From 4e15fb80fbddf8cf65413ff19091e9914304ba07 Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Mon, 9 Sep 2024 23:34:18 -0400
Subject: [PATCH] Add boxplots to interaction plots

---
 .../apps/r/calculate_interaction_zscores5.R   | 32 ++++++++++++++-----
 1 file changed, 24 insertions(+), 8 deletions(-)

diff --git a/workflow/apps/r/calculate_interaction_zscores5.R b/workflow/apps/r/calculate_interaction_zscores5.R
index d2f3bce6..2bcd7882 100644
--- a/workflow/apps/r/calculate_interaction_zscores5.R
+++ b/workflow/apps/r/calculate_interaction_zscores5.R
@@ -320,22 +320,22 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
       if (config$y_var == "delta_bg" && config$plot_type == "scatter") {
         plot <- plot + geom_point(shape = 3, size = 0.2, position = "jitter") +
           geom_errorbar(aes(ymin = !!sym(y_mean_col) - !!sym(y_sd_col),
-                            ymax = !!sym(y_mean_col) + !!sym(y_sd_col)), width = 0.1) +
+            ymax = !!sym(y_mean_col) + !!sym(y_sd_col)), width = 0.1) +
           geom_point(aes(y = !!sym(y_mean_col)), size = 0.6)
       } else if (config$error_bar %||% FALSE) {
         plot <- plot +
           geom_point(shape = 3, size = 0.2) +
           geom_errorbar(aes(ymin = !!sym(y_mean_col) - !!sym(y_sd_col),
-                            ymax = !!sym(y_mean_col) + !!sym(y_sd_col)), width = 0.1) +
+            ymax = !!sym(y_mean_col) + !!sym(y_sd_col)), width = 0.1) +
           geom_point(aes(y = !!sym(y_mean_col)), size = 0.6)
       }
     }
     
     plot <- switch(config$plot_type,
-                   "box" = plot + geom_boxplot(),
-                   "density" = plot + geom_density(),
-                   "bar" = plot + geom_bar(stat = "identity"),
-                   plot + geom_point() + geom_smooth(method = "lm", se = FALSE))
+      "box" = plot + geom_boxplot(),
+      "density" = plot + geom_density(),
+      "bar" = plot + geom_bar(stat = "identity"),
+      plot + geom_point() + geom_smooth(method = "lm", se = FALSE))
     
     if (!is.null(config$ylim_vals)) {
       plot <- plot + coord_cartesian(ylim = config$ylim_vals)
@@ -358,7 +358,7 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
   
   # If grid_layout is provided, arrange plots in a grid and save in a single PDF
   if (!is.null(grid_layout)) {
-    pdf(file.path(output_dir, paste0(file_name, "_grid.pdf")), width = 14, height = 9)
+    pdf(file.path(output_dir, paste0(file_name, ".pdf")), width = 14, height = 9)
     
     # Loop through plots in chunks defined by ncol and nrow
     for (start_idx in seq(1, length(plots), by = grid_layout$ncol * grid_layout$nrow)) {
@@ -426,7 +426,7 @@ interaction_plot_configs <- function(df, variables) {
         ifelse(variable == "r", -0.45, -4500))), label = paste("SM =", df$SM))
     )
 
-    # Append a new plot configuration for each variable
+    # Add scatter plot configuration for this variable
     plot_configs[[length(plot_configs) + 1]] <- list(
       df = df,
       x_var = "conc_num_factor",
@@ -443,11 +443,27 @@ interaction_plot_configs <- function(df, variables) {
       x_labels = unique(as.character(df$conc_num)),
       x_label = unique(df$Drug[1])
     )
+
+    # Add box plot configuration for this variable
+    plot_configs[[length(plot_configs) + 1]] <- list(
+      df = df,
+      x_var = "conc_num_factor",
+      y_var = variable,
+      plot_type = "box",
+      title = sprintf("%s      %s (Boxplot)", df$OrfRep[1], df$Gene[1]),
+      ylim_vals = ylim_vals,
+      annotations = annotations,
+      error_bar = FALSE,  # Boxplots typically don't need error bars
+      x_breaks = unique(df$conc_num_factor),
+      x_labels = unique(as.character(df$conc_num)),
+      x_label = unique(df$Drug[1])
+    )
   }
 
   return(plot_configs)
 }
 
+
 correlation_plot_configs <- function(df, lm_list, lm_summaries) {
   lapply(seq_along(lm_list), function(i) {
     r_squared <- round(lm_summaries[[i]]$r.squared, 3)