Coordinate-Based Genomic Visualization Package for R

---

Documentation for package ‘plotgardener’ version 1.13.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

plotgardener-package	plotgardener: Coordinate-based Genomic Visualization Package for R
.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
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
calcSignalRange	Calculate a score range for multiple signals
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
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
pgParams	pgParams: plotgardener parameters object
plotCircle	Plot a circle within a plotgardener layout
plotgardener	plotgardener: Coordinate-based Genomic Visualization Package for R
plotGenes	Plot a gene track for a specified genomic region
plotGenomeLabel	Plot genomic coordinates along the x or y-axis of a plotgardener plot
plotGG	Plot a ggplot2 plot, gtable, or grob object in a plotgardener layout
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
plotMultiSignal	Plot multiple signal tracks in line with each other
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
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