Package index • plotgardener

About plotgardener
	`plotgardener-package` `plotgardener`	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
	`readCool()`	Read a .(m)cool file and return Hi-C data as a dataframe
	`readCoolBpResolutions()`	Read basepair resolutions from an .(m)cool file
	`readCoolChroms()`	Read chromosomes included in .(m)cool files
	`readCoolNorms()`	Read normalizations included in .(m)cool files
	`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
Internal
	`.checkCool()`	Check for .(m)cool file and contents
	`.checkCoolErrors()`	Error checking function for .(m)cool files
	`.coolAutoResolution()`	Determine best resolution for size of region for .(m)cool files
	`.coolRegion()`	Add (alt)chromstart and (alt)chromend for NULL (alt)chrom region of .(m)cool files
	`.pullBinChunks()`	Read in data for a bin chunk
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

Reference

About plotgardener

Page layout functions

Reading functions

Plotting functions

Genomics

Shapes and Basic Elements

External

Internal

Annotation functions

Meta functions