",
"Stockholm")
for (i in (1:4)) tkinsert(tl,"end",city [i])
tkselection.set(tl,1)
tkgrid.configure(scr,rowspan=4,sticky="nsw")
4/2/2013 31

32. Create a Dialog Box
 OK button
OK.but <-tkbutton(tt,text=" OK ",
command=OnOK)
tkgrid(OK.but)
tkgrid.configure(OK.but)
tkfocus(tt)
4/2/2013 32

33. Run the function (OK button)
4/2/2013 33

34. Run the function (OK button)
OnOK <- function() {
NameVal <- tclvalue(Name)
rbVal <- as.character(tclvalue
(rbValue))
if (rbVal=="Male") pref = "Mr."
if (rbVal=="Female") pref = "Mrs.“
cityChoice <- city [as.numeric(tkcurselection(tl))+1]
tkdestroy(tt)
msg <- paste("Good morning ",pref , NameVal , "from", cityChoice,
sep=" ")
tkmessageBox(message=msg)
}
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35. Embeded R GUI: Rcmdr Plugin
 GUIs that are embedded/attached into another
GUI, i.e., R Commander (Rcmdr)
 Rcmdr was originally developed as a basic-
statistics graphical user interface (“GUI”) to R.
 Rcmdr needs extension for specific statistical
analysis
 More than 20 Rcmdr plugins today
4/2/2013 35

36. Rcmdr Plugin Advantages
 Does not need to develop GUI for common
procedures: Open, save and manipulate data.
 Can use standard statistical analysis.
 In term of programming: easier (standard tcltk
commands are provided)
 Users know how to work in command line
4/2/2013 36

37. R Commander (Rcmdr)
 Developed by John Fox from McMaster
University, Canada.
 Not only providing GUIs but also rendering users
to R commands
 Advantages:
• Ease of use. Beginners will have less problem to start to
use Rcmdr.
• Coverage. Offers wide range of basic statistics analysis
and data management.
4/2/2013 37

38. R Commander (Rcmdr)
 Advantages:
• Cross-platform functionality. Primarily under
Windows, but also available in Linux and Macintosh
OS/X.
• Extensibility: one can develop “plug-in" packages for
new methods/analysis.
• Protects the novices from errors. Limited options
related to the current context will minimize the errors
made by users.
• Exposes users to R commands.
4/2/2013 38

39. R Commander
Main Window:
 Script Window
 Output Window
 Messages
4/2/2013 39

40. RcmdrPlugin.biclustGUI
 An extension for the Rcmdr for biclustering
analysis.
Standard Rcmdr Menu
4/2/2013 40

41. RcmdrPlugin.biclustGUI
 An extension for the Rcmdr for biclustering
analysis.
Rcmdr with biclustering plugin
Standard Rcmdr Menu
4/2/2013 41

42. Create a Dialog Box
initializeDialog(title =
gettextRcmdr("Biclustering-CC"))
specFrame <- tkframe(top, borderwidth=5)
tkgrid(labelRcmdr(specFrame , text=gettextRcmdr("CC Specification:")))
deltaVal <- tclVar(“ ")
deltaField <- ttkentry(specFrame, width = "5",textvariable = deltaVal )
tkgrid(labelRcmdr(specFrame , text=gettextRcmdr("Delta:")), deltaField)
alphaVal <- tclVar("2")
alphaField <- ttkentry(specFrame, width = "5",textvariable = alphaVal )
tkgrid(labelRcmdr(specFrame , text=gettextRcmdr("Alpha:")), alphaField)
4/2/2013 42

43. Create a Dialog Box
numberVal <- tclVar("100")
numberField <- ttkentry(specFrame,
width = "5”, textvariable = numberVal)
tkgrid(labelRcmdr(specFrame , text=gettextRcmdr("Maximal Numbers : ")),
numberField)
OKbutton <- buttonRcmdr(specFrame , text = gettextRcmdr("Show Result"),
width = "12", command = onOK, default = "active", borderwidth = 3)
tkgrid(OKbutton,Plotbutton ,exitButton ,helpButton)
tkgrid(specFrame)
dialogSuffix()
4/2/2013 43

44. Submitting the job (OK button)
onOK <- function() {
.activeDataSet <- ActiveDataSet()
delta <- paste(tclvalue(deltaVal ))
alpha <- paste(tclvalue(alphaVal ))
number <- if (tclvalue( numberVal) == "") "100“
else paste(tclvalue(numberVal))
doItAndPrint(paste("CCbics <-biclust(as.matrix(",.activeDataSet,"),
method=BCCC(), delta=", delta, ", alpha= ", alpha, ", number=
",number ,")" , sep="") )
doItAndPrint("CCbics ")
tkfocus(CommanderWindow())
}
4/2/2013 44

