limmaGUI              package:limmaGUI              R Documentation

_G_r_a_p_h_i_c_a_l _U_s_e_r _I_n_t_e_r_f_a_c_e _f_o_r _t_h_e _l_i_m_m_a _m_i_c_r_o_a_r_r_a_y _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     Graphical User Interface for the limma microarray package

_U_s_a_g_e:

     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()
     limmaUsersGuide(view = TRUE)
     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()

_A_r_g_u_m_e_n_t_s:

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

    view: limmaUsersGuide:arg1

 whatFor: GetParametersAndOrContrasts:arg2

whichCoef: GetCoef:arg2

   Width: HTMLplotUsingFunction:arg10

  xlabel: GetPlotLabels:arg2

    xlim: GetNEWxlim:arg1

  ylabel: GetPlotLabels:arg3

_D_e_t_a_i_l_s:

     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.

_A_u_t_h_o_r(_s):

     James Wettenhall

