Plot prevalence of mutations

Plot the prevalence of mutations generated by mutation_prevalence(). The prevalence is plotted on the y-axis and the amino acid change is plotted on the x-axis. Data are grouped by the gene on which the mutation took place and coloured according to their groupings.

Usage

plot_mutation_prevalence(data)

# S3 method for mut_prev
autoplot(object, ...)

# S3 method for mut_prev
plot(x, ...)

Arguments

data, object, x

An object of class mut_prev. Derived from the output of mutation_prevalence().

...

Other arguments passed to specific methods.

See also

mutation_prevalence() for generating the data for plotting.

Examples

ref_file <- miplicorn_example("reference_AA_table.csv")
alt_file <- miplicorn_example("alternate_AA_table.csv")
cov_file <- miplicorn_example("coverage_AA_table.csv")
data <- read_tbl_ref_alt_cov(
  ref_file,
  alt_file,
  cov_file,
  gene == "atp6" | gene == "crt"
)
prevalence <- mutation_prevalence(data, 5)
plot(prevalence)