draw.clone

c("polygon", "triangle", "parabol")

shape:

width of the polygon (representing cellular fraction)

wid:

len:

col:

label:

cell.frac:

position for cell.frac =
c('top.left', 'top.right', 'top.mid',
'right.mid', 'right.top', 'right.bottom',
'side', 'top.out')

cell.frac.position:

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

cell.frac.top.out.space:

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

cell.frac.side.arrow.width:

list of variants to highlight inside the polygon

variant.names:

border.color:

vertical distance between the end point of clone
bell curve, and its mid point (increase this will make the curve steeper,
set this equal to zero will give no curve; use case: sometimes bell of
subclone cannot fit parent clone bell, so decrease this will help fitting

bell.curve.step:

scale the x length of the curve part of the bell plot by
this to make sure in a wider pdf output file, the curve part won't be
lengthen (wscale should be the ratio of the default width (currently
hard-coded as 7) and the pdf page width

wscale:

Draw a polygon representing a clone, annotated with cluster
label and cellular fraction

clonevol performs clonal ordering and visualization using
the variant clustering results. It uses a bootstrap resampling
technique to estimate the cellular prevalence of the clones within
samples and probabilistically model clonal ordering constraints
(sum and cross rules), hence it tolerates error and variability
in cellular prevalence estimates of individual variants.

draw.clone: Draw a bell/polygon representing a clone evolution, annotated with cluster label and cellular fraction

Description

Usage

Arguments