45. doItAndPrint(paste("CCbics <-biclust(as.matrix(",.activeDataSet,"),
method=BCCC(), delta=", delta, ", alpha= ", alpha, ", number= ",number ,")" ,
sep="") )
doItAndPrint("CCbics ")
4/2/2013 45

46. Output
4/2/2013 46

47. RcmdrPlugin.biclustGUI
4/2/2013 47

48. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
4/2/2013 48

49. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
 The first line in menus.txt defines the top-level biclustGUI
menu:
Menu biclustMenu topMenu ““ ““ ““ ““
4/2/2013 49

50. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
Define
 menu/item line in menus.txt defines the top-level biclustGUI
The first
menu:
Menu biclustMenu topMenu ““ ““ ““ ““
4/2/2013 50

51. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
Name of
 The first line in menus.txt defines the top-level biclustGUI
new menu
menu:
Menu biclustMenu topMenu ““ ““ ““ ““
4/2/2013 51

52. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
Parent of
 The first line in menus.txt defines the top-level biclustGUI
the menu
menu:
Menu biclustMenu topMenu ““ ““ ““ ““
4/2/2013 52

53. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
 The first line in menus.txt defines the top-level biclustGUI
menu:
Menu biclustMenu topMenu ““ ““ ““ ““
 The second line in menus.txt defines a menu item under biclust
menu:
item biclustMenu command "Biclustering Plaid " PlaidWin "" "packageAvailable
('RcmdrPlugin.BiclustGUI')"
4/2/2013 53

54. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
 The first line in menus.txt defines the top-level biclustGUI
menu:
Menu biclustMenu topMenu ““ ““ ““ ““
Define
menu item
The second line in menus.txt defines a menu item under biclust
menu:
item biclustMenu command "Biclustering Plaid " PlaidWin "" "packageAvailable
('RcmdrPlugin.BiclustGUI')"
4/2/2013 54

55. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
 The first line in menus.txt defines the top-level biclustGUI
menu:
Menu biclustMenu topMenu ““ ““ ““ ““
Menu item
 The second line
belongs to in menus.txt defines a menu item under biclust
menu:
item biclustMenu command "Biclustering Plaid " PlaidWin "" "packageAvailable
('RcmdrPlugin.BiclustGUI')"
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56. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
 The first line in menus.txt defines the top-level biclustGUI
menu:
Menu biclustMenu topMenu ““ ““ ““ ““
Menu item
 The second line in menus.txt
invokes a defines a menu item under biclust
command
menu:
item biclustMenu command "Biclustering Plaid " PlaidWin "" "packageAvailable
('RcmdrPlugin.BiclustGUI')"
4/2/2013 56

57. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
 The first line in menus.txt defines the top-level biclustGUI
menu:
Menu biclustMenu topMenu ““ ““ ““ ““
Text
 The second line in menus.txt defines
displayed a menu item under biclust
menu:
item biclustMenu command "Biclustering Plaid " PlaidWin "" "packageAvailable
('RcmdrPlugin.BiclustGUI')"
4/2/2013 57

58. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
 The first line in menus.txt defines the top-level biclustGUI
menu:
Menu biclustMenu topMenu ““ ““ ““ ““
Called
 The second line in menus.txt defines afunction
menu item under biclust
menu:
item biclustMenu command "Biclustering Plaid " PlaidWin "" "packageAvailable
('RcmdrPlugin.BiclustGUI')"
4/2/2013 58

59. RcmdrPlugin: Menu-Definition File
 The plugin menus are defined the file: menus.txt.
 The first line in menus.txt defines the top-level biclustGUI
menu:
Menu biclustMenu topMenu ““ ““ ““ ““
Conditional activation
 The second line in menus.txt defines a menu item under biclust
and installation
menu:
item biclustMenu command "Biclustering Plaid " PlaidWin "" "packageAvailable
('RcmdrPlugin.BiclustGUI')"
4/2/2013 59

60. Next Stage
 Error handling: message boxes, warnings, etc.
 Trial by other people.
 Compile as a package.
 Submit in a repository for development we can use R-
forge.
 When all ready, submit to a repository, Bioconductor, or
CRAN.
 Bioconductor more restrict and have to comply all
guidelines:
http://www.bioconductor.org/developers/package-
guidelines/ 4/2/2013 60

