draw.sample.clones: Draw clonal structures/evolution of a single sample

Description

Draw clonal structure for a sample with single or multiple clones/subclones using polygon and tree plots

Usage

draw.sample.clones(v, x = 1, y = 0, wid = 30, len = 9,
  clone.shape = "bell", bell.curve.step = 0.25, bell.border.width = 1,
  clone.time.step.scale = 1, label = NULL, text.size = 1,
  cell.frac.ci = FALSE, disable.cell.frac = FALSE,
  zero.cell.frac.clone.color = NULL,
  zero.cell.frac.clone.border.color = NULL,
  nonzero.cell.frac.clone.border.color = NULL,
  nonzero.cell.frac.clone.border.width = NULL,
  zero.cell.frac.clone.border.width = NULL, top.title = NULL,
  adjust.clone.height = TRUE, cell.frac.top.out.space = 0.75,
  cell.frac.side.arrow.width = 1.5, variants.to.highlight = NULL,
  variant.color = "blue", variant.angle = NULL, show.time.axis = TRUE,
  color.node.by.sample.group = FALSE, color.border.by.sample.group = TRUE,
  show.clone.label = TRUE, wscale = 1)

Arguments

clonal structure data frame (output of enumerate.clones)

clone.shape:

c("bell", polygon"); shape of the object used to present a clone in the clonal evolution plot.

adjust.clone.height:

if TRUE, rescale the width of polygon such that subclones should not have total vaf > that of parent clone when drawing polygon plot

cell.frac.top.out.space:

spacing between cell frac annotation when annotating on top of the plot

cell.frac.side.arrow.width:

width of the line and arrow pointing to the top edge of the polygon from the cell frac annotation on top

color.border.by.sample.group:

color border of bell plot based on sample grouping

variants.to.highlight:

a data frame of 2 columns: cluster, variant.name Variants in this data frame will be printed on the clone shape

bell.curve.step:

see draw.clone function's bell.curve.step param

drop.zero.cell.frac.clone:

c(TRUE,FALSE); if TRUE, do not display zero cell frac clones

clone.time.step.scale:

scaling factor for distance between the tips of the polygon/bell representing clone; see also wscale

zero.cell.frac.clone.color:

color clone with zero cell fraction in the sample with this color (default = NULL, color using matching color auto-generated)

disable.cell.frac:

disable cellular fraction display

show.clone.label:

show clone label in bell tip

nonzero.cell.frac.clone.border.color:

border color of nonzero cell frac clone; if = "fill", use clone fill color

nonzero.cell.frac.clone.border.width:

bell border with for nonzero cell frac clone