genomeChart: genomeChart

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

genomeChart

Description

Plotting of somatic variants using the circlize R package. Somatic variants plotted are single nucleotide variants (SNVs), Indels, copy number variants (CNVs) and structural variants (SVs or rearrangements). In addition to the circle visualisation of the variants, other data are plotted, such as SNV and SV mutational catalogues, indels classification summary counts and a copy number plot indicating estimates of total and minor allele copy numbers.

Usage

genomeChart(
  outfilename,
  sample_name,
  SNV_vcf_file = NULL,
  SNV_tab_file = NULL,
  Indels_vcf_file = NULL,
  Indels_tab_file = NULL,
  CNV_tab_file = NULL,
  SV_bedpe_file = NULL,
  plot_title = NULL,
  runKataegis = TRUE,
  genome.v = "hg19",
  debug = FALSE
)

Arguments

outfilename	file where the figure should be plotted. This also determines the file type of the output, use either pdf (recommended) or png
sample_name	name of sample
SNV_vcf_file	name of the vcf file containing the SNVs
SNV_tab_file	name of the tab separated file containing the SNVs. Column names should be: chr, position, REF and ALT. If SNV_vcf_file is also specified, these variants will be ignored and the variants in the vcf file will be used instead.
Indels_vcf_file	name of the vcf file containing the Indels
Indels_tab_file	name of the tab separated file containing the Indels. Column names should be: chr, position, REF and ALT. If Indels_vcf_file is also specified, these variants will be ignored and the variants in the vcf file will be used instead.
CNV_tab_file	name of the tab separated file containing the CNVs. Column names should be: 'seg_no', 'Chromosome', 'chromStart', 'chromEnd', 'total.copy.number.inNormal', 'minor.copy.number.inNormal', 'total.copy.number.inTumour', 'minor.copy.number.inTumour'
SV_bedpe_file	name of the tab separated bedpe file containing the SVs. The file should contain a rearrangement for each row (two breakpoint positions should be on one row as determined by a pair of mates of paired-end sequencing) and should already be filtered according to the user preference, as all rearrangements in the file will be used and no filter will be applied. The files should contain a header in the first line with the following columns: "chrom1", "start1", "end1", "chrom2", "start2", "end2" and "sample" (sample name). In addition, either two columns indicating the strands of the mates, "strand1" (+ or -) and "strand2" (+ or -), or one column indicating the structural variant class, "svclass": translocation, inversion, deletion, tandem-duplication. The column "svclass" should correspond to (Sanger BRASS convention): inversion (strands +/- or -/+ and mates on the same chromosome), deletion (strands +/+ and mates on the same chromosome), tandem-duplication (strands -/- and mates on the same chromosome), translocation (mates are on different chromosomes). In addition, columns 'non-template' and 'micro-homology' can be specified, including the non-templated insertion or micro-homology deletion sequence, which will be used to build an SV junctions catalogue.
plot_title	title of the plot. If NULL, then the sample_name will be used as title. Use "", the empty string, to have no title.
runKataegis	whether or not to run the kataegis algorithm (default is TRUE)
genome.v	genome version to use, either hg19 or hg38
debug	if TRUE, show debug guidelines and grid when plotting (default is FALSE)

Value

all computed results, like catalogues and clustering regions, will be returned

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.