Merge pull request #37 from morinlab/kdreval-viz-setup

bug fix: resolve function conflicts

.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 `<package>::function()` syntax.
+- [ ] I ensured not to add GAMBLR.data or GAMBLR.results to the `@import` section of the documentation

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)

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",

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 `<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.