Plot frequency of mutations

Plot the frequency of mutations generated by mutation_frequency(). The frequency 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_frequency(data)

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

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

Arguments

data, object, x

An object of class mut_freq. Derived from the output of mutation_frequency().

...

Other arguments passed to specific methods.

See also

mutation_frequency() 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"
)
frequency <- mutation_frequency(data, 5)
plot(frequency)