plotMutTypeProfile: Plot Mutation Signature Profiles.

In dami82/mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

Plot Mutation Signature Profiles.

Description

Build a barplot to visualize the relative abundance of mutation counts in a mutational signature or biological sample of interest.

Usage

plotMutTypeProfile(
  mutCounts,
  mutLabs,
  freq = TRUE,
  ylim = "auto",
  ylab = "Fraction of Variants",
  xlab = "Sequence Motifs",
  xaxis_cex = 0.475,
  cols = c("#4eb3d3", "#040404", "#b30000", "#bdbdbd", "#41ab5d", "#dd3497"),
  main = "MutType Profile"
)

Arguments

mutCounts	data.frame including mutation types counts or frequencies, such as a data.frame of mutation counts from samples, or mutation type frequencies from a mutational signature.
mutLabs	character vector, labels to be used for the mutation types
freq	logical, shall frequency be plotted rather than counts. Defaults to TRUE
ylim	values used for ylim. Defaults to "auto" (ylim automatically set)
ylab	string, used as y-axis title. Defaults to "Fraction of Variants"
xlab	string, used as x-axis title. Defaults to "Sequence Motifs"
xaxis_cex	numeric, cex value for the xaxis
cols	character vector, indicates the colors to be used for the bars. It typically requires 6 colors.
main	string, tutle of the plot. Defaults to "MutType Profile"

Details

This function is part of the user-interface set of tools included in mutSignatures. This is an exported function.

Value

NULL. A plot is printed to the active device.

Author(s)

Damiano Fantini, [e-mail]

References

More information and examples about mutational signature analysis can be found here:

1. Official website: http://www.mutsignatures.org

2. More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/

3. Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6

dami82/mutSignatures documentation built on Jan. 24, 2023, 12:21 a.m.