Plot mutational source and effect attributions

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,
  other_color = "white"
)

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 groupings and color palette as Cannataro et al. 2022. You can use Cannataro signature groupings with a different color palette by specifying viridis_option.

viridis_option

A viridis color mapping, specified with a single letter ('A' to 'H'). By default, map 'G' (mako) unless using Cannataro signature groupings.

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.

other_color

Color to use for signatures in the "other" group, supplied as a scalar character.