mutaliskRutils is an R package that produces cohort-level visualisations from the files output by mutalisk.
Note CRUX is a GUI tool that makes it easy to export data in mutalisk compatible formats, and also provides a GUI interface to this package in the ‘Mutational Signatures’ module. For a no-code solution, consider using the web app.
You can install the development version of mutaliskRutils from GitHub with:
# install.packages("remotes")
# remotes::install_github("selkamand/mutaliskRutils")
install.packages("mutaliskRutils", repos = c('https://selkamand.r-universe.dev', 'https://cloud.r-project.org'))
First you have to generate mutalisk file:
Start by following the instructions on the mutalisk website
Once the results are ready, Select
Mutational Signature (Best only)
Then click Get the selected result for all samples at once
Unzip the file
Parse the directory with
mutalisk_best_signature_directory_to_dataframe and plot with
plot_stacked_bar
library(mutaliskRutils)
# Read files in mutalisk_dir into
mutalisk_dir <- system.file("lusc_tcga", package = "mutaliskRutils")
mutalisk_df <- mutalisk_best_signature_directory_to_dataframe(mutalisk_dir)
# Plot Cohort Data
plot_stacked_bar(mutalisk_df)
#> Lumping together signatures with contributions < 0.1 in all samples as 'Other'
#> Metadata columns: SignaturesAllContributionsBelowMin
