annoDomains             Annotate domains in a Hi-C plot
annoGenomeLabel         Annotate genomic coordinates along the x or
                        y-axis of a plot
annoHeatmapLegend       Add a color scale legend for heatmap-style
                        plots
annoHighlight           Annotates a highlight box around a specified
                        genomic region of a plot
annoPixels              Annotate pixels in a Hi-C plot
annoSegments            Annotates a line segment within a plot
annoText                Annotates text within a plot
annoXaxis               Add an x-axis to a plot
annoYaxis               Add a y-axis to a plot
annoZoomLines           Annotates zoom lines for a specified genomic
                        region of a plot
assembly                Make a 'assembly' object for alternate TxDb,
                        OrgDb,and BSgenome genomic annotation packages
c                       Combine multiple pgParams objects into a vector
colorby                 Handle plotgardener color scaling parameters
defaultPackages         Display the default genomic annotation packages
                        associated with a genome build
genomes                 Display the included available default genome
                        assemblies
mapColors               Maps a numeric or character vector to a color
                        palette and returns the vector of colors
pageCreate              Create a page for a plotgardener layout
pageGuideHide           Remove guides from a plotgardener page
pageGuideHorizontal     Draw a horizontal guideline at a specified
                        y-coordinate on a plotgardener page
pageGuideShow           Reshow guides drawn with 'pageCreate',
                        'pageGuideHorizontal', and 'pageGuideVertical'
pageGuideVertical       Draw a vertical guideline at a specified
                        x-coordinate on a plotgardener page
pagePlotPlace           Place a plot that has been previously created
                        but not drawn
pagePlotRemove          Remove plotgardener plots and annotations
pgParams                pgParams: plotgardener parameters object
plotCircle              Plot a circle within a plotgardener layout
plotGG                  Plot a ggplot2 plot, gtable, or grob object in
                        a plotgardener layout
plotGenes               Plot a gene track for a specified genomic
                        region
plotGenomeLabel         Plot genomic coordinates along the x or y-axis
                        of a plotgardener plot
plotHicRectangle        Plot a triangular Hi-C interaction matrix in a
                        rectangular format
plotHicSquare           Plot a Hi-C interaction matrix in a square
                        format
plotHicTriangle         Plot a Hi-C interaction matrix in a triangular
                        format
plotIdeogram            Plot a chromosome ideogram with or without
                        cytobands
plotLegend              Plot a legend
plotManhattan           Plot a Manhattan plot
plotPairs               Plot paired-end genomic range elements
plotPairsArches         Plot paired-end genomic range data in an arch
                        style
plotPolygon             Plot a polygon within a plotgardener layout
plotRanges              Plot genomic range elements in a pileup or
                        collapsed format
plotRaster              Plot a raster object within a plotgardener
                        layout
plotRect                Plot a rectangle within a plotgardener layout
plotSegments            Draw a line segment within a plotgardener
                        layout
plotSignal              Plot any kind of signal track data for a single
                        chromosome
plotText                Plot text within a plotgardener layout
plotTranscripts         Plot gene transcripts in a pileup style for a
                        single chromosome
plotgardener            plotgardener: Coordinate-based Genomic
                        Visualization Package for R
readBigwig              Read a bigWig file and return it as a data
                        frame
readHic                 Read a .hic file and return Hi-C data as a
                        dataframe
