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Generate Bubble Plots

Source: R/plot_bubbles.R
plot_bubbles.Rd

Produces a ggplot object of bubble plots from given mutation data. Optionally, bubble plots can be facetted and coloured by a specified column.

Usage

plot_bubbles(
  mutation_data,
  size_by = "alt_depth",
  facet_col = NULL,
  color_by = "normalized_subtype",
  circle_spacing = 1,
  circle_outline = "none",
  circle_resolution = 50,
  custom_palette = NULL
)

Arguments

mutation_data

Data frame containing the mutation data.

size_by

The column name by which to size the circles. Recommended values are "alt_depth" or "vaf".

facet_col

The column name by which to facet . If NULL, no facetting will be done. Default is NULL.

color_by

The column name by which to colour the mutations. Default is "normalized_subtype".

circle_spacing

Numerical value to adjust the spacing between circles. Default is 1.

circle_outline

Colour for the circle outline. Default is "none", resulting in no outline colour. Other accepted values are colours in the R language.

circle_resolution

Number of points to use for the circle resolution. Default is 50.

custom_palette

A named vector of colors to be used for the mutation subtypes. The names of the vector should correspond to the levels in color_by. Alternatively, you can specify a color palette from the RColorBrewer package. See brewer.pal for palette options. You may visualize the palettes at the ColorBrewer website: https://colorbrewer2.org/. Default is NULL.

Value

A ggplot object with the bubble plot, facetted if specified.

Details

The function will plot a circle for each mutation in mutation_data. Mutations flagged by the filter_mut column will be excluded from the plot. The size of the circle is determined by the size_by parameter. Sizing by the "alt_depth" or the "vaf" will give users the ability to visualize the the distribution of recurrent mutations within their data with large multiplets having a large circle.

Examples

if (requireNamespace("MutSeqRData", quietly = TRUE)) {
  # Example data consists of 24 mouse bone marrow DNA samples imported
  # using import_mut_data() and filtered with filter_mut as in Example 4.
  # Sequenced on TS Mouse Mutagenesis Panel. Example data is
  # retrieved from MutSeqRData, an ExperimentHub data package.
  library(ExperimentHub)
  eh <- ExperimentHub()
  example_data <- eh[["EH9861"]]
  plot <- plot_bubbles(
    mutation_data = example_data,
    facet_col = "dose_group"
  )
}