plotMutTypeProfile {mutSignatures}

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. GitHub Repo: https://github.com/dami82/mutSignatures/

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

3. Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/

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