R/IsoGeneGUI.R

In IsoGeneGUI: A graphical user interface to conduct a dose-response analysis of microarray data

`IsoGeneGUI` <-
function () {

#############################################
# Creating a main window with menu and plot #
#############################################

tt <<- tktoplevel()
tkwm.title(tt,"IsoGene GUI 2.0")
##############################

#####################################
# Making a menu for the main widget #
#####################################

topMenu <- tkmenu(tt)           # Create a menu
tkconfigure(tt, menu = topMenu) # Add it to the 'tt' window
welcome <-tkframe(tt, borderwidth=2, width=1500, height=1000)
tclRequire("BWidget")
message <-tkframe(tt, borderwidth=2)

fileMenu <- tkmenu(topMenu, tearoff = FALSE)
analysisMenu<- tkmenu(topMenu, tearoff = FALSE)
PlotsMenu<- tkmenu(topMenu, tearoff = FALSE)
HelpMenu<- tkmenu(topMenu, tearoff = FALSE)
clusteringMenu<- tkmenu(topMenu, tearoff = FALSE)

loadMenu<- tkmenu(fileMenu, tearoff = FALSE)
SamMenu <- tkmenu(analysisMenu, tearoff = FALSE)
SamPlotMenu <- tkmenu(PlotsMenu, tearoff = FALSE)
IsoGeneHelpMenu<- tkmenu(HelpMenu, tearoff = FALSE)


tkadd(fileMenu,"cascade", label = "Open dataset", menu= loadMenu)
tkadd(loadMenu, "command", label = "R workspace", command = loadDataSet )
tkadd(loadMenu, "command", label = "Excel or Text files", command = openFile )
tkadd(fileMenu,"separator")

tkadd(fileMenu,"cascade", label = "Show dataset", command = showdata)

tkadd(fileMenu,"separator")
tkadd(fileMenu, "cascade", label = "Exit", command = exit)

tkadd(topMenu, "cascade", label = "File", menu = fileMenu)

tkadd(analysisMenu, "cascade", label = "Set Seed", command = Setseed)
tkadd(analysisMenu, "cascade", label = "Likelihood Ratio Test (E2): Asymptotic", command = ExactE2 )
tkadd(analysisMenu, "cascade", label = "Permutation", command = Permutation )

tkadd(analysisMenu, "cascade", label = "Significance Analysis of Microarrays", menu = SamMenu )
tkadd(SamMenu, "command", label = "SAM Permutation", command = PermuteSAM )
tkadd(SamMenu, "command", label = "SAM Analysis", command = IsoPlotSldr )

tkadd(analysisMenu, "cascade", label = "Likelihood Ratio Test (E2): orQA", command = orQAE2)
tkadd(analysisMenu, "cascade", label = "GORIC", command = doGORIC)

tkadd(topMenu, "cascade", label = "Analysis", menu = analysisMenu)


tkadd(clusteringMenu,"cascade", label = "ORCME", command= doORCME)
tkadd(clusteringMenu,"cascade", label = "ORIClust", command= doORIClust)
tkadd(topMenu, "cascade", label = "Clustering", menu = clusteringMenu)


tkadd(PlotsMenu, "cascade", label = "IsoPlot", command = Isoplot)
tkadd(PlotsMenu, "cascade", label = "Permutation P-values Plot", command = IsopvalPlot)
tkadd(PlotsMenu, "cascade", label = "SAM Plots", menu = SamPlotMenu)
tkadd(SamPlotMenu, "command", label = "Plot of FDR vs. Delta", command = PlotFdrDlt)
tkadd(SamPlotMenu, "command", label = "Plot of number of significant genes vs. Delta", command = PlotSigDlt)
tkadd(SamPlotMenu, "command", label = "Plot of number of FP vs. Delta", command = PlotFPDlt)
tkadd(PlotsMenu, "cascade", label = "User Defined Scatter Plot", command = UserPlotting)
tkadd(PlotsMenu, "cascade", label = "Plot ORCME clusters", command = plotORCME)

tkadd(topMenu, "cascade", label = "Plots", menu = PlotsMenu)
tkadd(HelpMenu, "cascade", label = "IsoGene Help", command = onHelpIsoGene )
#tkadd(HelpMenu, "cascade", label = "IsoGeneGUI Help", command = IsoGeneGUIHelp)

tkadd(HelpMenu, "cascade", label = "IsoGeneGUI Help", menu=IsoGeneHelpMenu)
tkadd(IsoGeneHelpMenu, "command", label = "IsoGeneGUI Help", command = IsoGeneGUIHelp)
tkadd(IsoGeneHelpMenu, "command", label = "IsoGeneGUI Vignette", command = IsoGeneGUIVignette)


tkadd(HelpMenu, "cascade", label = "About", command = about )
tkadd(topMenu, "cascade", label = "Help", menu = HelpMenu)



fontHeading <- tkfont.create(family="times",size=22,weight="bold",slant="italic")
fontTextLabel <- tkfont.create(family="times",size=10)

tkgrid(tklabel(welcome, text="                             ", font=fontHeading))
tkgrid(tklabel(welcome, text="    Welcome to IsoGene GUI 2.0  ", font=fontHeading))
tkgrid(tklabel(welcome, text=" A Graphical User Interface for dose response analysis in microarray experiments" ,font=fontTextLabel))
tkgrid(tklabel(welcome, text="                              ", font=fontHeading))

SeedNum <<- 1234
tkgrid(welcome)

yScr       <- tkscrollbar(tt,command=function(...)tkyview(treeWidget,...))
treeWidget <<- tkwidget(tt,"Tree", yscrollcommand=function(...)tkset(yScr,...), width=50, height=15)

tkgrid(tklabel(tt, text=" Infobox  ", font=fontTextLabel))
tkgrid(treeWidget, yScr)
tkgrid.configure(yScr, stick="nsw")


# Insert at the end of the nodes in "root" a new node, called
# "Record1Node", which displays the text "Record 1", etc.

tkinsert(treeWidget, "end", "root", "Record1Node", text="Data")
tkinsert(treeWidget, "end", "root", "Record2Node", text="LRT: Asymptotic")
tkinsert(treeWidget, "end", "root", "Record3Node", text="Permutation")
tkinsert(treeWidget, "end", "root", "Record4Node", text="SAM")
tkinsert(treeWidget, "end", "root", "Record5Node", text="LRT: orQA")
tkinsert(treeWidget, "end", "root", "Record6Node", text="GORIC")
tkinsert(treeWidget, "end", "root", "Record7Node", text="ORCME")
tkinsert(treeWidget, "end", "root", "Record8Node", text="ORIClust")

tkinsert(treeWidget, "end", "Record1Node", "data", text="Not Available")
tkinsert(treeWidget, "end", "Record2Node", "nodeAsymp", text="Not Available")
tkinsert(treeWidget, "end", "Record3Node", "nodePerm", text="Not Available")
tkinsert(treeWidget, "end", "Record4Node", "nodeSAM", text="Not Available")
tkinsert(treeWidget, "end", "Record5Node", "nodeORQA", text="Not Available")
tkinsert(treeWidget, "end", "Record6Node", "nodeGORIC", text="Not Available")
tkinsert(treeWidget, "end", "Record7Node", "nodeORCME", text="Not Available")
tkinsert(treeWidget, "end", "Record8Node", "nodeORIClust", text="Not Available")

tkgrid(tklabel(tt,text="") )

tkwait.window(tt)

}