plot_cnvkit: Plot CNR across bins

In TearsWillFall/ULPwgs: An implementation of a wrapper for estimating tumor fraction in ultra-low-pass whole genome sequencing (ULP-WGS) for cell-free DNA in GNU/Unix based systems

Plot CNR across bins

Description

Plot CNR across bins

Usage

plot_cnvkit(
  cnr = NULL,
  cns = NULL,
  chromosomes = NULL,
  genes = NULL,
  highlights = NULL,
  weights = NULL,
  threads = 5,
  show_lines = TRUE,
  trend = TRUE,
  save = TRUE,
  limits = 5,
  show = "panel",
  output_dir = "img",
  output_name = "img.png",
  plot_width = 1200,
  plot_height = 600
)

Arguments

cnr	REQUIRED Path to CNR as produced by fix_cnvkit command.
cns	OPTIONAL Path to CNS as produced by segment_cnvkit command.
genes	OPTIONAL Genes to focus on. Default NULL
highlights	OPTIONAL Highlights genes. Default NULL.
weights	OPTIONAL Filter bins by weight
trend	OPTIONAL Draw trend line across bins
save	OPTIONAL Save image

TearsWillFall/ULPwgs documentation built on April 18, 2024, 3:45 p.m.