Fix plate analysis plots, make error bar use aes color by default

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -556,37 +556,71 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
 
       # Add error bars if specified
       if (!is.null(config$error_bar) && config$error_bar) {
-        error_bar_color <- if (!is.null(config$error_bar_params$color)) {
-          config$error_bar_params$color
-        } else {
-          "red"
-        }
-
+        # Check if a fixed color is provided or if it should come from a data column
+        error_bar_color <- config$error_bar_params$color
+        
         if (!is.null(config$error_bar_params$ymin) && !is.null(config$error_bar_params$ymax)) {
           # Check if ymin and ymax are constants or column names
           if (is.numeric(config$error_bar_params$ymin) && is.numeric(config$error_bar_params$ymax)) {
-            plot <- plot + geom_errorbar(aes(x = .data[[config$x_var]]),
+            plot <- plot + geom_errorbar(
+              aes(x = .data[[config$x_var]]),
               ymin = config$error_bar_params$ymin,
-              ymax = config$error_bar_params$ymax,
-              color = error_bar_color)
+              ymax = config$error_bar_params$ymax
+            )
+            # Apply fixed color if specified
+            if (!is.null(error_bar_color)) {
+              plot <- plot + scale_color_manual(values = error_bar_color)
+            }
           } else {
-            plot <- plot + geom_errorbar(aes(
-              x = .data[[config$x_var]],
-              ymin = .data[[config$error_bar_params$ymin]],
-              ymax = .data[[config$error_bar_params$ymax]]
-            ), color = error_bar_color)
+            # If config$color_var exists, map the color aesthetic
+            if (!is.null(config$color_var)) {
+              plot <- plot + geom_errorbar(
+                aes(
+                  x = .data[[config$x_var]],
+                  ymin = .data[[config$error_bar_params$ymin]],
+                  ymax = .data[[config$error_bar_params$ymax]],
+                  color = .data[[config$color_var]]  # Map color_var to data
+                )
+              )
+            } else {
+              plot <- plot + geom_errorbar(
+                aes(
+                  x = .data[[config$x_var]],
+                  ymin = .data[[config$error_bar_params$ymin]],
+                  ymax = .data[[config$error_bar_params$ymax]]
+                )
+              )
+            }
           }
         } else {
           # Ensure the mean and sd columns exist
           y_mean_col <- paste0("mean_", config$y_var)
           y_sd_col <- paste0("sd_", config$y_var)
-          
+
           if (y_mean_col %in% colnames(df) && y_sd_col %in% colnames(df)) {
-            plot <- plot + geom_errorbar(aes(
-              x = .data[[config$x_var]],
-              ymin = .data[[y_mean_col]] - .data[[y_sd_col]],
-              ymax = .data[[y_mean_col]] + .data[[y_sd_col]]
-            ), color = error_bar_color)
+            # If config$color_var exists, map the color aesthetic
+            if (!is.null(config$color_var)) {
+              plot <- plot + geom_errorbar(
+                aes(
+                  x = .data[[config$x_var]],
+                  ymin = .data[[y_mean_col]] - .data[[y_sd_col]],
+                  ymax = .data[[y_mean_col]] + .data[[y_sd_col]],
+                  color = .data[[config$color_var]]  # Color based on aes()
+                )
+              )
+            } else {
+              plot <- plot + geom_errorbar(
+                aes(
+                  x = .data[[config$x_var]],
+                  ymin = .data[[y_mean_col]] - .data[[y_sd_col]],
+                  ymax = .data[[y_mean_col]] + .data[[y_sd_col]]
+                )
+              )
+            }
+            # Apply fixed color if specified
+            if (!is.null(error_bar_color)) {
+              plot <- plot + scale_color_manual(values = error_bar_color)
+            }
           }
         }
       }
@@ -734,7 +768,6 @@ generate_scatter_plot <- function(plot, config) {
     }
   }
 
-  
   # Set Y-axis limits if specified
   if (!is.null(config$ylim_vals)) {
     plot <- plot + scale_y_continuous(limits = config$ylim_vals)
@@ -746,8 +779,8 @@ generate_scatter_plot <- function(plot, config) {
       plot <- plot +
         annotate(
           "text",
-          x = annotation$x,
-          y = annotation$y,
+          x = ifelse(is.null(annotation$x), 0, annotation$x),
+          y = ifelse(is.null(annotation$y), 0, annotation$y),
           label = annotation$label,
           hjust = ifelse(is.null(annotation$hjust), 0.5, annotation$hjust),
           vjust = ifelse(is.null(annotation$vjust), 0.5, annotation$vjust),
@@ -806,9 +839,9 @@ generate_plate_analysis_plot_configs <- function(variables, df_before = NULL, df
         plot_type = plot_type,
         title = paste("Plate analysis by Drug Conc for", var, stage, "quality control"),
         color_var = "conc_num_factor_factor",
-        position = if (plot_type == "scatter") "jitter" else NULL,
         size = 0.2,
-        error_bar = (plot_type == "scatter")
+        error_bar = (plot_type == "scatter"),
+        legend_position = "bottom"
       )
 
       # Add config to plots list
@@ -1340,6 +1373,7 @@ main <- function() {
         list(
           df = df_na_l_outside_2sd_k_stats,
           x_var = "delta_bg",
+          x_label = "Delta Background",
           y_var = "K",
           plot_type = "scatter",
           title = "Delta Background vs K for strains falling outside 2SD of the K mean at each Conc",
@@ -1348,9 +1382,12 @@ main <- function() {
           tooltip_vars = c("OrfRep", "Gene", "delta_bg"),
           annotations = list(
             list(
-              x = median(df_na_l_outside_2sd_k_stats$delta_bg, na.rm = TRUE) / 2,
-              y = median(df_na_l_outside_2sd_k_stats$K, na.rm = TRUE) / 2,
-              label = paste("Total strains:", nrow(df_na_l_outside_2sd_k_stats))
+              x = 0.05,
+              y = 0.95,
+              hjust = 0,
+              vjust = 1,
+              label = paste("Total strains:", nrow(df_na_l_outside_2sd_k_stats)),
+              size = 5
             )
           ),
           error_bar = FALSE,
@@ -1384,9 +1421,9 @@ main <- function() {
         plot_configs = delta_bg_outside_2sd_k_plot_configs)
     )
 
-    # furrr::future_map(plot_configs, function(config) {
-    #   generate_and_save_plots(config$out_dir, config$filename, config$plot_configs)
-    # }, .options = furrr_options(seed = TRUE))
+    furrr::future_map(plot_configs, function(config) {
+      generate_and_save_plots(config$out_dir, config$filename, config$plot_configs)
+    }, .options = furrr_options(seed = TRUE))
 
     bg_strains <- c("YDL227C")
     lapply(bg_strains, function(strain) {