plot_from_tsv: Allow tunable reformatting of plots

In brucemoran/somenone: R functions required by the somenone NextFlow nf-core pipeline

Allow tunable reformatting of plots

Description

Allow tunable reformatting of plots

Usage

plot_from_tsv(
  pattern,
  dict_file,
  which_genome,
  tag,
  write_out = FALSE,
  max_cna_maxd = 8,
  sample_map = NULL,
  work_dir
)

Arguments

pattern	string e.g. "facets.CNA.CGC.tsv" as output by main functions
dict_file	dictionary file of fasta used to align BAMs
which_genome	the genome assembly used, "hg19" or "hg38"
tag	write output with this tag prefix
write_out	write tsv output?
max_cna_maxd	maximum CNA to show on plot
sample_map	named vector, names are filenames before first dot, elements are new names
work_dir	character path of where files should be found, written (default: ./)

Value

none, prints a plot and writes output if flag used

brucemoran/somenone documentation built on Nov. 1, 2022, 3:56 p.m.