R/IsoGeneGUI.R

`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)
    
    analysisVecMenu <- 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(HD)", menu = analysisMenu)
    
    
    tkadd(analysisVecMenu, "cascade", label = "Set Seed", command = Setseed)
    tkadd(analysisVecMenu, "cascade", label = "Likelihood Ratio Test (E2): Asymptotic", command = ExactE2Vec )
    tkadd(analysisVecMenu, "cascade", label = "Permutation", command = PermutationVec )
    tkadd(analysisVecMenu, "cascade", label = "GORIC", command = doGORICVec)
    tkadd(analysisVecMenu, "cascade", label = "IsoPlot", command = IsoplotVec)
    tkadd(analysisVecMenu, "cascade", label = "Permutation P-values Plot", command = IsopvalPlotVec)
       
    tkadd(topMenu, "cascade", label = "Analysis(SD)", menu = analysisVecMenu)
    
    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)
    
  }

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IsoGeneGUI documentation built on May 2, 2019, 4:49 p.m.