Developing R

Graphical User

Interfaces

SETIA PRAMANA

Outlines

• Motivations

• R GUI• IsoGeneGUI

• neaGUI

• How to develop an R GUI?• Independent GUI

• Embedded GUI (RcmdrPlugin.BiclustGUI)

• Summary

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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.

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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.

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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

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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

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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).

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R Studio

Download from

Rstudio.com

Powerfull IDE

(Integrated

Development

Environment) for

R.

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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/) Shiny C++, C# Other extensions connect R to graphical

toolboxes for developing menus and dialog boxes: Tcltk, Gtk.

We focus on Tcltk and Shiny

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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.

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RGUI Developed using

tcltk R G

UI

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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)

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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)

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Independent

GUI

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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)

• Rcommander (Fox, 2005)

• RcmdrPlugin.biclustGUI (Pramana, 2011)

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Embeded

GUI

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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.

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neaGUI Output 16R

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neaGUI Output 17R

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RGUI: RCommander

Rcommander.com

Helpful for R

beginner

Install inside R

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RGUI using C#: Wires

Developed by STIS

students

For Spatial Data

Analysis

Still developing…

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RGUI using C#: WiresR

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RGUI: Web Based App

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WebBUGS

Conducting

Bayesian Statistical

Analysis Online

Combines

OpenBUGS and R

www.webbugs.psychstat.org

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RGUI: Shiny

A new package from Rstudio to build

interactive web applications with R.

Really Easy!

Build useful web applications with only a

few lines of code—no JavaScript required.

Self learning: http://shiny.rstudio.com/

http://www.showmeshiny.com/

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RGUI using Shiny: FAST

Figure 5. FAST main page

Figure 7. Cluster Analysis in FAST

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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?

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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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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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getXls <- function () {

fileName <- tclvalue(tkgetOpenFile(filetypes=

gettext(' {"Excel Files" {".xls"}} {"All Files"

{"*"}}')))

data <- get( fileName) }

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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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Create a Dialog Box

Create the windowrequire(tcltk)

tt<-tktoplevel()

tkwm.title(tt,"Input Window")

Edit BoxName <- tclVar("")

entry.Name <-tkentry(tt,width="20",

textvariable=Name)

tkgrid(tklabel(tt,text="Name:"), entry.Name)

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Create a Dialog Box

Radio buttonrb1 <- 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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Create a Dialog Box

List box with scroll barscr <- 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")

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Create a Dialog Box

OK buttonOK.but <-tkbutton(tt,text=" OK ",

command=OnOK)

tkgrid(OK.but)

tkgrid.configure(OK.but)

tkfocus(tt)

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Run the function (OK

button)

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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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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.

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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

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Summary

Make sure GUI is simple and user friendly.

Design Development Trial Packaging and Storing

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