Changed color scheme for batch detection plots back to default

mpip · Nov 4, 2023 · 7a5fffb · 7a5fffb
1 parent b154f07
commit 7a5fffb
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Showing 3 changed files with 0 additions and 10 deletions.
diff --git 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
@@ -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
@@ -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]])
   }