# Coordinate-Based Genomic Visualization Package for R

## Documentation for package ‘plotgardener’ version 1.16.0

- 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