plots HiC interaction matrix

plots HiC interaction matrix

bb_plotHicSquare(
  hic,
  chrom,
  params = NULL,
  chromstart = NULL,
  chromend = NULL,
  half = "both",
  resolution = "auto",
  zrange = NULL,
  palette = colorRampPalette(c("white", "dark red")),
  assembly = "hg19",
  width = NULL,
  height = NULL,
  x = NULL,
  y = NULL,
  just = c("left", "top"),
  default.units = "inches",
  draw = TRUE,
  altchrom = NULL,
  altchromstart = NULL,
  altchromend = NULL,
  althalf = NULL,
  norm = "KR",
  dataType = "observed"
)

Arguments

hic	path to .hic file or 3 column dataframe of counts
chrom	chromosome of region to be plotted
params	an optional "bb_params" object space containing relevant function parameters
chromstart	start position
chromend	end position
half	what sides of square plot; options are "both", top", or "bottom"
resolution	the width in bp of each pixel; for hic files, "auto" will attempt to choose a resolution based on the size of the region; for dataframes, "auto" will attempt to detect the resolution the dataframe contains
zrange	the range of interaction scores to plot, where extreme values will be set to the max or min
palette	ColorRamp palette to use for representing interaction scores
assembly	default genome assembly as a string or a bb_assembly object
width	A numeric or unit object specifying width
height	A numeric or unit object specifying height
x	A numeric or unit object specifying x-location
y	A numeric or unit object specifying y-location
just	a string or numeric vector specifying the justification of the viewport relative to its (x, y) location
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
altchrom	alternate chromosome for off-diagonal plotting or interchromosomal plotting
altchromstart	alternate chromosome start for off-diagonal plotting or interchromosomal plotting
altchromend	alternate chromosome end for off-diagonal plotting or interchromosomal plotting
althalf	if plotting altchrom region, which side off diagonal to plot; options are "top" or "bottom"
norm	if giving .hic file, hic data normalization; must be found in hic file
dataType	type of data to be returned; options are "observed" and "oe"

Value

Function will plot a HiC interaction matrix and return a bb_hic object

Examples