affylmGUI {affylmGUI} | R Documentation

## Graphical User Interface for the limma microarray package

### Description

Graphical User Interface for Affy analysis using the limma microarray package

### Usage

    AboutaffylmGUI()
    affyHelp()
    affylmGUI(BigfontsForaffylmGUIpresentation=FALSE)
    affylmGUIhelp()
    affyPlotMA()
    affyPlotMAcontrast()
    ALGlimmaUsersGuide(view=TRUE)
    ChooseCDF()
    ChooseContrastParameterization()
    chooseDir()
    ChooseEbayesStatistic()
    ComputeContrasts()
    ComputeLinearModelFit()
    CopyGraph(img)
    DeleteContrastParameterization()
    deleteItemFromList(list1,itemName=NULL,index=NULL)
    DensityPlot()
    DensityPlotAll()
    evalRcode()
    ExportHTMLreport()
    ExportNormalizedExpressionValues()
    ExportTopTable()
    fixSeps(string)
    generalPlotFunction(code="",WindowTitle="")
    GetComponentsToExportInHTMLreport(contrastParameterizationIndex=NULL)
    GetContrast(contrastParameterizationIndex)
    GetContrastNamesForHeatDiagram(numContrasts=2,ContrastNames=c("Contrast 1","Contrast 2"))
    GetContrastParameterizationName()
    GetContrasts(NumContrasts=0)
    GetDEcutoff()
    GetGeneLabelsOptions()
    GetJpegOrPngParams(graphFileType)
    GetJpegOrPngX11Params(graphFileType)
    GetlimmaDataSetName()
    GetLogPLMDataChoice()
    GetMultipleContrasts(contrastParameterizationIndex)
    GetNormalizationMethod()
    getPackageVersion(pkgName)
    GetParameterizationName()
    GetPlotLabels(plottitle="",xlabel="",ylabel="")
    GetPlotSize()
    GetPlotTitle(plottitle="")
    GetPValueCutoff(p.value=0.01)
    GetResidualTypeChoice()
    GetRNATypesFrom.ContrastsFromDropDowns.String(string)
    GetSetNames(numSets=2,set1="",set2="",set3="")
    GetSlideNum(all=FALSE)
    GetSlideNums()
    GetWhichProbes(includeBoth=FALSE)
    GetWtAreaParams()
    GetWtFlagParams()
    HeatDiagramDialog(parameterName)
    HeatDiagramPlot()
    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()
    ImageQualityResidualPlot()
    ImageQualityWeightPlot()
    initGlobals()
    IntensityHistogram()
    IntensityHistogramAll()
    limmaHelp()
    LogOddsPlot()
    NewLimmaFile()
    NormalizedIntensityBoxPlot()
    NormalizeNow()
    nstrstr(haystack,needle)
    NUSEPlotAll()
    onDestroy()
    onExit()
    OpenALimmaFile(FileName)
    OpenCDFandTargetsfiles()
    OpenCDFFile()
    OpenLimmaFile()
    OpenTargetsFile()
    PlotOptions()
    QQTplot()
    RawIntensityBoxPlot()
    Require(pkg)
    Resize(img,plotFunction)
    RLEPlotAll()
    RNADegradationPlotAll()
    SaveAsLimmaFile()
    SaveGraphAsJpeg(initialfile, plotFunction)
    SaveGraphAsPDF(initialfile, plotFunction)
    SaveGraphAsPNG(initialfile, plotFunction)
    SaveGraphAsPostscript(initialfile, plotFunction)
    SaveLimmaFile()
    SetupPlotKeyBindings(tt,img)
    SetupPlotMenus(tt,initialfile,plotFunction,img)
    SetWD()
    showChangeLog(n = 20)
    showCitations()
    showTopTable(...,export=FALSE)
    SimplifyContrastsExpression(string)
    strstr(haystack, needle)
    tclArrayVar()
    TclRequire(tclPkg)
    topTable2(fit, coef = 1, number = 10, genelist = NULL,adjust.method = "holm", sort.by = "B")
    toptable2(fit, coef = 1, number = 10, genelist = NULL, A = NULL,eb = NULL, adjust.method = "holm", sort.by = "B", ...)
    Try(expr)
    TryReadImgProcFile(expr)
    UpDownOrBoth()
    vennDiagramaffylmGUI(object, include = "both", names, cex = 1.5, mar = rep(1, 4), ...)
    VennDiagramPlot()
    ViewContrastsMatrixAsPairs(contrastsMatrix, contrastsMatrixList,contrastParameterizationIndex = NULL)
    ViewContrastsMatrixInTable(contrastsMatrixList, contrastParameterizationIndex = NULL)
    ViewExistingContrastParameterization()
    ViewRNATargets()

