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Tumour mutational burden bar chart

Source: R/plot_tmb.R
plot_tmb.Rd

Plots per-sample tumour mutational burden (TMB): the number of mutations carried by each sample, optionally normalised to mutations per megabase.

Usage

plot_tmb(
  variants,
  samples = NULL,
  mb_size = NULL,
  sample_order = NULL,
  palette = NULL,
  interactive = FALSE
)

Arguments

variants

A gvf object from read_vcf() or coerce_variants(), or any data.frame with sample and pos columns.

samples

Character vector of sample names to include. NULL (default) uses every sample present in variants.

mb_size

Numeric. Size, in megabases, of the sequenced region used to normalise mutation counts into mutations/Mb. NULL (default) plots raw mutation counts instead.

sample_order

Character vector giving an explicit left-to-right sample order, e.g. to align with plot_oncoprint()'s memo-sorted column order. NULL (default) orders samples by descending TMB.

palette

Single hex colour string for the bars. NULL uses a built-in default.

interactive

Logical. Returns a plotly object if TRUE.

Value

A ggplot object (or a plotly object when interactive = TRUE).

Details

The per-sample mutation count is computed by an internal helper shared with any future plot_oncoprint() TMB marginal, so the two always agree. Pass mb_size (the size, in megabases, of the sequenced region) to convert raw counts into mutations/Mb, the conventional TMB unit; leave it NULL to plot raw counts.

References

Chalmers ZR, Connelly CF, Fabrizio D, et al. (2017). Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Medicine, 9(1), 34. doi:10.1186/s13073-017-0424-2

See also

plot_oncoprint(), gv_palette()

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

Examples

vcf_file <- system.file("extdata", "example.vcf", package = "ggvariant")
variants <- read_vcf(vcf_file)
#> ℹ Reading VCF: example.vcf
#> ✔ Reading VCF: example.vcf [11ms]
#> 
#> Loaded 19 variant records across 7 chromosomes.

# Raw mutation counts, samples ordered by descending TMB
plot_tmb(variants)


# Normalised to mutations/Mb for a 38 Mb exome
plot_tmb(variants, mb_size = 38)


# Aligned to a specific sample order, e.g. from plot_oncoprint()
plot_tmb(variants, sample_order = c("TUMOR_S1", "TUMOR_S2"))