Remove references to ranked df

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -660,73 +660,69 @@ generate_plate_analysis_plot_configs <- function(variables, stages = c("before",
   return(plots)
 }
 
-generate_interaction_plot_configs <- function(df, variables) {
-
-  configs <- list()
-
-  # Set the y-limits for each variable
-  df_filtered <- df %>%
-    filter(
-      !is.na(L) & between(L, -65, 65),
-      !is.na(K) & between(K, -65, 65),
-      !is.na(r) & between(r, -0.65, 0.65),
-      !is.na(AUC) & between(AUC, -6500, 6500)
+generate_interaction_plot_configs <- function(df, variables, limits_map = NULL) {
+  # Default limits_map if not provided
+  if (is.null(limits_map)) {
+    limits_map <- list(
+      L = c(-65, 65),
+      K = c(-65, 65),
+      r = c(-0.65, 0.65),
+      AUC = c(-6500, 6500)
     )
+  }
 
-  # Define annotation label functions
-  generate_annotation_labels <- function(df, var, annotation_name) {
-    switch(annotation_name,
-      ZShift = paste("ZShift =", round(df[[paste0("Z_Shift_", var)]], 2)),
-      lm_ZScore = paste("lm ZScore =", round(df[[paste0("Z_lm_", var)]], 2)),
-      NG = paste("NG =", df$NG),
-      DB = paste("DB =", df$DB),
-      SM = paste("SM =", df$SM),
-      NULL  # Default case for unrecognized annotation names
-    )
+  # Filter data
+  df_filtered <- df
+  for (var in names(limits_map)) {
+    df_filtered <- df_filtered %>%
+      filter(!is.na(!!sym(var)) &
+        !!sym(var) >= limits_map[[var]][1] &
+        !!sym(var) <= limits_map[[var]][2])
   }
 
-  # Define annotation positions relative to the y-axis range
-  calculate_annotation_positions <- function(y_range) {
+  configs <- list()
+
+  for (variable in variables) {
+    y_range <- limits_map[[variable]]
+    
+    # Calculate annotation positions
     y_min <- min(y_range)
     y_max <- max(y_range)
     y_span <- y_max - y_min
-
-    list(
+    annotation_positions <- list(
       ZShift = y_max - 0.1 * y_span,
       lm_ZScore = y_max - 0.2 * y_span,
       NG = y_min + 0.2 * y_span,
       DB = y_min + 0.1 * y_span,
       SM = y_min + 0.05 * y_span
     )
-  }
-
-  # Create configurations for each variable
-  for (variable in variables) {
 
-    y_range <- limits_map[[variable]]
-    annotation_positions <- calculate_annotation_positions(y_range)
+    # Prepare linear model line
     lm_line <- list(
       intercept = df_filtered[[paste0("lm_intercept_", variable)]],
       slope = df_filtered[[paste0("lm_slope_", variable)]]
     )
 
-    # Determine x-axis midpoint
+    # Calculate x-axis position for annotations
     num_levels <- length(levels(df_filtered$conc_num_factor))
-    x_pos <- (1 + num_levels) / 2  # Midpoint of x-axis
+    x_pos <- (1 + num_levels) / 2
 
     # Generate annotations
     annotations <- lapply(names(annotation_positions), function(annotation_name) {
-      label <- generate_annotation_labels(df_filtered, variable, annotation_name)
-      y_pos <- annotation_positions[[annotation_name]]
+      label <- switch(annotation_name,
+        ZShift = paste("ZShift =", round(df_filtered[[paste0("Z_Shift_", variable)]], 2)),
+        lm_ZScore = paste("lm ZScore =", round(df_filtered[[paste0("Z_lm_", variable)]], 2)),
+        NG = paste("NG =", df_filtered$NG),
+        DB = paste("DB =", df_filtered$DB),
+        SM = paste("SM =", df_filtered$SM),
+        NULL
+      )
       if (!is.null(label)) {
-        list(x = x_pos, y = y_pos, label = label)
+        list(x = x_pos, y = annotation_positions[[annotation_name]], label = label)
       } else {
-        message(paste("Warning: No annotation found for", annotation_name))
         NULL
       }
     })
-
-    # Remove NULL annotations
     annotations <- Filter(Negate(is.null), annotations)
 
     # Shared plot settings
@@ -740,7 +736,7 @@ generate_interaction_plot_configs <- function(df, variables) {
       x_breaks = levels(df_filtered$conc_num_factor),
       x_labels = levels(df_filtered$conc_num_factor),
       x_label = unique(df_filtered$Drug[1]),
-      coord_cartesian = y_range  # Use the actual y-limits
+      coord_cartesian = y_range
     )
 
     # Scatter plot config
@@ -1422,7 +1418,7 @@ main <- function() {
 
       message("Generating filtered ranked plots")
       rank_plot_filtered_configs <- generate_rank_plot_configs(
-        df = zscores_interactions_filtered_ranked,
+        df = zscores_interactions_filtered,
         variables = interaction_vars,
         is_lm = FALSE,
         adjust = FALSE,
@@ -1437,7 +1433,7 @@ main <- function() {
 
       message("Generating filtered ranked linear model plots")
       rank_plot_lm_filtered_configs <- generate_rank_plot_configs(
-        df = zscores_interactions_filtered_ranked,
+        df = zscores_interactions_filtered,
         variables = interaction_vars,
         is_lm = TRUE,
         adjust = FALSE,