Merge pull request #124 from UMCUGenetics/hotfix/v2.7.4

Hotfix/v2.7.4

Author: ALuesink

DIMS/export/generate_violin_plots_functions.R

@@ -713,9 +713,15 @@ create_violin_plot <- function(metab_zscores_df, patient_zscore_df, sub_perpage,
   colors_plot <- c("#22E4AC", "#00B0F0", "#504FFF", "#A704FD", "#F36265", "#DA0641")
 
   y_order <- attr(metab_zscores_df, "y_order")
-  metab_zscores_df$HMDB_name <- rev(factor(metab_zscores_df$HMDB_name, levels = rev(y_order)))
-  patient_zscore_df$HMDB_name <- rev(factor(patient_zscore_df$HMDB_name, levels = rev(y_order)))
-
+  
+  metab_zscores_df <- metab_zscores_df %>%
+    mutate(HMDB_name = factor(HMDB_name, levels = y_order)) %>%
+    arrange(HMDB_name)
+  
+  patient_zscore_df <- patient_zscore_df %>%
+    mutate(HMDB_name = factor(HMDB_name, levels = y_order)) %>%
+    arrange(HMDB_name)
+  
   ggplot_object <- ggplot(metab_zscores_df, aes(x = Z_score, y = HMDB_name)) +
     # Make violin plots
     geom_violin(scale = "width", na.rm = TRUE) +

DIMS/tests/testthat/_snaps/generate_violin_plots.md

@@ -4,8 +4,8 @@
       content_pdf_violinplots
     Output
       [1] "Top deviating metabolites for patient: P2025M1\n                Metabolite  Z.score\n               Increased\n               metab1      2.45\n               Decreased\n               metab11     −1.51\n"                                                                                                                                                                                 
-      [2] "                       Results for patient P2025M1\n                       test acyl carnitines\n              metab1                                          Z=2.34\nMetabolites\n              metab3                                          Z=0.31\n                        −5        0           5     10   15            20\n                                              Z−scores\n"
-      [3] "                        Results for patient P2025M1\n                        test crea gua\n              metab4                                       Z=−0.46\nMetabolites\n              metab11                                      Z=0.84\n                         −5       0     5     10      15            20\n                                        Z−scores\n"                   
+      [2] "                       Results for patient P2025M1\n                       test acyl carnitines\n              metab1                                          Z=0.31\nMetabolites\n              metab3                                          Z=2.34\n                        −5        0           5     10   15            20\n                                              Z−scores\n"
+      [3] "                        Results for patient P2025M1\n                        test crea gua\n              metab4                                       Z=0.84\nMetabolites\n              metab11                                      Z=−0.46\n                         −5       0     5     10      15            20\n                                        Z−scores\n"                   
       [4] "          Unit test Generate Violin Plots\nUnit test Generate Violin Plots\n"                                                                                                                                                                                                                                                                                                                 
 
 # save_prob_scores_to_excel: Saving the probability score dataframe as an Excel file