plot_signatures: Plots the mutational signatures
In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

plot_signatures

R Documentation

Plots the mutational signatures

Description

After mutational signature discovery has been performed, this function can be used to display the distribution of each mutational signature. The color_variable and color_mapping parameters can be used to change the default color scheme of the bars.

Usage

plot_signatures(
  result,
  plotly = FALSE,
  color_variable = NULL,
  color_mapping = NULL,
  text_size = 10,
  show_x_labels = TRUE,
  show_y_labels = TRUE,
  same_scale = TRUE,
  y_max = NULL,
  annotation = NULL
)

Arguments

`result`	A `musica_result` object generated by a mutational discovery or prediction tool.
`plotly`	If `TRUE`, the the plot will be made interactive using `plotly`. Default `FALSE`.
`color_variable`	Name of the column in the variant annotation data.frame to use for coloring the mutation type bars. The variant annotation data.frame can be found within the count table of the `musica` object. If `NULL`, then the default column specified in the count table will be used. Default `NULL`.
`color_mapping`	A character vector used to map items in the `color_variable` to a color. The items in `color_mapping` correspond to the colors. The names of the items in `color_mapping` should correspond to the uniqeu items in `color_variable`. If `NULL`, then the default `color_mapping` specified in the count table will be used. Default `NULL`.
`text_size`	Size of axis text. Default `10`.
`show_x_labels`	If `TRUE`, the labels for the mutation types on the x-axis will be shown. Default `TRUE`.
`show_y_labels`	If `TRUE`, the y-axis ticks and labels will be shown. Default `TRUE`.
`same_scale`	If `TRUE`, the scale of the probability for each signature will be the same. If `FALSE`, then the scale of the y-axis will be adjusted for each signature. Default `TRUE`.
`y_max`	Vector of maximum y-axis limits for each signature. One value may also be provided to specify a constant y-axis limit for all signatures. Vector length must be 1 or equivalent to the number of signatures. Default `NULL`.
`annotation`	Vector of annotations to be displayed in the top right corner of each signature. Vector length must be equivalent to the number of signatures. Default `NULL`.