internal: Internal Functions

In affylmGUI: GUI for limma Package with Affymetrix Microarrays

Description

Internal functions defined by the affylmGUI package.

Usage

AboutaffylmGUI()
affyHelp()
affylmGUIhelp()
affyPlotMA()
affyPlotMAcontrast()
ChooseCDF()
ChooseContrastParameterization()
chooseDir()
ChooseEbayesStatistic()
ComputeContrasts()
ComputeLinearModelFit()
CopyGraph(img)
DeleteContrastParameterization()
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 = "plot.html", 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()
showCitations()
showTopTable(...,export=FALSE)
SimplifyContrastsExpression(string)
strstr(haystack, needle)
tclArrayVar()
TclRequire(tclPkg)
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

...	HTMLplotUsingFunction:arg14:and:showTopTable:arg1: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
initialfile	SetupPlotMenus:arg2:and:SaveGraphAsJpeg:arg1:and:SaveGraphAsPDF:arg1:and:SaveGraphAsPNG:arg1:and:SaveGraphAsPostscript:arg1
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
Width	HTMLplotUsingFunction:arg10
WindowTitle	generalPlotFunction: arg2: a title
xlabel	GetPlotLabels:arg2
ylabel	GetPlotLabels:arg3
object	vennDiagramaffylmGUI:arg1
include	vennDiagramaffylmGUI:arg2
names	vennDiagramaffylmGUI:arg3
cex	vennDiagramaffylmGUI:arg4
mar	vennDiagramaffylmGUI:arg5
contrastsMatrix	ViewContrastsMatrixAsPairs:arg1
contrastsMatrixList	ViewContrastsMatrixAsPairs:arg2:and:ViewContrastsMatrixInTable:arg1
PointSize	HTMLplotUsingFunction:arg12

Details

These functions are called by affylmGUI() via the GUI and are not intended to be called directly by users.

Author(s)

Created by James Wettenhall between 2003 and September 2006. Maintained by Keith Satterley between September 2006 and July 2015. Currently maintained by Gordon Smyth.

See Also

affylmGUI

affylmGUI documentation built on Nov. 8, 2020, 11 p.m.