Installation

We recommend installing the package directly from GitHub (requires devtools dependency).

if (!require("devtools")) install.packages("devtools")

devtools::install_github(
    "morinlab/GAMBLR.viz",
    repos = BiocManager::repositories()
)

You can confirm successful installation by running one of the most popular functions:

library(GAMBLR.data)

maf_metadata <- get_gambl_metadata(seq_type_filter = "genome") %>%
    dplyr::filter(pathology %in% c("FL", "DLBCL"))

maf_data <- get_ssm_by_samples(
    these_samples_metadata = maf_metadata
)

#define some genes of interest
fl_genes = c("RRAGC", "CREBBP", "VMA21", "ATP6V1B2")
dlbcl_genes = c("EZH2", "KMT2D", "MEF2B", "CD79B", "MYD88", "TP53")
genes = c(fl_genes, dlbcl_genes)

prettyOncoplot(
    maf_df = maf_data,
    genes = genes,
    these_samples_metadata = maf_metadata
)

There is a lot of functionality to hand-craft this plot exactly in the way you want. Interested? Read more in the tutorials section.

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