Entry: GetColor
Aliases: GetColor dChip.colors greenred.colors
Keywords: manip
Description: A function to get the Red-Blue color scheme used by dChip
URL: ../../../library/geneplotter/html/GetColor.html

Entry: Makesense
Aliases: Makesense Makesense,matrix,character-method Makesense,exprSet,character-method Makesense,exprSet,missing-method Makesense,eSet,missing-method Makesense,eSet,character-method
Keywords: dplot
Description: Produce Smoothed Sense/Anti-sense For All Chromosomes
URL: ../../../library/geneplotter/html/Makesense.html

Entry: alongChrom
Aliases: alongChrom buildACMainLabel doACImagePlot fixACPhysPoints getACGeneSyms limitACXRange cullACXPoints doACLocalPlot getACClosestPos getACPlotLabs scaleACData dispACXaxis doACMatPlot getACDataEnv getACStrandVals doACCumPlot emptyACPlot getACExprs highlightACDups
Keywords: utilities
Description: A function for plotting expression data from an exprset for a given chromosome.
URL: ../../../library/geneplotter/html/alongChrom.html

Entry: amplicon.plot
Aliases: amplicon.plot
Keywords: hplot
Description: Create an amplicon plot
URL: ../../../library/geneplotter/html/amplicon.plot.html

Entry: cColor
Aliases: cColor
Keywords: utilities
Description: A function for marking specific probes on a cPlot.
URL: ../../../library/geneplotter/html/cColor.html

Entry: cPlot
Aliases: cPlot
Keywords: utilities
Description: A plotting function for chromosomes.
URL: ../../../library/geneplotter/html/cPlot.html

Entry: cScale
Aliases: cScale
Keywords: utilities
Description: A function for mapping chromosome length to a number of points.
URL: ../../../library/geneplotter/html/cScale.html

Entry: connection-class
Aliases: connection-class file-class
Keywords: classes
Description: Virtual S4 classes for method dispatching
URL: ../../../library/geneplotter/html/classes.html

Entry: expressionSet133a
Aliases: expressionSet133a
Keywords: datasets
Description: A small dataset for testing
URL: ../../../library/geneplotter/html/eset133a.html

Entry: histStack
Aliases: histStack
Keywords: hplot
Description: Stacked histogram
URL: ../../../library/geneplotter/html/histStack.html

Entry: identifyLines
Aliases: identifyLines
Keywords: utilities
Description: A function for identifying sample lines on an alongChrom() plot.
URL: ../../../library/geneplotter/html/identifyLines.html

Entry: imageMap-methods
Aliases: imageMap imageMap-methods imageMap,matrix-method imageMap,matrix,connection,list,character-method
Keywords: manip
Description: Write an HTML IMG tag together with a MAP image map.
URL: ../../../library/geneplotter/html/imageMap.html

Entry: make.chromOrd
Aliases: make.chromOrd
Keywords: utilities
Description: Make a chromOrd object
URL: ../../../library/geneplotter/html/make.chromOrd.html

Entry: multiecdf
Aliases: multiecdf multiecdf.default multiecdf.formula multidensity multidensity.default multidensity.formula
Keywords: hplot
Description: Multiple empirical cumulative distribution functions (ecdf) and densities
URL: ../../../library/geneplotter/html/multiecdf.html

Entry: openHtmlPage
Aliases: openHtmlPage closeHtmlPage
Keywords: IO
Description: Open and close an HTML file for writing.
URL: ../../../library/geneplotter/html/openHtmlPage.html

Entry: plotChr
Aliases: plotChr
Keywords: hplot
Description: Plot Smoothed Sense/Anti-sense of Specified Chromosomes
URL: ../../../library/geneplotter/html/plotChr.html

Entry: plotExpressionGraph
Aliases: plotExpressionGraph getPlotExpressionColors defMapFun
Keywords: utilities graphs hplot
Description: A function to plot a graph colored by expression data
URL: ../../../library/geneplotter/html/plotExpressionGraph.html

Entry: savepng
Aliases: savepdf saveeps savepng savetiff
Keywords: programming error
Description: Save the contents of the current graphics device to a file
URL: ../../../library/geneplotter/html/savepng.html

Entry: smoothScatter
Aliases: smoothScatter densCols
Keywords: hplot
Description: Scatterplots with smoothed densities color representation
URL: ../../../library/geneplotter/html/smoothscatter.html