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bb_annoHeatmapLegend()
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adds color scale legend for heatmap plots |
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bb_annoLoops()
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annotates loops in a Hi-C plot |
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bb_annoXaxis()
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wrapper function for plotting an x axis in its own viewport |
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bb_annoYaxis()
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wrapper function for plotting an y axis in its own viewport |
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bb_assembly()
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Makes a bb_assembly object for alternate TxDB, OrgDb,and BSgenome packages |
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bb_calcApa()
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Extract BEDPE interactions from a Hi-C matrix |
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bb_calcBedpe()
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Calculates all potential paired interactions from a BED file |
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bb_defaultPackages()
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Displays the default data packages associated with a genome build |
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bb_filterBedpe()
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Filters out short BEDPE interactions |
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bb_genomes()
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Displays the included available default genome assemblies |
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bb_maptocolors()
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Maps numeric vector to color palette |
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bb_pageCreate()
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Creates a page for a BentoBox layout |
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bb_pageHideGuides()
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Removes guides from a BentoBox page |
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bb_pageHorizontalGuide()
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draws a horizontal guideline at a specified y-coordinate on a BentoBox page |
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bb_pagePlacePlot()
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places a plot that has been previously created but not drawn |
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bb_pageRemovePlot()
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Removes BentoBox plots and annotations |
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bb_pageShowGuides()
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Reshows guides drawn with bb_makePage() |
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bb_pageVerticalGuide()
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draws a vertical guideline at a specified y-coordinate on a BentoBox page |
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bb_params()
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bb_params: BentoBox parameters object |
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bb_plotApa()
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Plots Aggregate Peak Analysis Matrix |
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bb_plotBase()
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adds a plot created with baseR to a BentoBox layout |
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bb_plotBedpe()
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plots paired-end data for a single chromosome |
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bb_plotBedpeArches()
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plots data stored in BEDPE format in a "ribbon arch" style |
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bb_plotCircle()
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wrapper to draw a circleGrob based on BentoBox page coordinates and units |
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bb_plotGG()
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adds a plot created with ggplot2 to a BentoBox layout |
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bb_plotGenes()
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plots a gene track for a specified region |
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bb_plotGenomeLabel()
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Plots genomic coordinates for the axis of a BentoBox plot |
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bb_plotHicSquare()
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plots HiC interaction matrix |
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bb_plotHicTriangle()
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plots HiC interaction matrix in triangular format |
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bb_plotIdeogram()
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plots and highlights a chromosome with its cytobands |
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bb_plotLegend()
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plots a legend |
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bb_plotManhattan()
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plots a Manhattan plot |
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bb_plotPileup()
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plots data stored in BED format in a pileup style |
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bb_plotRect()
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wrapper to draw a rectGrob based on BentoBox page coordinates and units |
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bb_plotSignal()
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plots signal track data |
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bb_plotText()
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wrapper to draw a textGrob based on BentoBox page coordinates and units |
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bb_plotTranscripts()
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plots gene transcripts in a pileup style |
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bb_readBigwig()
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Reads a bigwig file and returns it as a data frame. |
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bb_readHic()
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extracts Hi-C data from a .hic file |