GAMBLR Improvements and Bugfixes

[mattssca]

This PR is providing a fix for many of the active issues on GAMBLR, as well as other quality-of-life improvements. The following issues have been addressed in this PR:

• https://github.com/morinlab/GAMBLR/issues/161

• https://github.com/morinlab/GAMBLR/issues/160

• https://github.com/morinlab/GAMBLR/issues/159

• https://github.com/morinlab/GAMBLR/issues/157

• https://github.com/morinlab/GAMBLR/issues/156

• https://github.com/morinlab/GAMBLR/issues/153

• https://github.com/morinlab/GAMBLR/issues/128

• https://github.com/morinlab/GAMBLR/issues/102

• This PR also includes updates that are ensuring that the thematic vignettes can be knitted in remote sessions as well.

• Many updates in this PR are related to the function documentation overhaul.

• All functions that are using the config in any way to get file paths have been updated to encapsulate these statements in the newly added helper function that checks the config keys.

• README.md has been updated with a new section called "For Developers". This section details what the best practices are for designing and adding a new function to GAMBLR, complete with examples and a function template that can be used for designing new functions as well as an example of an adequately documented GAMBLR function.

• Minor hot fixes prevented the vignettes from being knitted. For some reason, the vignettes errors out when a warning gets thrown. Even if the warnings in the chunk option is set to FALSE.

• This branch was tested by running the vignettes as well as the test_funcitons.R script.

• the vignettes have also been updated to rely on modified code.

• The package documentation has also been re-generated to match all the updates included in this PR.

Pull Request Checklists

Important: When opening a pull request, keep only the applicable checklist and delete all other sections.

Checklist for all PRs

Required

• [x] I tested the new code for my use case (please provide a reproducible example of how you tested the new functionality)

• [x] I ensured all dplyr functions that commonly conflict with other packages are fully qualified.

This can be checked and addressed by running check_functions.pl and responding to the prompts. Test your code after you do this.

• [x] I generated the documentation and checked for errors relating to the new function (e.g. devtools::document()) and added NAMESPACE and all other modified files in the root directory and under man.

Optional but preferred with PRs

• [x] I updated and/or successfully knitted a vignette that relies on the modified code (which ones?)

Checklist for New Functions

Required

• [x] I documented my function using ROxygen style.)

• [x] All parameters for the function are described in the documentation and the function has a decriptive title.

Example:

#' Use GISTIC2.0 scores output to reproduce maftools::chromoplot with more flexibility
#'
#' @param scores output file scores.gistic from the run of GISTIC2.0
#' @param genes_to_label optional. Provide a data frame of genes to label (if mutated). The first 3 columns must contain chromosome, start, and end coordinates. Another required column must contain gene names and be named `gene`. (truncated for example)
#' @param cutoff optional. Used to determine which regions to color as aberrant. Must be float in the range [0-1]. (truncated for example)

• [ ] My function uses a library that isn't already a dependency of GAMBLR and I made the package aware of this dependency using the function documentation import statment.

Example:

#' @return nothing
#' @export
#' @import tidyverse ggrepel

Checklist for changes to existing code

• [ ] I added/removed arguments to a function and updated documentation for all changed/new arguments

• [ ] I tested the new code for compatability with existing functionality in the Master branch (please provide a reprex of how you tested the original functionality)

[mattssca]

Thanks for your comments @Kdreval, I'll work on an update addressing the issues you raised. Stay tuned for a re-review!