Simplify SD bands

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -508,28 +508,26 @@ generate_scatter_plot <- function(plot, config) {
   }
   
   # Add SD Bands if specified
-  if (!is.null(config$sd_band_values)) {
-    for (sd_band in config$sd_band_values) {
-      plot <- plot +
-        annotate(
-          "rect",
-          xmin = -Inf, xmax = Inf,
-          ymin = sd_band, ymax = Inf,
-          fill = "#542788",
-          alpha = 0.3
-        ) +
-        annotate(
-          "rect",
-          xmin = -Inf, xmax = Inf,
-          ymin = -sd_band, ymax = -Inf,
-          fill = "orange",
-          alpha = 0.3
-        ) +
-        geom_hline(
-          yintercept = c(-sd_band, sd_band),
-          color = "gray"
-        )
-    }
+  if (!is.null(config$sd_band)) {
+    plot <- plot +
+      annotate(
+        "rect",
+        xmin = -Inf, xmax = Inf,
+        ymin = config$sd_band, ymax = Inf,
+        fill = "#542788",
+        alpha = 0.3
+      ) +
+      annotate(
+        "rect",
+        xmin = -Inf, xmax = Inf,
+        ymin = -config$sd_band, ymax = -Inf,
+        fill = "orange",
+        alpha = 0.3
+      ) +
+      geom_hline(
+        yintercept = c(-config$sd_band, config$sd_band),
+        color = "gray"
+      )
   }
 
   # Add Rectangles if specified
@@ -770,18 +768,19 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
   
   # SD-based plots for L and K
   for (variable in c("L", "K")) {
+
+    if (is_lm) {
+      rank_var <- paste0("Rank_lm_", variable)
+      zscore_var <- paste0("Z_lm_", variable)
+      y_label <- paste("Int Z score", variable)
+    } else {
+      rank_var <- paste0("Rank_", variable)
+      zscore_var <- paste0("Avg_Zscore_", variable)
+      y_label <- paste("Avg Z score", variable)
+    }
+
     for (sd_band in sd_bands) {
-      # Determine columns based on whether it's lm or not
-      if (is_lm) {
-        rank_var <- paste0("Rank_lm_", variable)
-        zscore_var <- paste0("Z_lm_", variable)
-        y_label <- paste("Int Z score", variable)
-      } else {
-        rank_var <- paste0("Rank_", variable)
-        zscore_var <- paste0("Avg_Zscore_", variable)
-        y_label <- paste("Avg Z score", variable)
-      }
-      
+
       num_enhancers <- sum(df_filtered[[zscore_var]] >= sd_band, na.rm = TRUE)
       num_suppressors <- sum(df_filtered[[zscore_var]] <= -sd_band, na.rm = TRUE)
       
@@ -805,7 +804,6 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
             label = paste("Deletion Suppressors =", num_suppressors)
           )
         ),
-        sd_band_values = sd_band,
         shape = 3,
         size = 0.1,
         y_label = y_label,
@@ -822,7 +820,6 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
         title = paste(y_label, "vs. Rank for", variable, "above", sd_band, "SD No Annotations"),
         sd_band = sd_band,
         annotations = NULL,
-        sd_band_values = sd_band,
         shape = 3,
         size = 0.1,
         y_label = y_label,
@@ -873,7 +870,6 @@ generate_rank_plot_configs <- function(df_filtered, variables, is_lm = FALSE) {
             label = paste("R-squared =", round(lm_summary$r.squared, 2))
           )
         ),
-        sd_band_values = NULL, # Not applicable
         shape = 3,
         size = 0.1,
         add_smooth = TRUE,
@@ -997,7 +993,6 @@ filter_data <- function(df, variables, nf = FALSE, missing = FALSE, adjust = FAL
   return(df)
 }
 
-
 main <- function() {
   lapply(names(args$experiments), function(exp_name) {
     exp <- args$experiments[[exp_name]]