(temp) test bugfix to brewer pal

Author: marsiwiec

R/999_plot_palettes.R

@@ -5,45 +5,54 @@
 # Applies palettes to <ggplot> objects
 # TODO add proper documentation.
 apply_palette <- function(ggplot_object, palette_name) {
-  ggplot_object <- switch(palette_name,
-    "npg" =
-      ggplot_object + ggsci::scale_color_npg() + ggsci::scale_fill_npg(),
-    "aaas" =
-      ggplot_object + ggsci::scale_color_aaas() + ggsci::scale_fill_aaas(),
-    "nejm" =
-      ggplot_object + ggsci::scale_color_nejm() + ggsci::scale_fill_nejm(),
-    "lancet" =
-      ggplot_object + ggsci::scale_color_lancet() + ggsci::scale_fill_lancet(),
-    "jama" =
-      ggplot_object + ggsci::scale_color_jama() + ggsci::scale_fill_jama(),
-    "jco" =
-      ggplot_object + ggsci::scale_color_jco() + ggsci::scale_fill_jco(),
-    "ucscgb" =
-      ggplot_object + ggsci::scale_color_ucscgb() + ggsci::scale_fill_ucscgb(),
-    "d3" =
-      ggplot_object + ggsci::scale_color_d3() + ggsci::scale_fill_d3(),
-    "locuszoom" =
-      ggplot_object + ggsci::scale_color_locuszoom() + ggsci::scale_fill_locuszoom(),
-    "igv" =
-      ggplot_object + ggsci::scale_color_igv() + ggsci::scale_fill_igv(),
-    "cosmic" =
-      ggplot_object + ggsci::scale_color_cosmic() + ggsci::scale_fill_cosmic(),
-    "uchicago" =
-      ggplot_object + ggsci::scale_color_uchicago() + ggsci::scale_fill_uchicago(),
-    "brewer" =
-      ggplot_object + ggplot2::scale_color_brewer() + ggplot2::scale_fill_brewer(),
-    "ordinal" =
-      ggplot_object + ggplot2::scale_color_ordinal() + ggplot2::scale_fill_ordinal(),
-    "viridis_d" =
-      ggplot_object + ggplot2::scale_color_viridis_d() + ggplot2::scale_fill_viridis_d()
+  ggplot_object <- switch(
+    palette_name,
+    "npg" = ggplot_object + ggsci::scale_color_npg() + ggsci::scale_fill_npg(),
+    "aaas" = ggplot_object +
+      ggsci::scale_color_aaas() +
+      ggsci::scale_fill_aaas(),
+    "nejm" = ggplot_object +
+      ggsci::scale_color_nejm() +
+      ggsci::scale_fill_nejm(),
+    "lancet" = ggplot_object +
+      ggsci::scale_color_lancet() +
+      ggsci::scale_fill_lancet(),
+    "jama" = ggplot_object +
+      ggsci::scale_color_jama() +
+      ggsci::scale_fill_jama(),
+    "jco" = ggplot_object + ggsci::scale_color_jco() + ggsci::scale_fill_jco(),
+    "ucscgb" = ggplot_object +
+      ggsci::scale_color_ucscgb() +
+      ggsci::scale_fill_ucscgb(),
+    "d3" = ggplot_object + ggsci::scale_color_d3() + ggsci::scale_fill_d3(),
+    "locuszoom" = ggplot_object +
+      ggsci::scale_color_locuszoom() +
+      ggsci::scale_fill_locuszoom(),
+    "igv" = ggplot_object + ggsci::scale_color_igv() + ggsci::scale_fill_igv(),
+    "cosmic" = ggplot_object +
+      ggsci::scale_color_cosmic() +
+      ggsci::scale_fill_cosmic(),
+    "uchicago" = ggplot_object +
+      ggsci::scale_color_uchicago() +
+      ggsci::scale_fill_uchicago(),
+    "brewerDark2" = ggplot_object +
+      ggplot2::scale_color_brewer(palette = "Dark2") +
+      ggplot2::scale_fill_brewer(palette = "Dark2"),
+    "ordinal" = ggplot_object +
+      ggplot2::scale_color_ordinal() +
+      ggplot2::scale_fill_ordinal(),
+    "viridis_d" = ggplot_object +
+      ggplot2::scale_color_viridis_d() +
+      ggplot2::scale_fill_viridis_d()
   )
 
   return(ggplot_object)
 }
 
 get_palette_colours <- function(palette_name, num_colours) {
   # palette function by name
-  colours <- switch(palette_name,
+  colours <- switch(
+    palette_name,
     "npg" = ggsci::pal_npg()(num_colours),
     "aaas" = ggsci::pal_aaas()(num_colours),
     "nejm" = ggsci::pal_nejm()(num_colours),
@@ -56,7 +65,7 @@ get_palette_colours <- function(palette_name, num_colours) {
     "igv" = ggsci::pal_igv()(num_colours),
     "cosmic" = ggsci::pal_cosmic()(num_colours),
     "uchicago" = ggsci::pal_uchicago()(num_colours),
-    "brewer" = RColorBrewer::brewer.pal()(num_colours),
+    "brewerDark2" = RColorBrewer::brewer.pal(name = "Dark2", n = num_colours),
     "ordinal" = viridisLite::viridis(n = num_colours, option = "viridis"),
     "viridis_d" = viridisLite::viridis(n = num_colours, option = "viridis")
   )