Fix error bars and points for interaction plots

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -377,8 +377,17 @@ calculate_interaction_scores <- function(df, max_conc, bg_stats, group_vars, ove
       Z_Shift_L, Z_Shift_K, Z_Shift_r, Z_Shift_AUC
     )
 
+  calculations_no_overlap <- calculations %>%
+    # DB, NG, SM are same as in interactions, the rest may be different and need to be checked
+    select(-any_of(c(
+      "DB", "NG", "SM",
+      "Raw_Shift_L", "Raw_Shift_K", "Raw_Shift_r", "Raw_Shift_AUC",
+      "Z_Shift_L", "Z_Shift_K", "Z_Shift_r", "Z_Shift_AUC",
+      "Z_lm_L", "Z_lm_K", "Z_lm_r", "Z_lm_AUC"
+    )))
+
   # Use left_join to avoid dimension mismatch issues
-  full_data <- calculations %>%
+  full_data <- calculations_no_overlap %>%
     left_join(interactions, by = group_vars)
 
   # Return full_data and the two required dataframes (calculations and interactions)
@@ -471,12 +480,12 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
 
     dev.off()
 
-    out_html_file <- file.path(out_dir, paste0(filename, ".html"))
-    message("Saving combined HTML file: ", out_html_file)
-    htmltools::save_html(
-      htmltools::tagList(plotly_plots),
-      file = out_html_file
-    )
+    # out_html_file <- file.path(out_dir, paste0(filename, ".html"))
+    # message("Saving combined HTML file: ", out_html_file)
+    # htmltools::save_html(
+    #   htmltools::tagList(plotly_plots),
+    #   file = out_html_file
+    # )
   }
 }
 
@@ -570,11 +579,23 @@ generate_scatter_plot <- function(plot, config) {
   # Add error bars if specified
   if (!is.null(config$error_bar) && config$error_bar && !is.null(config$y_var)) {
     if (!is.null(config$error_bar_params)) {
-      plot <- plot + geom_errorbar(aes(ymin = config$error_bar_params$ymin, ymax = config$error_bar_params$ymax))
+      error_bar_color <- if (!is.null(config$error_bar_params$color)) {
+        config$error_bar_params$color
+      } else {
+        "red"
+      }
+      
+      plot <- plot + geom_errorbar(aes(
+        ymin = config$error_bar_params$ymin,
+        ymax = config$error_bar_params$ymax,
+        color = error_bar_color))
     } else {
       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)))
+      plot <- plot + geom_errorbar(aes(
+        ymin = !!sym(y_mean_col) - !!sym(y_sd_col),
+        ymax = !!sym(y_mean_col) + !!sym(y_sd_col),
+        color = "red"))
     }
   }
 
@@ -727,8 +748,9 @@ generate_interaction_plot_configs <- function(df, type) {
       plot_type = "scatter",
       x_var = "conc_num_factor_factor",
       y_var = var,
+      shape = 16,
       x_label = unique(df$Drug)[1],
-      title = sprintf("Scatter RF for %s with SD", var),
+      title = sprintf("%s Scatter RF for %s with SD", OrfRep, var),
       coord_cartesian = y_limits,
       error_bar = TRUE,
       x_breaks = unique(df$conc_num_factor_factor),
@@ -769,7 +791,7 @@ generate_interaction_plot_configs <- function(df, type) {
       # Z_Shift and lm values
       Z_Shift_value <- round(first(group_data[[paste0("Z_Shift_", var)]], default = 0), 2)
       Z_lm_value <- round(first(group_data[[paste0("Z_lm_", var)]], default = 0), 2)
-      R_squared_value <- round(first(group_data[[paste0("R_squared_", var)]], default = 0), 2)
+      R_squared_value <- round(first(group_data[[paste0("R_Squared_", var)]], default = 0), 2)
 
       # NG, DB, SM values
       NG_value <- first(group_data$NG, default = 0)