plots gene transcripts in a pileup style

plots gene transcripts in a pileup style

bb_plotTranscripts(
  chrom,
  params = NULL,
  assembly = "hg19",
  chromstart = NULL,
  chromend = NULL,
  boxHeight = unit(2, "mm"),
  spaceHeight = 0.3,
  spaceWidth = 0.02,
  fillcolor = c("#8a8aff", "#ff7e7e"),
  colorbyStrand = TRUE,
  labels = "transcript",
  fontsize = 8,
  strandSplit = FALSE,
  stroke = 0.1,
  x = NULL,
  y = NULL,
  width = NULL,
  height = NULL,
  just = c("left", "top"),
  default.units = "inches",
  draw = TRUE
)

Arguments

chrom	chromsome of region to be plotted
params	an optional "bb_params" object space containing relevant function parameters
assembly	desired genome assembly
chromstart	start position
chromend	end position
boxHeight	A numeric or unit object specifying total height of each transcript
spaceHeight	height of spacing between transcripts, as a fraction of boxHeight
spaceWidth	width of minimum spacing between transcripts, as a fraction of the plot's genomic range
fillcolor	single value or vector specifying colors of transcripts
colorbyStrand	a logical value indicating whether to color strands by the first two colors in a fillcolor vector
labels	how labels should be determined; options are NULL for no labels, "transcript" for transcript names, "gene" for gene names, or "both" for combined transcript and gene names
fontsize	the size of gene label text (in points)
strandSplit	logical indicating whether plus and minus-stranded elements should be separated
stroke	numerical value indicating the stroke width for transcript body outlines
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	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 of transcripts and return a bb_transcripts object