plot_signatures: Plots the mutational signatures

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

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(
  musica,
  model_id,
  modality = "SBS96",
  result_name = "result",
  color_variable = NULL,
  color_mapping = NULL,
  text_size = 10,
  show_x_labels = TRUE,
  show_y_labels = TRUE,
  same_scale = FALSE,
  y_max = NULL,
  annotation = NULL,
  percent = TRUE,
  plotly = FALSE
)

Arguments

musica	A musica object containing a mutational discovery or prediction.
model_id	The name of the model to plot.
modality	The modality of the signatures to plot. Must be "SBS96", "DBS78", or "IND83". Default "SBS96".
result_name	Name of the result list entry containing the signatures to plot. Default "result".
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 unique 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 FALE.
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.
percent	If TRUE, the y-axis will be represented in percent format instead of mutation counts. Default TRUE.
plotly	If TRUE, the the plot will be made interactive using plotly. Default FALSE.

Value

Generates a ggplot or plotly object

Examples

data(res)
plot_signatures(res, model_id = "res")

campbio/musicatk documentation built on Dec. 25, 2024, 9:34 p.m.