fixed square for Z > 20 in DIMS/export/generate_violin_plots_functions.R

Author: mraves2

DIMS/export/generate_violin_plots_functions.R

@@ -665,14 +665,20 @@ create_pdf_violin_plots <- function(pdf_dir, patient_id, metab_perpage, top_meta
   for (metab_class in names(metab_perpage)) {
     # extract list of metabolites to plot on a page
     metab_zscores_df <- metab_perpage[[metab_class]]
-    # extract original data for patient of interest (pt_name) before cut-offs
-    patient_zscore_df <- metab_zscores_df %>% filter(Sample == patient_id)
-
-    # Remove patient column and change Z-score. If under -5 to -5 and if above 20 to 20.
+    # copy Z-scores to Z_score_original for displaying values
+    metab_zscores_df$Z_score_original <- metab_zscores_df$Z_score
+    # Cap Z-scores under -5 to -5 and above 20 to 20
     metab_zscores_df <- metab_zscores_df %>%
-      filter(Sample != patient_id) %>%
       mutate(Z_score = pmin(pmax(Z_score, -5), 20))
 
+    # extract original data for patient of interest (pt_name)
+    patient_zscore_df <- metab_zscores_df %>%
+      filter(Sample == patient_id)
+
+    # Remove patient of interest and retain only other patient data
+    metab_zscores_df <- metab_zscores_df %>%
+      filter(Sample != patient_id)
+
     # subtitle per page
     sub_perpage <- gsub("_", " ", metab_class)
     # for IEM plots, put subtitle on two lines
@@ -733,7 +739,7 @@ create_violin_plot <- function(metab_zscores_df, patient_zscore_df, sub_perpage,
     # Add the Z-score at the right side of the plot
     geom_text(
       data = patient_zscore_df,
-      aes(16, label = paste0("Z=", round(Z_score, 2))),
+      aes(16, label = paste0("Z=", round(Z_score_original, 2))),
       hjust = "left", vjust = +0.2, size = 3, na.rm = TRUE
     ) +
     # Set colour for the Z-score of the selected patient