About plotgardener

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

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

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