some minor updates to aSHM code

[rdmorin]

Pull Request Checklists

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

Checklist for all PRs

Required

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

get_mutation_frequency_bin_matrix(these_samples_metadata = some_meta,
                                  cluster_rows_heatmap = FALSE,
                                  regions_df = some_regions,
                                  customColour=col_list,
                                  min_bin_recurrence = 20,
                                  window_size = 500,
                                  slide_by = 500,
                                  orientation = "sample_rows", #change to "gene_rows" to rotate
                                  min_count_per_bin = 1,
                                  sortByColumns = c("pathology","genetic_subgroup","manta_MYC_sv","manta_MYC_partner"),
                                  metadataColumns=
                                    c("manta_MYC_sv","manta_MYC_partner","genetic_subgroup",
                                      "pathology"))

• 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.

• 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

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

Checklist for New Functions

Required

• I documented my function using ROxygen style.)

• 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)

[Kdreval]

This probably needs an update to be pathology == "HGBL" since this came back from path review