Rename vars in data processing

workflow/apps/r/calculate_interaction_zscores5.R

@@ -115,15 +115,17 @@ load_and_process_data <- function(easy_results_file, sd = 3) {
   df <- df %>%
     filter(!(.[[1]] %in% c("", "Scan"))) %>%
     filter(!is.na(ORF) & ORF != "" & !Gene %in% c("BLANK", "Blank", "blank") & Drug != "BMH21") %>%
+    # Rename columns
+    rename(L = l, num = Num., AUC = AUC96, scan = Scan) %>%
     mutate(
-      across(c(Col, Row, Num.), as.numeric),
-      across(c(L, K, r, scan, AUC96, LstBackgrd, X1stBackgrd), as.numeric),
+      across(c(Col, Row, num), as.numeric),
+      across(c(L, K, r, scan, AUC, LstBackgrd, X1stBackgrd), as.numeric),
       delta_bg = last_bg - first_bg,
       delta_bg_tolerance = mean(delta_bg, na.rm = TRUE) + (sd * sd(delta_bg, na.rm = TRUE)),
       NG = if_else(L == 0 & !is.na(L), 1, 0),
       DB = if_else(delta_bg >= delta_bg_tolerance, 1, 0),
       SM = 0,
-      OrfRep = if_else(ORF == "YDL227C", "YDL227C", OrfRep),
+      OrfRep = if_else(ORF == "YDL227C", "YDL227C", OrfRep), # should these be hardcoded?
       conc_num = as.numeric(gsub("[^0-9\\.]", "", Conc)),
       conc_num_factor = as.numeric(as.factor(conc_num)) - 1
     )
@@ -290,7 +292,6 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
   return(list(zscores_calculations = interaction_scores_all, zscores_interactions = interaction_scores))
 }
 
-
 interaction_plot_configs <- function(df, variable) {
   ylim_vals <- switch(variable,
     "L" = c(-65, 65),
@@ -321,7 +322,6 @@ interaction_plot_configs <- function(df, variable) {
   )
 }
 
-
 generate_plot <- function(df, x_var, y_var = NULL, plot_type, color_var = "conc_num",
   title, x_label = NULL, y_label = NULL, ylim_vals = NULL) {
 
@@ -376,7 +376,7 @@ generate_and_save_plots <- function(df, output_dir, file_prefix, plot_configs) {
     # If custom annotations for interaction plots are required
     if (!is.null(config$annotations)) {
       for (annotation in config$annotations) {
-        plot <- plot + 
+        plot <- plot +
           annotate(
             "text", x = annotation$x, y = annotation$y, label = annotation$label
           )
@@ -390,8 +390,6 @@ generate_and_save_plots <- function(df, output_dir, file_prefix, plot_configs) {
   save_plots(file_prefix, plots, output_dir)
 }
 
-
-
 # Ensure all plots are saved and printed to PDF
 save_plots <- function(file_name, plot_list, output_dir) {
   # Save to PDF