| 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... |
| 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... |
| 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... |
| genomes | Display the included available default genome assemblies |
| mapColors | Maps a numeric or character vector to a color palette and... |
| 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... |
| pageGuideShow | Reshow guides drawn with 'pageCreate', 'pageGuideHorizontal',... |
| pageGuideVertical | Draw a vertical guideline at a specified x-coordinate on a... |
| pageLayoutCol | Generate column positions for a number of plot elements with... |
| pageLayoutRow | Generate row positions for a number of plot elements with a... |
| 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... |
| plotGenes | Plot a gene track for a specified genomic region |
| plotGenomeLabel | Plot genomic coordinates along the x or y-axis of a... |
| plotGG | Plot a ggplot2 plot, gtable, or grob object in a plotgardener... |
| plotHicRectangle | Plot a triangular Hi-C interaction matrix in a rectangular... |
| 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... |
| 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 |
