# Grapics related functions for Bioconductor

## Documentation for package ‘geneplotter’ version 1.20.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

alongChrom | A function for plotting expression data from an ExpressionSet for a given chromosome.
amplicon.plot | Create an amplicon plot
buildACMainLabel | A function for plotting expression data from an ExpressionSet for a given chromosome.
cColor | A function for marking specific probes on a cPlot.
closeHtmlPage | Open and close an HTML file for writing.
connection-class | Virtual S4 classes for method dispatching
cPlot | A plotting function for chromosomes.
cScale | A function for mapping chromosome length to a number of points.
cullACXPoints | A function for plotting expression data from an ExpressionSet for a given chromosome.
dChip.colors | A function to get the Red-Blue color scheme used by dChip
defMapFun | A function to plot a graph colored by expression data
densCols | Scatterplots with smoothed densities color representation
dispACXaxis | A function for plotting expression data from an ExpressionSet for a given chromosome.
doACCumPlot | A function for plotting expression data from an ExpressionSet for a given chromosome.
doACImagePlot | A function for plotting expression data from an ExpressionSet for a given chromosome.
doACLocalPlot | A function for plotting expression data from an ExpressionSet for a given chromosome.
doACMatPlot | A function for plotting expression data from an ExpressionSet for a given chromosome.
emptyACPlot | A function for plotting expression data from an ExpressionSet for a given chromosome.
expressionSet133a | A small dataset for testing
file-class | Virtual S4 classes for method dispatching
fixACPhysPoints | A function for plotting expression data from an ExpressionSet for a given chromosome.
getACClosestPos | A function for plotting expression data from an ExpressionSet for a given chromosome.
getACDataEnv | A function for plotting expression data from an ExpressionSet for a given chromosome.
getACExprs | A function for plotting expression data from an ExpressionSet for a given chromosome.
getACGeneSyms | A function for plotting expression data from an ExpressionSet for a given chromosome.
getACPlotLabs | A function for plotting expression data from an ExpressionSet for a given chromosome.
getACStrandVals | A function for plotting expression data from an ExpressionSet for a given chromosome.
GetColor | A function to get the Red-Blue color scheme used by dChip
getPlotExpressionColors | A function to plot a graph colored by expression data
greenred.colors | A function to get the Red-Blue color scheme used by dChip
groupedHeatmap | Heatmap of a matrix with grouped rows and columns
highlightACDups | A function for plotting expression data from an ExpressionSet for a given chromosome.
histStack | Stacked histogram
imageMap | Write an HTML IMG tag together with a MAP image map.
imageMap,matrix,connection,list,character-method | Write an HTML IMG tag together with a MAP image map.
imageMap,matrix-method | Write an HTML IMG tag together with a MAP image map.
imageMap-methods | Write an HTML IMG tag together with a MAP image map.
IMCAEntrezLink | A function to plot a graph colored by expression data
limitACXRange | A function for plotting expression data from an ExpressionSet for a given chromosome.
make.chromOrd | Make a chromOrd object
Makesense | Produce Smoothed Sense/Anti-sense For All Chromosomes
Makesense,ExpressionSet,character-method | Produce Smoothed Sense/Anti-sense For All Chromosomes
Makesense,ExpressionSet,missing-method | Produce Smoothed Sense/Anti-sense For All Chromosomes
Makesense,matrix,character-method | Produce Smoothed Sense/Anti-sense For All Chromosomes
multidensity | Multiple empirical cumulative distribution functions (ecdf) and densities
multiecdf | Multiple empirical cumulative distribution functions (ecdf) and densities
openHtmlPage | Open and close an HTML file for writing.
panel.smoothScatter | Lattice panel function analogous to smoothScatter
plotChr | Plot Smoothed Sense/Anti-sense of Specified Chromosomes
plotExpressionGraph | A function to plot a graph colored by expression data
saveeps | Save the contents of the current graphics device to a file
savepdf | Save the contents of the current graphics device to a file
savepng | Save the contents of the current graphics device to a file
savetiff | Save the contents of the current graphics device to a file
scaleACData | A function for plotting expression data from an ExpressionSet for a given chromosome.
smoothScatter | Scatterplots with smoothed densities color representation