From 7a5fffb5b4b33fd4f816d0c753182eed49a5a2ea Mon Sep 17 00:00:00 2001
From: "Vera N. Karlbauer" <vera@karlbauer.org>
Date: Sat, 4 Nov 2023 17:00:36 +0100
Subject: [PATCH] Changed color scheme for batch detection plots back to
 default

---
 scripts/10_correction_batch_effects_unfiltered.Rmd     | 3 ---
 scripts/8_removal_of_outliers_detect_batch_effects.Rmd | 4 ----
 scripts/9_correction_batch_effects_filtered.Rmd        | 3 ---
 3 files changed, 10 deletions(-)

diff --git a/scripts/10_correction_batch_effects_unfiltered.Rmd b/scripts/10_correction_batch_effects_unfiltered.Rmd
index 1ff132b..31d08a5 100644
--- a/scripts/10_correction_batch_effects_unfiltered.Rmd
+++ b/scripts/10_correction_batch_effects_unfiltered.Rmd
@@ -141,7 +141,6 @@ if (correction_variable_1 == "PLEASE FILL IN"){
     technical_batch_plots[[i]] <- PCs %>%
       ggplot(aes(x = PC1, y = PC2)) +
       geom_point(aes(color = .data[[i]], fill = .data[[i]])) +
-      scale_colour_brewer(palette = "Dark2") +
       ggtitle(i) + theme(legend.title = element_blank())
     print(technical_batch_plots[[i]])
   }
@@ -301,7 +300,6 @@ if (correction_variable_2 == "PLEASE FILL IN"){
     technical_batch_plots[[i]] <- PCs %>%
       ggplot(aes(x = PC1, y = PC2)) +
       geom_point(aes(color = .data[[i]], fill = .data[[i]])) +
-      scale_colour_brewer(palette = "Dark2") +
       ggtitle(i) + theme(legend.title = element_blank())
     print(technical_batch_plots[[i]])
   }
@@ -461,7 +459,6 @@ if (correction_variable_3 == "PLEASE FILL IN"){
     technical_batch_plots[[i]] <- PCs %>%
       ggplot(aes(x = PC1, y = PC2)) +
       geom_point(aes(color = .data[[i]], fill = .data[[i]])) +
-      scale_colour_brewer(palette = "Dark2") +
       ggtitle(i) + theme(legend.title = element_blank())
     print(technical_batch_plots[[i]])
   }
diff --git a/scripts/8_removal_of_outliers_detect_batch_effects.Rmd b/scripts/8_removal_of_outliers_detect_batch_effects.Rmd
index bf12934..73f59b4 100644
--- a/scripts/8_removal_of_outliers_detect_batch_effects.Rmd
+++ b/scripts/8_removal_of_outliers_detect_batch_effects.Rmd
@@ -198,7 +198,6 @@ for (i in technical_batch_variables){
                      size = 3, box.padding = unit(0.35, "lines"),
                      segment.colour = "black",
                      point.padding = unit(0.3, "lines")) +
-    scale_colour_brewer(palette = "Dark2") +
     ggtitle(i) + theme(legend.title = element_blank())
   print(technical_batch_plots[[i]])
 }
@@ -332,7 +331,6 @@ if(!identical(extreme_outliers_filtered %>% pull(personid),character(0))){
                        size = 3, box.padding = unit(0.35, "lines"),
                        segment.colour = "black",
                        point.padding = unit(0.3, "lines")) +
-      scale_colour_brewer(palette = "Dark2") +
       ggtitle(i) + theme(legend.title = element_blank())
     print(technical_batch_plots[[i]])
   }
@@ -546,7 +544,6 @@ for (i in technical_batch_variables){
                      size = 3, box.padding = unit(0.35, "lines"),
                      segment.colour = "black",
                      point.padding = unit(0.3, "lines")) +
-    scale_colour_brewer(palette = "Dark2") +
     ggtitle(i) + theme(legend.title = element_blank())
   print(technical_batch_plots[[i]])
 }
@@ -681,7 +678,6 @@ if(!identical(extreme_outliers_unfiltered %>% pull(personid),character(0))){
                        size = 3, box.padding = unit(0.35, "lines"),
                        segment.colour = "black",
                        point.padding = unit(0.3, "lines")) +
-      scale_colour_brewer(palette = "Dark2") +
       ggtitle(i) + theme(legend.title = element_blank())
     print(technical_batch_plots[[i]])
   }
diff --git a/scripts/9_correction_batch_effects_filtered.Rmd b/scripts/9_correction_batch_effects_filtered.Rmd
index 7462e35..6091378 100644
--- a/scripts/9_correction_batch_effects_filtered.Rmd
+++ b/scripts/9_correction_batch_effects_filtered.Rmd
@@ -151,7 +151,6 @@ if (correction_variable_1 == "PLEASE FILL IN"){
     technical_batch_plots[[i]] <- PCs %>%
       ggplot(aes(x = PC1, y = PC2)) +
       geom_point(aes(color = .data[[i]], fill = .data[[i]])) +
-      scale_colour_brewer(palette = "Dark2") +
       ggtitle(i) + theme(legend.title = element_blank())
     print(technical_batch_plots[[i]])
   }
@@ -311,7 +310,6 @@ if (correction_variable_2 == "PLEASE FILL IN"){
     technical_batch_plots[[i]] <- PCs %>%
       ggplot(aes(x = PC1, y = PC2)) +
       geom_point(aes(color = .data[[i]], fill = .data[[i]])) +
-      scale_colour_brewer(palette = "Dark2") +
       ggtitle(i) + theme(legend.title = element_blank())
     print(technical_batch_plots[[i]])
   }
@@ -471,7 +469,6 @@ if (correction_variable_3 == "PLEASE FILL IN"){
     technical_batch_plots[[i]] <- PCs %>%
       ggplot(aes(x = PC1, y = PC2)) +
       geom_point(aes(color = .data[[i]], fill = .data[[i]])) +
-      scale_colour_brewer(palette = "Dark2") +
       ggtitle(i) + theme(legend.title = element_blank())
     print(technical_batch_plots[[i]])
   }