# affylmGUI Menu Definitions

# last modified 18 Dec 03 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         "Export Normalized Expression Values"           ExportNormalizedExpressionValues
    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    RNATargetsMenu  topMenu         ""                                              ""
    item    RNATargetsMenu  command         "RNA Targets"                                   ViewRNATargets
    item    topMenu         cascade         "RNA Targets"                                   RNATargetsMenu
    menu    normalizeMenu   topMenu         ""                                              ""
    item    normalizeMenu   command         "Normalize"                                     NormalizeNow
    item    normalizeMenu   command         "Export Normalized Expression Values"           ExportNormalizedExpressionValues
    item    topMenu         cascade         "Normalization"                                 normalizeMenu
    menu    linearModelMenu topMenu         ""                                              ""
    item    linearModelMenu command         "Compute Linear Model Fit"                      ComputeLinearModelFit
    item    linearModelMenu separator       ""                                              ""
    item    linearModelMenu command         "Compute Contrasts"                             ComputeContrasts
    item    linearModelMenu command         "View Existing Contrasts Parameterization"      ViewExistingContrastParameterization
    item    linearModelMenu command         "Delete Contrasts Parameterization"             DeleteContrastParameterization
    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         "Intensity Density Plot"                        DensityPlotAll
    item    plotMenu        command         "Raw Intensity Box Plot"                        RawIntensityBoxPlot
    item    plotMenu        command         "Normalized Intensity Box Plot"                 NormalizedIntensityBoxPlot
    item    plotMenu        command         "RNA Degradation Plot"                          RNADegradationPlotAll
    item    plotMenu        command         "NUSE-Normalized Unscaled Std.Errors Plot"      NUSEPlotAll
    item    plotMenu        command         "RLE-Relative Log Expression Plot"              RLEPlotAll
    item    plotMenu        command         "Weights pseudo chip Image(s) Plot"             ImageQualityWeightPlot
    item    plotMenu        command         "Residuals pseudo chip Image(s) Plot"           ImageQualityResidualPlot
    item    plotMenu        command         "M A Plot (for two slides)"                     affyPlotMA
    item    plotMenu        command         "Image Array Plot(One slide)"                   ImageArrayPlot
    item    plotMenu        separator       ""                                              ""
    item    plotMenu        command         "M A Plot (for one contrast)"                   affyPlotMAcontrast
    item    plotMenu        command         "Quantile-Quantile t Statistic Plot (for one contrast)"  QQTplot
    item    plotMenu        command         "Log Odds (Volcano) Plot (for one contrast)"    LogOddsPlot
    item    plotMenu        command         "Heat Diagram"                                  HeatDiagramPlot
    item    plotMenu        command         "Venn Diagram"                                  VennDiagramPlot
    item    plotMenu        separator       ""                                              ""
    item    plotMenu        command         "Options"                                       PlotOptions
    item    topMenu         cascade         "Plot"                                          plotMenu
    menu    helpMenu        topMenu         ""                                              ""
    item    helpMenu        command         "affylmGUI Help"                                affylmGUIhelp
    item    helpMenu        command         "affy Help"                                     affyHelp
    item    helpMenu        command         "Limma Help"                                    limmaHelp
    item    helpMenu        separator       ""                                              ""
    item    helpMenu        command         "Citations"                                     showCitations
    item    helpMenu        command         "ChangeLog"                                     showChangeLog
    item    helpMenu        command         "About affylmGUI"                               AboutaffylmGUI
    item    topMenu         cascade         "Help"                                          helpMenu
