Coordinate-Based Genomic Visualization Package for R

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Documentation for package ‘plotgardener’ version 1.0.0

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

Help Pages

plotgardener-package	plotgardener: Coordinate-based Genomic Visualization Package for R
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
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
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
readHic	Read a .hic file and return Hi-C data as a dataframe