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Plot the Mutation Frequency

Source: R/plot_mf.R
plot_mf.Rd

This function creates a plot of the mutation frequency.

Usage

plot_mf(
  mf_data,
  group_col,
  plot_type = "bar",
  mf_type = "min",
  fill_col = NULL,
  custom_palette = NULL,
  group_order = "none",
  group_order_input = NULL,
  labels = "count",
  scale_y_axis = "linear",
  x_lab = NULL,
  y_lab = NULL,
  title = NULL,
  rotate_labels = FALSE,
  label_size = 3
)

Arguments

mf_data

A data frame containing the mutation frequency data. This is obtained from the calculate_mf function with SUMMARY = TRUE.

group_col

The name of the column containing the sample/group names for the x-axis.

plot_type

The type of plot to create. Options are "bar" or "point".

mf_type

The type of mutation frequency to plot. Options are "min", "max", "both", or "stacked". If "both", the min and max mutation frequencies are plotted side by side. "stacked" can be chosen for bar plot_type only. If "stacked", the difference between the min and max MF is stacked on top of the min MF such that the total height of both bars represent the max MF.

fill_col

The name of the column containing the fill variable.

custom_palette

A character vector of colour codes to use for the plot. If NULL, a default palette is used

group_order

The order of the samples/groups along the x-axis. ' Options include:

  • none: No ordering is performed. Default.

  • smart: Samples are ordered based on the sample names.

  • arranged: Samples are ordered based on one or more factor column(s) in mf_data. Factor column names are passed to the function using the group_order_input.

  • custom: Samples are ordered based on a custom vector of sample names. The custom vector is passed to the function using the group_order_input.

group_order_input

The order of the samples/groups if group_order is "custom". The column name by which to arrange samples/groups if group_order is "arranged"

labels

The data labels to display on the plot. Either "count", "MF", or "none". Count labels display the number of mutations, MF labels display the mutation frequency.

scale_y_axis

The scale of the y axis. Either "linear" or "log".

x_lab

The label for the x axis.

y_lab

The label for the y axis.

title

The title of the plot.

rotate_labels

A logical value aplied when labels is not "none". Indicates whether the labels should be rotated 90 degrees. Default is FALSE.

label_size

A numeric value that adjusts the size of the labels. Default is 3.

Value

A ggplot object

Examples

example_file <- system.file("extdata", "Example_files",
                            "example_mutation_data_filtered.rds",
                            package = "MutSeqR")
example_data <- readRDS(example_file)
example_data$dose_group <- factor(example_data$dose_group,
                                  levels = c("Control", "Low",
                                             "Medium", "High"))
mf <- calculate_mf(mutation_data = example_data,
                   cols_to_group = "sample",
                   subtype_resolution = "none",
                   retain_metadata_cols = "dose_group")
#> Performing internal depth correction to prevent double-counting...
#> Internal depth correction complete.
#> Joining with `by = join_by(sample)`
#> Joining with `by = join_by(sample)`
plot <- plot_mf(mf_data = mf,
                group_col = "sample",
                plot_type = "bar",
                mf_type = "min",
                fill_col = "dose_group",
                group_order = "arranged",
                group_order_input = "dose_group",
                labels = "count",
                title = "Mutation Frequency per Sample")