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Mutational spectrum (SBS) bar chart

Source: R/plot_functions.R
plot_variant_spectrum.Rd

Plots the single-base substitution (SBS) spectrum — the relative frequency of each of the 6 substitution classes (C>A, C>G, C>T, T>A, T>C, T>G) — optionally broken down by trinucleotide context.

Usage

plot_variant_spectrum(
  variants,
  sample = NULL,
  context = FALSE,
  genome = NULL,
  facet_by_sample = FALSE,
  palette = NULL,
  normalize = TRUE,
  interactive = FALSE
)

Arguments

variants

A gvf object or compatible data.frame containing SNVs. Indels are automatically excluded.

sample

Character. Sample name to filter on. NULL uses all variants pooled (or facets by sample if facet_by_sample = TRUE).

context

Logical. 96-trinucleotide context bars are not yet implemented; passing TRUE aborts with an error. Default FALSE, which produces the 6-class SBS spectrum. See https://github.com/josh45-source/ggvariant/issues/1.

genome

Not yet implemented; passing a non-NULL value aborts with an error. Reserved for future BSgenome-based trinucleotide context extraction. See https://github.com/josh45-source/ggvariant/issues/1.

facet_by_sample

Logical. If TRUE, facets the plot by sample. Default FALSE.

palette

Named character vector with names matching substitution classes ("C>A", "C>G", etc.). NULL uses COSMIC-style colours.

normalize

Logical. If TRUE (default), shows relative proportions. If FALSE, shows raw counts.

interactive

Logical. If TRUE, returns a plotly interactive plot (requires the plotly package).

Value

A ggplot object.

References

Alexandrov LB, Kim J, Haradhvala NJ, et al.; PCAWG Consortium (2020). The repertoire of mutational signatures in human cancer. Nature, 578(7793), 94-101. doi:10.1038/s41586-020-1943-3

Blokzijl F, Janssen R, van Boxtel R, Cuppen E (2018). MutationalPatterns: comprehensive genome-wide analysis of mutational processes. Genome Medicine, 10(1), 33. doi:10.1186/s13073-018-0539-0

See also

plot_lollipop(), plot_consequence_summary(), gv_palette()

Other ggvariant plots: plot_consequence_summary(), plot_lollipop(), plot_oncoprint(), plot_tmb()

Examples

vcf_file <- system.file("extdata", "example.vcf", package = "ggvariant")
variants <- read_vcf(vcf_file)
#> ℹ Reading VCF: example.vcf
#> ✔ Reading VCF: example.vcf [10ms]
#> 
#> Loaded 19 variant records across 7 chromosomes.

# Basic 6-class SBS spectrum
plot_variant_spectrum(variants)
#> Excluded 2 non-SNV records from spectrum plot.


# Faceted by sample
plot_variant_spectrum(variants, facet_by_sample = TRUE)
#> Excluded 2 non-SNV records from spectrum plot.