Add back error bars to scatter plots

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -461,7 +461,7 @@ generate_scatter_plot <- function(plot, config, interactive = FALSE) {
     aes_params, shape = config$shape %||% 3,
     size = config$size %||% 0.2, 
     position = if (!is.null(config$position) && config$position == "jitter") "jitter" else "identity")
-
+  
   # Add smooth line if specified
   if (!is.null(config$add_smooth) && config$add_smooth) {
     plot <- if (!is.null(config$lm_line)) {
@@ -471,6 +471,16 @@ generate_scatter_plot <- function(plot, config, interactive = FALSE) {
     }
   }
 
+  # Add error bars if specified
+  if (!is.null(config$error_bar) && config$error_bar) {
+    y_mean_col <- paste0("mean_", config$y_var)
+    y_sd_col <- paste0("sd_", config$y_var)
+    plot <- plot + geom_errorbar(aes(
+      ymin = !!sym(y_mean_col) - !!sym(y_sd_col),
+      ymax = !!sym(y_mean_col) + !!sym(y_sd_col)
+    ), alpha = 0.3)
+  }
+
   # Add x-axis customization if specified
   if (!is.null(config$x_breaks) && !is.null(config$x_labels) && !is.null(config$x_label)) {
     plot <- plot + scale_x_continuous(
@@ -615,10 +625,7 @@ generate_interaction_plot_configs <- function(df, variables) {
       ylim_vals = var_info$ylim,
       annotations = annotations,
       lm_line = lm_line,  # Precomputed linear model
-      error_bar = list(
-        ymin = 0 - (2 * df[[var_info$sd_col]][1]),
-        ymax = 0 + (2 * df[[var_info$sd_col]][1])
-      ),
+      error_bar = TRUE,
       x_breaks = unique(df$conc_num_factor),
       x_labels = unique(as.character(df$conc_num)),
       x_label = unique(df$Drug[1]),
@@ -637,7 +644,7 @@ generate_interaction_plot_configs <- function(df, variables) {
       title = sprintf("%s      %s (Boxplot)", df$OrfRep[1], df$Gene[1]),
       ylim_vals = var_info$ylim,
       annotations = annotations,
-      error_bar = FALSE,  # Boxplots typically don't need error bars
+      error_bar = FALSE,
       x_breaks = unique(df$conc_num_factor),
       x_labels = unique(as.character(df$conc_num)),
       x_label = unique(df$Drug[1]),