61. Summary
 A GUI could help novice R users for utilizing all the power of
R.
 Increase the use of our package/methods especially by scientists
with no/less knowledge of R.
4/2/2013 61

62. Summary
 A GUI could help novice R users for utilizing all the power of
R.
 Increase the use of our package/methods especially by scientists
with no/less knowledge of R.
 Things to consider in developing a GUI:
• Type of GUI (spreadsheets, menu/dialog boxes),
• Tool to develop (tcltk, java)
• Embedded/Independent.
• Single/Multi dialog boxes
4/2/2013 62

63. Summary
 Independent GUI: really for a specific use, no need of “useless”
capabilities, simpler.
 Rcmdr PlugIn in: easier, all standard data manipulation and
analysis is ready, users can learn the command.
4/2/2013 63

64. Summary
 Independent GUI: really for a specific use, no need of “useless”
capabilities, simpler.
 Rcmdr PlugIn in: easier, all standard data manipulation and
analysis is ready, users can learn the command.
 Make sure GUI is simple and user friendly.
 Design  Development  Trial  Packaging and Storing
4/2/2013 64

65. The GUIs
 IsoGeneGUI:http://www.bioconductor.org/packages/2.11/
bioc/html/IsoGeneGUI.html
 neaGUI: https://r-forge.r-project.org/projects/neagui/
 biclustGUI:
http://www.ibiostat.be/software/BiclustGUI/index.html
 Examples of RGUI:
• http://www.sciviews.org/_rgui/
• http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/
• http://setiopramono.wordpress.com/r-programming/
4/2/2013 65

66. Next Development:
 Isogene RSB : Web based development using R Service
Bus: http://www.openanalytics.eu/r-service-bus
 R Service Bus: plug R into a processes independently of
the technology used by other software applications
involved in the workflow.
 Web Based neaGUI using shiny
 Shiny: Easy web applications in R:
http://www.rstudio.com/shiny/
4/2/2013 66

67. RSB-IsoGene
4/2/2013 67

68. Web based neaGUI
4/2/2013 68

69. Collaborator
 Karolinska Institutet, Sweden: Yudi Pawitan & Woojoo Lee
 Scilifelab, Sweden: Andrey Alexeyenko
 Johnson & Johnson Research and Development, Belgium: Luc
Bijnes & Willem Talloen.
 Hasselt University, Belgium: Ziv Shkedy, Dan Lin, Philippe H,
Martin O Pushpike, Tatsiana K.
 Open Analytics, Belgium: Tobias Verbeke
 Johannes Kepler University of Linz, Austria: Sepp Hochreiter’s
Group
 LMU Munich, Germany: Sebastian Kaiser
4/2/2013 69

70. Thank you for your attention…
4/2/2013 70

71. References
 Pramana, S., Lin, D., and Shkedy Z., (2010), IsoGeneGUI
Bioconductor Package Vignette.
 Pramana, S., Lin, D., Haldermans, P., Shkedy Z., and Verbeke, T., De
Bondt, A., Talloen, W., Göehlmann,. H and Bijnens, L. (2010).
“IsoGene: An R Package for Analyzing Dose-response Studies in
Microarray Experiments", R Journal 2/1.
 Pramana, S., Lin, D., Haldermans P., and Verbeke, T. (2102). “A
User Friendly Interface for Analyzing Dose-response Studies in
Microarray Experiments: The IsoGene-GUI package”, in Lin, D.,
Shkedy, Z., Yekutieli, D., Amaratunga, D. and Bijnens L. (editors).
Modeling Dose-response Microarray Data in Early Drug
Development Experiments Using R, Springer.
4/2/2013 71

72. References
 Pramana (2011) RcmdrPlugin.BiclustGUI: A User Friendly Interface
for Biclustering Analysis, a chapter of PhD: “Statistical Methods for
Microarray Experiments: Analysis Dose-response Studies and
Software Development in R”, Hasselt University, Belgium.
 Pramana, S., Lee, W., Alexeyenko, A., Pawitan., Y. (2012). neaGUI:
A Graphical User Interface for Network Enrichment Analysis.
 Fox J (2005). The R Commander: A Basic-Statistics Graphical User
Interface to R." Journal of Statistical Software, 14(9), 1-42.
 Valero-Mora, P.M and Ledesma R.D. (2012) “Graphical User
Interfaces for R”. Journal of Statistical Software.
 Verzani J (2007). An Introduction to gWidgets." R News, 7(3), 26-33.
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