limmaGUI {limmaGUI} | R Documentation

## Graphical User Interface for the limma microarray package

### Description

Graphical User Interface for the limma microarray package

### Usage

    AboutLimmaGUI()
    AboutNormalization()
    BChelp()
    ChooseContrastsParameterization(parameterizationTreeIndex)
    ChooseEbayesStatistic()
    ChooseParameterization()
    ChoosePlotSymbolByClicking(spotType, cex)
    ChooseSpotType(parameterizationTreeIndex)
    ComputeContrasts()
    CopyGraph(img)
    CreateNewParameterization()
    DeleteContrastsParameterization()
    deleteItemFromList(list1, itemName = NULL, index = NULL)
    DeleteParameterization()
    DupCorBoxPlot()
    ebayesBoxPlots()
    evalRcode()
    ExportHTMLreport()
    ExportTopTable()
    fixSeps(string)
    GetBackgroundCorrectionMethod()
    GetBetweenArrayNormalizationMethod()
    GetCoef(parameterizationTreeIndex, whichCoef = "onlyOne")
    GetComponentsToExportInHTMLreport(parameterizationIndex = NULL)
    GetContrastsParameterizationName()
    GetContrastsParameterizationNames(parameterizationTreeIndex)
    GetDEcutoff()
    GetDesignOrContrasts(Design = FALSE, Contrasts = FALSE, NumContrasts = 0,
                         parameterizationIndex = 0)
    GetGeneLabelsOptions()
    GetImageAnalysisColumnHeadings()
    GetImageProcessingFileType()
    GetJpegOrPngParams(graphFileType)
    GetJpegOrPngX11Params(graphFileType)
    GetlimmaDataSetName()
    GetlmFitMethod()
    GetLowessType()
    GetNEWxlim(xlim)
    GetNormexpOffsetValue(CurrentNormexpOffsetValue)
    GetNumParametersNoTargets()
    getPackageVersion(pkgName)
    GetParameterizationName()
    GetParameterNames(parameterizationTreeIndex)
    GetParametersAndOrContrasts(parameterizationTreeIndex, whatFor = "heat")
    GetPlotLabels(plottitle = "", xlabel = "", ylabel = "")
    GetPlotSize()
    GetPlotTitle(plottitle = "")
    GetPValueCutoff(p.value = 0.01)
    GetReducedDuplicateSpacing(parameterizationTreeIndex)
    GetRNATypesFrom.ContrastsFromDropDowns.String(string)
    GetSlideNum()
    GetSpotTypesForLinearModel()
    GetSpotTypesIncludedNames(parameterizationTreeIndex)
    GetWithinArrayNormalizationMethod()
    GetWtAreaParams()
    HeatDiagramDialog(parameterName)
    HeatDiagramPlot()
    HowManyDups()
    HTMLplotUsingFunction(Caption = "", File = .HTML.file,
                     GraphRelativeDirectory = ".", GraphAbsoluteDirectory =
                     NULL, GraphFileName = "", GraphSaveAs = "png",
                     GraphBorder = 1, Align = "center", plotFunction =
                     NULL, Width = 600, Height = 600, PointSize = 12,
                     BG ="white", res = 72, ...)
    ImageArrayPlot()
    ImageArrayPlotDialog(slidenum)
    ImportMA()
    ImportMADialog()
    initGlobals()
    InitNewParameterization()
    limmaGUI(BigfontsForlimmaGUIpresentation = FALSE)
    limmaHelp()
    lmFitMethodHelp()
    LogOddsPlot()
    MAPlot()
    MAPlotAvg()
    MBoxPlot()
    MMPlot()
    NewLimmaFile()
    NormalizeNow()
    nstrstr(haystack, needle)
    onDestroy()
    onExit()
    OpenALimmaFile(FileName)
    OpenGALandTargetsandSpotTypesfiles()
    OpenGALFile()
    OpenLimmaFile()
    OpenSpotTypesFile()
    OpenTargetsFile()
    plotMAColorCoded()
    PlotOptions()
    PrintTipGroupMAPlot()
    QQTplot()
    read.marrayTools(MFile,AFile, path, verbose, sep, quote, header, ...)
    ReadImageProcessingFiles()
    Require(pkg)
    Resize(img, plotFunction)
    SaveAsLimmaFile()
    SaveGraphAsJpeg(initialfile, plotFunction)
    SaveGraphAsPDF(initialfile, plotFunction)
    SaveGraphAsPNG(initialfile, plotFunction)
    SaveGraphAsPostscript(initialfile, plotFunction)
    SaveLimmaFile()
    SelectPlotSymbols(SpotTypes)
    SetLayoutParameters()
    SetupPlotKeyBindings(tt, img)
    SetupPlotMenus(tt, initialfile, plotFunction, img)
    SetWD()
    showChangeLog()
    showCitations()
    showGAL()
    showTopTable(..., export = FALSE)
    SimplifyContrastsExpression(string)
    strstr(haystack, needle)
    tclArrayVar()
    TclRequire(tclPkg)
    TryReadImgProcFile(expr)
    UpdateSpotTypesStatus()
    UpDownOrBoth()
    VennDiagramPlot()
    ViewDesignOrContrastsMatrixAsPairs(DesignOrContrasts, designOrContrastsList,
                     parameterizationIndex, contrastsParameterizationIndex
                     = NULL)
    ViewDesignOrContrastsMatrixInTable(DesignOrContrasts, designOrContrastsList,
                     parameterizationIndex, contrastsParameterizationIndex
                     = NULL)
    ViewExistingContrastsParameterization()
    ViewExistingParameterization()
    ViewRNATargets()
    ViewSpotTypes()

