morinlab / GAMBLR.viz

Collection of functions to make plots for Genomic Analysis of Mature B-cell Lymphomas in R

GAMBLR.viz

Collection of functions to make plots for Genomic Analysis of Mature B-cell Lymphomas in R.

For detailed information about how to install, bundled resources, functionality overview, tutorials, frequently asked questions and much more please visit the website morinlab.github.io/GAMBLR.viz

Contributing

Cloning repo for the code development

The easiest way to obtain and contribute to GAMBLR.viz is to do this via cloning the repository

cd
git clone [e-mail]:morinlab/GAMBLR.viz.git

In your R editor of choice, set your working directory to the place you just cloned the repo.

setwd("~/GAMBLR.viz")

Install the package in R by running the following command (requires the devtools package)

devtools::install()

As GAMBL users (GAMBLRs, so to speak) rely on the functionality of this package, the Master branch is protected. All commits must be submitted via pull request on a branch. Please refer to the GAMBL documentation for details on how to do this.

Function conflicts

This package relies on the use of some functions (e.g. get_gambl_metadata(), get_coding_ssm() etc) that exist in 2 different versions: GAMBLR.data for the users who do not have access to GSC and GAMBLR.results for the Morin Lab users with access to GSC. If your contribution relies on the use of such functions, please follow these 2 steps:

• DO NOT prepend the function use with <package>:: (for example, <package>::function()), and
• DO NOT add the corresponding package to the @import section of the function

Following these steps will ensure correct usage of the proper function depending on which package is loaded in the session and will avoid functionality conflicts.