diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..ea1f667 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,10 @@ +# 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 ensured not to prepend the functions existing in both GAMBLR.data and GAMBLR.results with `::function()` syntax. +- [ ] I ensured not to add GAMBLR.data or GAMBLR.results to the `@import` section of the documentation diff --git a/NAMESPACE b/NAMESPACE index 8ce5265..6d09e29 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -31,7 +31,6 @@ export(pretty_lollipop_plot) export(splendidHeatmap) export(ssm_to_proteinpaint) import(ComplexHeatmap) -import(GAMBLR.data) import(GAMBLR.helpers) import(GAMBLR.utils) import(RCircos) diff --git a/R/prettyRainfallPlot.R b/R/prettyRainfallPlot.R index 9e7c03e..0d8092b 100644 --- a/R/prettyRainfallPlot.R +++ b/R/prettyRainfallPlot.R @@ -35,7 +35,7 @@ #' @return a ggplot2 object #' #' @rawNamespace import(data.table, except = c("last", "first", "between", "transpose", "melt", "dcast")) -#' @import ggplot2 dplyr readr stringr tidyr reshape2 GAMBLR.data GAMBLR.helpers GAMBLR.utils +#' @import ggplot2 dplyr readr stringr tidyr reshape2 GAMBLR.helpers GAMBLR.utils #' @export #' #' @examples @@ -110,7 +110,7 @@ prettyRainfallPlot = function( # allow to zoom in to a specific region if (!missing(zoom_in_region)) { region <- zoom_in_region - zoom_in_region <- GAMBLR.data::region_to_chunks(zoom_in_region) + zoom_in_region <- region_to_chunks(zoom_in_region) zoom_in_region$chromosome <- GAMBLR.helpers::standardize_chr_prefix( incoming_vector = zoom_in_region$chromosome, projection = projection @@ -121,7 +121,7 @@ prettyRainfallPlot = function( if (label_ashm_genes) { if (projection == "grch37") { - ashm_regions <- GAMBLR.data::grch37_ashm_regions %>% + ashm_regions <- grch37_ashm_regions %>% dplyr::rename( "start" = "hg19_start", "end" = "hg19_end", @@ -134,7 +134,7 @@ prettyRainfallPlot = function( ) ) } else if (projection == "hg38") { - ashm_regions <- GAMBLR.data::hg38_ashm_regions %>% + ashm_regions <- hg38_ashm_regions %>% dplyr::rename( "start" = "hg38_start", "end" = "hg38_end", diff --git a/README.md b/README.md index 6fffe32..ebef2b1 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,37 @@ # GAMBLR.viz + Collection of functions to make plots for Genomic Analysis of Mature B-cell Lymphomas in R + +# 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 git@github.com: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](https://github.com/morinlab/gambl#contribution-guidelines) 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](https://github.com/morinlab/GAMBLR.data) for the users who do not have access to GSC and [GAMBLR.results](https://github.com/morinlab/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 `::` (for example, `::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. diff --git a/man/ashm_multi_rainbow_plot.Rd b/man/ashm_multi_rainbow_plot.Rd index bbc2696..df7ec0c 100644 --- a/man/ashm_multi_rainbow_plot.Rd +++ b/man/ashm_multi_rainbow_plot.Rd @@ -13,11 +13,12 @@ ashm_multi_rainbow_plot( custom_colours, classification_column = "lymphgen", maf_data, + projection = "grch37", verbose = TRUE ) } \arguments{ -\item{regions_bed}{Bed file with chromosome coordinates, should contain columns chr, start, end, name (with these exact names).} +\item{regions_bed}{Bed file with chromosome coordinates, should contain columns chr, start, end, name (with these exact names). Not required if selecting from many common regions; bonus regions also exist in grch37.} \item{regions_to_display}{Optional vector of names from default regions_bed to use.} @@ -31,7 +32,9 @@ ashm_multi_rainbow_plot( \item{classification_column}{Optional. Override default column for assigning the labels used for colouring in the figure.} -\item{maf_data}{An already loaded maf, if no provided, this function will call `get_ssm_by_region`, using the regions supplied into `regions_bed`.} +\item{maf_data}{An already loaded maf. If not provided, this function will call `get_ssm_by_region`, using the regions supplied into `regions_bed`. Ensure your maf matches the genome projection.} + +\item{projection}{Provide genome build; default is grch37. Bonus regions are only available in grch37.} \item{verbose}{Set to FALSE to prevent printing the full regions bed file to the console. Default is TRUE.} }