pp_plot: pp_plot

In mskilab/skitools: Various mskilab R utilties

pp_plot

Description

pp_plot

Usage

pp_plot(
  jabba_rds = NULL,
  cov.fname = NULL,
  hets.fname = NULL,
  allele = FALSE,
  field = NULL,
  plot.min = -2,
  plot.max = 2,
  scatter = FALSE,
  bins = 500,
  height = 800,
  width = 800,
  output.fname = "./plot.png",
  verbose = FALSE
)

Arguments

jabba_rds	(character) JaBbA output
cov.fname	(character) path to coverage GRanges (supply if allele = FALSE)
hets.fname	(character) path to sites.txt (supply if allele = TRUE)
allele	(logical) allelic CN? default FALSE
field	(character) default ratio if allele is FALSE and count if allele is TRUE
plot.min	(numeric) minimum CN default -2
plot.max	(numeric) max CN (factor times ploidy) default 2
scatter	(logical) default FALSE
bins	(numeric) number of histogram bins default 500
height	(numeric) plot height
width	(numeric) plot width
output.fname	(character) path of output directory
verbose	(logical)

Details

create histogram of estimated copy number given purity and ploidy

Value

output.fname

Author(s)

Zi-Ning Choo

mskilab/skitools documentation built on March 5, 2025, 11:52 p.m.