Skip to contents

Plot the trinucleotide spectrum

Source: R/plot_trinucleotide.R
plot_trinucleotide.Rd

Creates barplots of the trinucleotide spectrum for all levels of a given group.

Usage

plot_trinucleotide(
  mf_96,
  response = "proportion",
  mf_type = "min",
  group_col = "dose",
  indiv_y = FALSE,
  sum_totals = TRUE,
  output_path = NULL,
  output_type = "svg"
)

Arguments

mf_96

A data frame containing the mutation frequency data at the 96-base resolution. This should be obtained using the 'calculate_mf' with subtype_resolution set to 'base_96'. Generally, cols_to_group should be the same as 'group_col'.

response

A character string specifying the type of response to plot. Must be one of 'frequency', 'proportion', or 'sum'.

mf_type

A character string specifying the mutation count method to plot. Must be one of 'min' or 'max'. Default is 'min'.

group_col

A character string specifying the column(s) in 'mf_96' to group the data by. Default is 'sample'. The sum, proportion, or frequency will be plotted for all unique levels of this group. You can specify more than one column to group by. Generally the same as the 'cols_to_group' parameter in 'calculate_mf' when generating mf_96.

indiv_y

A logical value specifying whether the the max response value for the y-axis should be scaled independently for each group (TRUE) or scaled the same for all groups (FALSE). Default is FALSE.

sum_totals

A logical value specifying whether to display the total sum of mutations in the mutation labels. Default is TRUE.

output_path

An optional file path to an output directory. If provided, the plots will be automatically exported using the graphics device specified in output_type. The function will create the output directory if it doesn't already exist. If NULL, plots will not be exported. Default is NULL.

output_type

A character string specifying the type of output file. Options are 'eps', 'ps', 'tex', 'pdf', or 'jpeg', 'tiff', 'png', 'bmp', 'svg', or 'wmf' (windows only). Default is 'svg'.

Value

A named list containing ggplots.

Details

The function plots the trinucleotide spectrum for all levels of a given group from the provided mf_96 data; the output of calculate_mf with subtype_resolution = "base_96".

Examples

# Load example data
example_file <- system.file(
 "extdata", "Example_files",
 "example_mutation_data_filtered.rds",
 package = "MutSeqR"
)
example_data <- readRDS(example_file)

# Calculate the mutation frequency data at the 96-base resolution
mf_96 <- calculate_mf(
 mutation_data = example_data,
 cols_to_group = "dose_group",
 subtype_resolution = "base_96",
 variant_types = "snv"
)
#> Performing internal depth correction to prevent double-counting...
#> Internal depth correction complete.
#> Joining with `by = join_by(dose_group, normalized_context)`
# Plot the trinucleotide proportions for each dose group
# Scale y-axis the same for all groups
plots <- plot_trinucleotide(
 mf_96 = mf_96,
 response = "proportion",
 mf_type = "min",
 group_col = "dose_group",
 indiv_y = FALSE,
 output_path = NULL
)