# limmaGUI Menu Definitions

# last modified 10 Jun 04 by J. Wettenhall

# Based on Rcmdr-menus.txt from the Rcmdr package by John Fox, 

#   type    menu/item      operation/parent  label                                              command/menu
    
    menu    fileMenu        topMenu         ""                                                  ""
    item    fileMenu        command         "New     Ctrl+N"                                    NewLimmaFile
    item    fileMenu        command         "Open    Ctrl+O"                                    OpenLimmaFile
    item    fileMenu        command         "Save    Ctrl+S"                                    SaveLimmaFile
    item    fileMenu        command         "Save As"                                           SaveAsLimmaFile
    item    fileMenu        separator       ""                                                  ""
    item    fileMenu        command         "Import marrayTools Data"                           ImportMA
    item    fileMenu        separator       ""                                                  ""    
    item    fileMenu        command         "Export M values (log ratios)"                      ExportMvalues
    item    fileMenu        command         "Export A values (log intensities)"                 ExportAvalues
    item    fileMenu        command         "Export TopTable (differentially expressed genes)"  ExportTopTable
    item    fileMenu        command         "Export HTML Report"                                ExportHTMLreport
    item    fileMenu        separator       ""                                                  ""
    item    fileMenu        command         "Working Directory"                                 SetWD
    item    fileMenu        separator       ""                                                  ""
    item    fileMenu        command         "Exit"                                              onExit
    item    topMenu         cascade         "File"                                              fileMenu   
    menu    SpotTypesMenu   topMenu         ""                                                  ""
    item    SpotTypesMenu   command         "Spot Types"                                        ViewSpotTypes
    item    topMenu         cascade         "Spot Types"                                        SpotTypesMenu
    menu    RNATargetsMenu  topMenu         ""                                                  ""
    item    RNATargetsMenu  command         "RNA Targets"                                       ViewRNATargets
    item    topMenu         cascade         "RNA Targets"                                       RNATargetsMenu
    menu    layoutMenu      topMenu         ""                                                  ""
    item    layoutMenu      command         "Layout Parameters"                                 SetLayoutParameters
    item    layoutMenu      command         "View Gene List"                                    showGAL
    item    topMenu         cascade         "Layout"                                            layoutMenu
    menu    normalizeMenu   topMenu         ""                                                  ""
    item    normalizeMenu   command         "Select Within-Array Normalization Method"          GetWithinArrayNormalizationMethod
    item    normalizeMenu   command         "Select Between-Array Normalization Method"         GetBetweenArrayNormalizationMethod    
    item    normalizeMenu   command         "Normalize / Update M and A"                        NormalizeNow
    item    normalizeMenu   command         "Export M values (log ratios)"                      ExportMvalues
    item    normalizeMenu   command         "Export A values (log intensities)"                 ExportAvalues
    item    normalizeMenu   command         "About Normalization"                               AboutNormalization
    item    topMenu         cascade         "Normalization"                                     normalizeMenu
    menu    linearModelMenu topMenu         ""                                                  ""
    item    linearModelMenu command         "Compute Linear Model Fit"                          ComputeLinearModelFit
    item    linearModelMenu separator       ""                                                  ""
    item    linearModelMenu command         "Create New Parameterization"                       CreateNewParameterization
    item    linearModelMenu command         "View Existing Parameterization"                    ViewExistingParameterization
    item    linearModelMenu command         "Delete Parameterization"                           DeleteParameterization    
    item    linearModelMenu separator       ""                                                  ""
    item    linearModelMenu command         "Compute Contrasts"                                 ComputeContrasts
    item    linearModelMenu command         "View Existing Contrasts Parameterization"          ViewExistingContrastsParameterization
    item    linearModelMenu command         "Delete Contrasts Parameterization"                 DeleteContrastsParameterization        
    item    topMenu         cascade         "Linear Model"                                      linearModelMenu    
    menu    evaluateMenu    topMenu         ""                                                  ""
    item    evaluateMenu    command         "Evaluate R Code"                                   evalRcode
    item    topMenu         cascade         "Evaluate"                                          evaluateMenu
    menu    toptableMenu    topMenu         ""                                                  ""
    item    toptableMenu    command         "Table of Genes Ranked in order of Differential Expression"   showTopTable
    item    topMenu         cascade         "TopTable"                                          toptableMenu
    menu    plotMenu        topMenu         ""                                                  ""
    item    plotMenu        command         "M A Plot with lowess curves (for one slide)"       MAPlot
    item    plotMenu        command         "Color-Coded M A Plot (for one slide)"              plotMAColorCoded
    item    plotMenu        command         "Print-Tip Group M A Plot (for one slide)"          PrintTipGroupMAPlot
    item    plotMenu        command         "M Box Plot"                                        MBoxPlot
    item    plotMenu        command         "Image Array Plot"                                  ImageArrayPlot
    item    plotMenu        separator       ""                                                  ""
    item    plotMenu        command         "Quantile-Quantile t Statistic Plot"                QQTplot
    item    plotMenu        command         "M A Plot (using fitted M values)"                  MAPlotAvg
    item    plotMenu        command         "M M Plot (using fitted M values)"                  MMPlot
    item    plotMenu        command         "Log Odds Plot"                                     LogOddsPlot
    item    plotMenu        command         "Heat Diagram"                                      HeatDiagramPlot
    item    plotMenu        command         "Duplicate Correlation Box Plot"                    DupCorBoxPlot
    item    plotMenu        command         "Empirical Bayes Statistics Box Plots"              ebayesBoxPlots
    item    plotMenu        command         "Venn Diagram"                                      VennDiagramPlot
#    item    plotMenu        command         "Histogram"                                        HistogramPlot
    item    plotMenu        separator       ""                                                  ""
    item    plotMenu        command         "Options"                                           PlotOptions    
    item    topMenu         cascade         "Plot"                                              plotMenu
    menu    helpMenu        topMenu         ""                                                  ""
    item    helpMenu        command         "LimmaGUI Help"                                     limmaGUIhelp
    item    helpMenu        command         "Limma Help"                                        limmaHelp
    item    helpMenu        separator       ""                                                  ""
    item    helpMenu        command         "Normalization"                                     AboutNormalization
    item    helpMenu        separator       ""                                                  ""    
    item    helpMenu        command         "Citations"                                         showCitations
    item    helpMenu        command         "ChangeLog"                                         showChangeLog
    item    helpMenu        command         "About LimmaGUI"                                    AboutLimmaGUI
    item    topMenu         cascade         "Help"                                              helpMenu
