Function that makes a plot with TMB boxplots for reference cohorts, highlighting the TMB estimate for a given sample and the cohort/primary site of interest

Function that makes a plot with TMB boxplots for reference cohorts, highlighting the TMB estimate for a given sample and the cohort/primary site of interest

Usage

plot_tmb_primary_site_tcga(
  tmb_reference,
  p_site = "Liver",
  tmb_estimates = NULL,
  tmb_display_type = "missense_only",
  tumor_only = FALSE
)

Arguments

tmb_reference

data frame with TMB estimates for reference samples (e.g. TCGA)

p_site

primary tumor_site (sample)

tmb_estimates

data frame with estimates of mutational burden (sample)

tmb_display_type

TMB estimation used for display (e.g. missense_only)

tumor_only

logical, if TRUE color using tumor-only color