plot_signature_effects: Plot mutational source and effect attributions

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

Plot mutational source and effect attributions

Description

Compare the extent to which mutational signatures contribute mutations (mutational source share) to the degree to which they contribute high-effect mutations (cancer effect share).

Usage

plot_signature_effects(
  mutational_effects = NULL,
  signature_groupings = "auto",
  viridis_option = NULL,
  num_sig_groups = 7
)

Arguments

mutational_effects	Output from mutational_signature_effects(). To compare groups of samples, supply a named list with each element corresponding to output from a separate run of mutational_signature_effects().
signature_groupings	A data.table of signature names and descriptions; signatures with identical descriptions are grouped together. Only signatures present in the data get displayed. Setting to "auto" (the default) uses the table returned by cosmic_signature_info(), which only makes sense when using COSMIC signatures. A custom table should have columns "name", "short_name", and "description". Additional options: To force a signature group to appear in the plot even if it has a low effect share, add a column called "prioritize" and set to TRUE where desired. To make a signature appear in its own group, make its description unique. Add a "color" column to manually specify colors for each group. Alternatively, setting signature_groupings = "cannataro" applies the same signature grouping and color palette as Cannataro et al. 2022.
viridis_option	A viridis color mapping, specified with a single letter ('A' to 'H'). By default, map 'G' (mako) is used.
num_sig_groups	How many groups of signatures to display. Groups are ordered by their highest effect shares, and the rest get lumped into an "other signatures" group.

Townsend-Lab-Yale/cancereffectsizeR documentation built on April 28, 2024, 6:14 p.m.