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Plot the Mean Mutatation Frequency

Source: R/plot_mean_mf.r
plot_mean_mf.Rd

This function calculates the mean mutation frequency across samples for given groups and plots the results.

Usage

plot_mean_mf(
  mf_data,
  group_col = "dose",
  fill_col = NULL,
  mf_type = "both",
  plot_type = "line",
  plot_error_bars = TRUE,
  plot_indiv_vals = TRUE,
  group_order = "none",
  group_order_input = NULL,
  add_labels = "mean_count",
  scale_y_axis = "linear",
  x_lab = NULL,
  y_lab = NULL,
  plot_title = NULL,
  custom_palette = NULL,
  plot_legend = TRUE,
  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 column(s) in mf_data by which to calculate the mean. When supplying more than one column, the values of all group columns will be concatenated into a single value by which to calculate the mean. Values will be displayed along the x-axis. Ex. "dose" or c("dose", "tissue").

fill_col

An optional column name in the data used to define the fill aesthetic in the plot. If fill_col has multiple levels within each group_col level, the mean will be calculated for each level of fill_col (recommend plot_type = "line" for this use case). Default is NULL.

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. Default is "min".

plot_type

The type of plot to create. Options are "bar" or "line". Default is "bar".

plot_error_bars

Whether to plot the error bars. Default is TRUE. Error bars are standard error of the mean.

plot_indiv_vals

Whether to plot the individual values as data points. Default is FALSE.

group_order

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

  • none: No ordering is performed. Default.

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

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

group_order_input

The order of the groups if group_order is "custom". The column name by which to arrange groups if group_order is "arranged". If "custom", and using more than one group_col, values are concatenated in the order listed, separated by a "_".

add_labels

The data labels to display on the plot. Either "indiv_count", "indiv_MF", "mean_count", "mean_MF", or "none". Count labels display the number of mutations, MF labels display the mutation frequency. Mean plots the mean value. Indiv plots the labels for individual data points (only if plot_indiv_vals = TRUE). Default is "none".

scale_y_axis

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

x_lab

The x-axis label. Default is the value of group_col.

y_lab

The y-axis label. Default is "Mutation Frequency (mutations/bp)".

plot_title

The title of the plot. Default is "Mean Mutation Frequency".

custom_palette

A custom color palette to use for the plot. Input a character vector of colours. Input a named character vector to specify olours to specific groups. Fill labels will be constructed by the following components

  1. "Mean/Individual" if plot_indiv_vals = TRUE, fill labels will specify Mean/Individual values.

  2. "min/max" if mf_type = "both" or "stacked", fill labels will specify min/max values.

  3. fill_col value. Name colours to match the fill labels. Default is NULL. If no custom_palette, a rainbow palette is generated. Min/Max values and Mean/Individual values will be the same colour, different shades.

plot_legend

Logical. Whether to show the fill (and color) legend. Default is TRUE.

rotate_labels

A logical value indicating whether data labels should be rotated 90 degrees. Default is FALSE.

label_size

A numeric value that controls the size of the data labels.

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_mean_mf(mf_data = mf,
                     group_col = "dose_group",
                     mf_type = "min",
                     plot_type = "line",
                     fill_col = "dose_group",
                     plot_error_bars = TRUE,
                     plot_indiv_vals = TRUE,
                     add_labels = "none")