From d037878b0b94cd487f463088d699c8aa7f66ad58 Mon Sep 17 00:00:00 2001
From: Kdreval <k.dreval@gmail.com>
Date: Thu, 1 Feb 2024 10:44:42 -0800
Subject: [PATCH] bug fix: resolve function conflicts

---
 NAMESPACE                      | 1 -
 R/prettyRainfallPlot.R         | 8 ++++----
 man/ashm_multi_rainbow_plot.Rd | 7 +++++--
 3 files changed, 9 insertions(+), 7 deletions(-)

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/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.}
 }