Reference

About plotgardener
	plotgardener plotgardener-package	plotgardener: Coordinate-based Genomic Visualization Package for R
Page layout functions
	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
	pageLayoutCol()	Generate column positions for a number of plot elements with a specified width and space between them
	pageLayoutRow()	Generate row positions for a number of plot elements with a specified height and space between them
	pagePlotPlace()	Place a plot that has been previously created but not drawn
	pagePlotRemove()	Remove plotgardener plots and annotations
Reading functions
	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
Plotting functions
Genomics
	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
	plotManhattan()	Plot a Manhattan plot
	plotPairs()	Plot paired-end genomic range elements
	plotPairsArches()	Plot paired-end genomic range data in an arch style
	plotRanges()	Plot genomic range elements in a pileup or collapsed format
	plotSignal()	Plot any kind of signal track data for a single chromosome
	plotMultiSignal()	Plot multiple signal tracks in line with each other
	plotTranscripts()	Plot gene transcripts in a pileup style for a single chromosome
Shapes and Basic Elements
	plotCircle()	Plot a circle within a plotgardener layout
	plotLegend()	Plot a legend
	plotPolygon()	Plot a polygon within a plotgardener layout
	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
	plotText()	Plot text within a plotgardener layout
External
	plotGG()	Plot a ggplot2 plot, gtable, or grob object in a plotgardener layout
Annotation functions
	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
Meta functions
	assembly()	Make a assembly object for alternate TxDb, OrgDb,and BSgenome genomic annotation packages
	defaultPackages()	Display the default genomic annotation packages associated with a genome build
	genomes()	Display the included available default genome assemblies
	pgParams()	pgParams: plotgardener parameters object
	c()	Combine multiple pgParams objects into a vector
	colorby()	Handle plotgardener color scaling parameters
	mapColors()	Maps a numeric or character vector to a color palette and returns the vector of colors
	calcSignalRange()	Calculate a score range for multiple signals