plots data stored in BED format in a pileup style

plots data stored in BED format in a pileup style

bb_plotPileup(
  bed,
  chrom,
  params = NULL,
  chromstart = NULL,
  chromend = NULL,
  assembly = "hg19",
  fillcolor = "black",
  linecolor = NA,
  colorby = NULL,
  colorbyrange = NULL,
  strandSplit = FALSE,
  boxHeight = unit(2, "mm"),
  spaceHeight = 0.3,
  spaceWidth = 0.02,
  x = NULL,
  y = NULL,
  width = NULL,
  height = NULL,
  just = c("left", "top"),
  default.units = "inches",
  draw = TRUE,
  ...
)

Arguments

bed	genomic data to be plotted; can be any data in BED format, a .bam file where a bam index file (.bam.bai) is in the same directory, or a GRanges
chrom	chromosome of region to be plotted
params	an optional "bb_params" object space containing relevant function parameters
chromstart	start position
chromend	end position
assembly	desired genome assembly
fillcolor	single value, vector, or palette specifying colors of pileup elements
linecolor	linecolor of line outlining pileup elements
colorby	name of column in bed data to scale colors by
colorbyrange	the range of values to apply a colorby palette scale to, if colorby values are numeric
strandSplit	logical indicating whether plus and minus-stranded elements should be separated
boxHeight	A numeric or unit object specifying height of pileup element boxes
spaceHeight	height of spacing between pileup element boxes, as a fraction of boxHeight
spaceWidth	width of minimum spacing between pileup element boxes, as a fraction of the plot's genomic range
x	A numeric or unit object specifying x-location
y	A numeric or unit object specifying y-location
width	A numeric or unit object specifying width
height	A numeric or unit object specifying height
just	A string or numeric vector specifying the justification of the viewport relative to its (x, y) location: "left", "right", "centre", "center", "bottom", "top"
default.units	A string indicating the default units to use if x, y, width, or height are only given as numerics
draw	A logical value indicating whether graphics output should be produced

Value

Function will plot a pileup style plot and return a bb_pileup object