plots data stored in BEDPE format in a "ribbon arch" style

plots data stored in BEDPE format in a "ribbon arch" style

bb_plotBedpeArches(
  bedpe,
  chrom,
  params = NULL,
  chromstart = NULL,
  chromend = NULL,
  cutoffArches = FALSE,
  archHeight = NULL,
  style = "2D",
  arch = 5,
  position = "top",
  fillcolor = "lightgrey",
  linecolor = NA,
  colorby = NULL,
  colorbyrange = NULL,
  assembly = "hg19",
  alpha = 0.4,
  x = NULL,
  y = NULL,
  width = NULL,
  height = NULL,
  just = c("left", "top"),
  default.units = "inches",
  draw = T,
  ...
)

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
cutoffArches	a logical value indicating whether to include arches that get cutoff in the region
archHeight	single value or vector specifying the arch heights; when NULL, all arches will be the same height, filling up the given viewport
style	style of arches: "2D" or "3D"
arch	arch curvature, determined by number of points along the curve
position	position of arches above or below the x-axis: "top" or "bottom"
fillcolor	single value, vector, or palette specifying colors of arches
linecolor	linecolor of line outlining arches
colorby	name of column in bedpe data to scale colors by
colorbyrange	the range of values to apply a colorby palette scale to, if colorby values are numeric
assembly	desired genome assembly
alpha	transparency of arches
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 ribbon arches plot and return a bb_arches object