### Arguments

`BigfontsForlimmaGUIpresentation` | If set to TRUE, larger fonts are used. However, some font sizes are not controlled by limmaGUI and so must be adjusted in the operating system, e.g. in the Control Panel in Windows under Display, Appearance.
`...` | HTMLplotUsingFunction:arg15, showTopTable:arg1
`AFile` | Flat-file of log-intensities output by marrayTools
`Align` | HTMLplotUsingFunction:arg8
`BG` | HTMLplotUsingFunction:arg13
`Caption` | HTMLplotUsingFunction:arg1
`cex` | ChoosePlotSymbolByClicking:arg2
`contrastsParameterizationIndex` | ViewDesignOrContrastsMatrixInTable:arg4, ViewDesignOrContrastsMatrixAsPairs:arg4
`Contrasts` | GetDesignOrContrasts:arg2
`CurrentNormexpOffsetValue` | GetNormexpOffsetValue:arg1
`designOrContrastsList` | ViewDesignOrContrastsMatrixInTable:arg2, ViewDesignOrContrastsMatrixAsPairs:arg2
`DesignOrContrasts` | ViewDesignOrContrastsMatrixInTable:arg1, ViewDesignOrContrastsMatrixAsPairs:arg1
`Design` | GetDesignOrContrasts:arg1
`export` | showTopTable:arg2
`expr` | TryReadImgProcFile:arg1
`FileName` | A file name.
`File` | HTMLplotUsingFunction:arg2
`GraphAbsoluteDirectory` | HTMLplotUsingFunction:arg4
`GraphBorder` | HTMLplotUsingFunction:arg7
`GraphFileName` | HTMLplotUsingFunction:arg5
`graphFileType` | GetJpegOrPngParams:arg1, GetJpegOrPngX11Params:arg1
`GraphRelativeDirectory` | HTMLplotUsingFunction:arg3
`GraphSaveAs` | HTMLplotUsingFunction:arg6
`haystack` | nstrstr:arg1, strstr:arg1
`header` | See help for read.table
`Height` | HTMLplotUsingFunction:arg11
`img` | SetupPlotMenus:arg1, Resize:arg1, CopyGraph:arg1, SetupPlotKeyBindings:arg2
`index` | deleteItemFromList:arg1
`initialfile` | SaveGraphAsJpeg:arg1, SaveGraphAsPDF:arg1, SaveGraphAsPNG:arg1, SaveGraphAsPostscript:arg1, SetupPlotMenus:arg2
`itemName` | deleteItemFromList:arg1
`list1` | deleteItemFromList:arg1
`MFile` | Flat-file of log-ratios output by marrayTools
`needle` | nstrstr:arg2, strstr:arg2
`NumContrasts` | GetDesignOrContrasts:arg3
`p.value` | A p-value cutoff.
`parameterizationIndex` | GetDesignOrContrasts:arg4, GetComponentsToExportInHTMLreport:arg1, GetDesignOrContrasts:arg4, ViewDesignOrContrastsMatrixInTable:arg3, ViewDesignOrContrastsMatrixAsPairs:arg3
`parameterizationTreeIndex` | GetParametersAndOrContrasts:arg1, ChooseContrastsParameterization:arg1, ChooseSpotType:arg1,GetCoef:arg1, GetParameterNames:arg1, GetReducedDuplicateSpacing:arg1, GetContrastsParameterizationNames:arg1, GetSpotTypesIncludedNames:arg1
`parameterName` | HeatDiagramDialog:arg1
`path` | Path to the directory containing the MFile and AFile
`pkgName` | getPackageVersion:arg1
`pkg` | Require:arg1
`plotFunction` | SetupPlotMenus:arg1, HTMLplotUsingFunction:arg9, Resize:arg1, SaveGraphAsJpeg:arg2, SaveGraphAsPDF:arg2, SaveGraphAsPNG:arg2, SaveGraphAsPostscript:arg2
`plottitle` | GetPlotLabels:arg1,GetPlotTitle:arg1
`PointSize` | HTMLplotUsingFunction:arg12
`quote` | See help for read.table
`res` | HTMLplotUsingFunction:arg14
`sep` | Column separator. ("\t" for tab-delimited text)
`slidenum` | ImageArrayPlotDialog:arg1
`spotType` | ChoosePlotSymbolByClicking:arg1
`SpotTypes` | SelectPlotSymbols:arg1
`string` | fixSeps:arg1,SimplifyContrastsExpression:arg1, GetRNATypesFrom.ContrastsFromDropDowns.String:arg1
`tclPkg` | TclRequire:arg1
`tt` | SetupPlotKeyBindings:arg1, SetupPlotMenus:arg1
`verbose` | Optional diagnostic messages
`whatFor` | GetParametersAndOrContrasts:arg2
`whichCoef` | GetCoef:arg2
`Width` | HTMLplotUsingFunction:arg10
`xlabel` | GetPlotLabels:arg2
`xlim` | GetNEWxlim:arg1
`ylabel` | GetPlotLabels:arg3

### Details

This function launches a Graphical User Interface for the limma package by Gordon Smyth. The GUI uses Tk widgets (via the R TclTk interface by Peter Dalgaard) in order to provide a simple interface to the limma functions for linear modelling of microarrays and identification of differentially expressed genes.

### Author(s)

James Wettenhall

[Package limmaGUI version 1.64.0 Index]