plots paired-end data for a single chromosome

plots paired-end data for a single chromosome

bb_plotBedpe(
  bedpe,
  chrom,
  params = NULL,
  chromstart = NULL,
  chromend = NULL,
  fillcolor = "black",
  colorby = NULL,
  colorbyrange = NULL,
  linecolor = NA,
  assembly = "hg19",
  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

bedpe	bed paired end data to be plotted
chrom	chromsome of region to be plotted
params	an optional "bb_params" object space containing relevant function parameters
chromstart	start position
chromend	end position
fillcolor	single value, vector, or palette specifying colors of bedpe elements
colorby	name of column in bedpe data to scale fillcolors by
colorbyrange	the range of values to apply a colorby palette scale to, if colorby values are numeric
linecolor	border color
assembly	default genome assembly as a string or a bb_assembly object
boxHeight	A numeric or unit object specifying height of boxes at either end of bedpe element
spaceHeight	height of space between boxes of different bedpe elements
spaceWidth	width of spacing between bedpe elements, as a fraction of the plot's genomic range
x	A numeric vector or unit object specifying x-location
y	A numeric vector or unit object specifying y-location
width	A numeric vector or unit object specifying width
height	A numeric vector or unit object specifying height
just	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 numeric vectors
draw	A logical value indicating whether graphics output should be produced