plot_out_list: Plotting from 'out_list' object

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

Plotting from 'out_list' object

Description

Plotting from 'out_list' object

Usage

plot_out_list(
  cna_list,
  pp_list,
  dict_file,
  which_genome,
  tag,
  samples,
  write_out = TRUE,
  max_cna_maxd = 8,
  sample_map = NULL,
  work_dir
)

Arguments

cna_list	GRanges in list of facets results
pp_list	ploidy/purity list
dict_file	dictionary file of fasta used to align BAMs
which_genome	the genome assembly used, "hg19" or "hg38"
tag	runID and annotation strategy, "ENS" or "CGC"
samples	vector of sampleIDs (use sample_map to change naming in plots)
write_out	runID and annotation strategy, "ENS" or "CGC"
max_cna_maxd	runID and annotation strategy, "ENS" or "CGC"
sample_map	named vector, names are all in samples, elements are new names
work_dir	character path of where files should be found, written

Value

none writes output files

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