### Arguments

`BigfontsForaffylmGUIpresentation` | affylmGUI:arg1:If set to TRUE, larger fonts are used. However, some font sizes are not controlled by affylmGUI and so must be adjusted in the operating system, e.g. in the Control Panel in Windows under Display, Appearance.
`...` | HTMLplotUsingFunction:arg14:and:showTopTable:arg1:and:toptable2:arg9:and:vennDiagramaffylmGUI:arg6
`Align` | HTMLplotUsingFunction:arg8
`all` | GetSlideNum:arg1
`BG` | HTMLplotUsingFunction:arg12
`Caption` | HTMLplotUsingFunction:arg1
`code` | generalPlotFunction: arg1: a code
`ContrastNames` | GetContrastNamesForHeatDiagram:arg2
`contrastParameterizationIndex` | GetComponentsToExportInHTMLreport:arg1:and:contrastParameterizationIndex:arg1:and:GetContrast:arg1:and:HTMLplotUsingFunction:arg3:and:ViewContrastsMatrixInTable:arg2
`export` | showTopTable:arg2
`expr` | Try:arg1:and:TryReadImgProcFile:arg1
`File` | HTMLplotUsingFunction:arg2
`FileName` | OpenALimmaFile:arg1
`GraphAbsoluteDirectory` | HTMLplotUsingFunction:arg4
`GraphBorder` | HTMLplotUsingFunction:arg7
`GraphFileName` | HTMLplotUsingFunction:arg5
`graphFileType` | GetJpegOrPngParams:arg1:and:GetJpegOrPngX11Params:arg1
`GraphRelativeDirectory` | HTMLplotUsingFunction:arg3
`GraphSaveAs` | HTMLplotUsingFunction:arg6
`haystack` | nstrstr:arg1:and:strstr:arg1
`Height` | HTMLplotUsingFunction:arg11
`img` | Resize:arg1:and:SetupPlotMenus:arg4:and:CopyGraph:arg1:and:SetupPlotKeyBindings:arg2
`includeBoth` | GetWhichProbes:arg1
`index` | deleteItemFromList:arg3:an index
`initialfile` | SetupPlotMenus:arg2:and:SaveGraphAsJpeg:arg1:and:SaveGraphAsPDF:arg1:and:SaveGraphAsPNG:arg1:and:SaveGraphAsPostscript:arg1
`itemName` | deleteItemFromList:arg2:an item name
`list1` | deleteItemFromList:arg1:a list
`needle` | nstrstr:arg2:and:strstr:arg2
`NumContrasts` | GetContrasts:arg1
`numContrasts` | GetContrastNamesForHeatDiagram:arg1
`numSets` | GetSetNames:arg1
`p.value` | GetPValueCutoff:arg1:A p-value cutoff.
`parameterName` | HeatDiagramDialog:arg1
`pkgName` | getPackageVersion:arg1
`pkg` | Require:arg1
`plotFunction` | Resize:arg2:and:HTMLplotUsingFunction:arg9:and:SetupPlotMenus:arg3:and:SaveGraphAsJpeg:arg2:and:SaveGraphAsPDF:arg2:and:SaveGraphAsPNG:arg2:and:SaveGraphAsPostscript:arg2
`plottitle` | GetPlotLabels:arg1:and:GetPlotTitle:arg1
`res` | HTMLplotUsingFunction:arg13
`set1` | GetSetNames:arg2
`set2` | GetSetNames:arg3
`set3` | GetSetNames:arg4
`string` | fixSeps:arg1:A character string:and:GetRNATypesFrom.ContrastsFromDropDowns.String:arg1:and:SimplifyContrastsExpression:arg1
`tclPkg` | TclRequire:arg1
`tt` | SetupPlotMenus:arg1:and:SetupPlotKeyBindings:arg1
`view` | ALGlimmaUsersGuide:arg1:A boolean determinig if the users'd guide will be viewed
`Width` | HTMLplotUsingFunction:arg10
`WindowTitle` | generalPlotFunction: arg2: a title
`xlabel` | GetPlotLabels:arg2
`ylabel` | GetPlotLabels:arg3
`fit` | topTable2:arg1:and:toptable2:arg1
`coef` | topTable2:arg2:and:toptable2:arg2
`number` | topTable2:arg3:and:toptable2:arg3
`genelist` | topTable2:arg4:and:toptable2:arg4
`A` | toptable2:arg5
`eb` | toptable2:arg6
`adjust.method` | topTable2:arg5:and:toptable2:arg7
`sort.by` | topTable2:arg6:and:toptable2:arg8
`object` | vennDiagramaffylmGUI:arg1
`include` | vennDiagramaffylmGUI:arg2
`names` | vennDiagramaffylmGUI:arg3
`cex` | vennDiagramaffylmGUI:arg4
`mar` | vennDiagramaffylmGUI:arg5
`contrastsMatrix` | ViewContrastsMatrixAsPairs:arg1
`contrastsMatrixList` | ViewContrastsMatrixAsPairs:arg2:and:ViewContrastsMatrixInTable:arg1
`n` | showChangeLog:arg1
`PointSize` | HTMLplotUsingFunction:arg12

### 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 affylmGUI version 1.54.1 Index]