Use WT values for error bars

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -463,9 +463,21 @@ 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 <- config$error_bar_params$color %||% "red"
+        error_bar_color <- if (!is.null(config$error_bar_params$color)) {
-        y_mean_col <- paste0("mean_", config$y_var)
+          config$error_bar_params$color
-        y_sd_col <- paste0("sd_", config$y_var)
+        } else {
+          "red"
+        }
+
+        y_mean_col <- paste0("mean_mean_", config$y_var)
+
+        # Dynamically set y_sd_col based on the provided prefix in error_bar_params
+        y_sd_prefix <- if (!is.null(config$error_bar_params$y_sd_prefix)) {
+          config$error_bar_params$y_sd_prefix
+        } else {
+          "sd_"
+        }
+        y_sd_col <- paste0(y_sd_prefix, config$y_var)
 
         if (!is.null(config$error_bar_params$center_point)) {
           plot <- plot + geom_point(aes(
@@ -489,6 +501,8 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
         }
       }
 
+
+
       # Convert ggplot to plotly for interactive version
       plotly_plot <- suppressWarnings(plotly::ggplotly(plot))
 
@@ -511,19 +525,18 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
         nrow = grid_layout$nrow
       )
     }
-
   }
 
   # Close the PDF device after all plots are done
   dev.off()
 
   # Save HTML file with interactive plots if needed
-  # out_html_file <- file.path(out_dir, paste0(filename, ".html"))
+  out_html_file <- file.path(out_dir, paste0(filename, ".html"))
-  # message("Saving combined HTML file: ", out_html_file)
+  message("Saving combined HTML file: ", out_html_file)
-  # htmltools::save_html(
+  htmltools::save_html(
-  #   htmltools::tagList(plotly_plots),
+    htmltools::tagList(plotly_plots),
-  #   file = out_html_file
+    file = out_html_file
-  # )
+  )
 }
 
 generate_scatter_plot <- function(plot, config) {
@@ -650,7 +663,7 @@ generate_scatter_plot <- function(plot, config) {
           label = annotation$label,
           hjust = ifelse(is.null(annotation$hjust), 0.5, annotation$hjust),
           vjust = ifelse(is.null(annotation$vjust), 0.5, annotation$vjust),
-          size = ifelse(is.null(annotation$size), 6, annotation$size),
+          size = ifelse(is.null(annotation$size), 3, annotation$size),
           color = ifelse(is.null(annotation$color), "black", annotation$color)
         )
     }
@@ -759,6 +772,7 @@ generate_interaction_plot_configs <- function(df, type) {
         plot_config$title <- sprintf("%s Scatter RF for %s with SD", OrfRep, var)
         plot_config$error_bar <- TRUE
         plot_config$error_bar_params <- list(
+          y_sd_prefix = "WT_sd_",
           color = "red",
           center_point = TRUE
         )

qhtcp-workflow/qhtcp-workflow

@@ -1442,6 +1442,7 @@ wrapper calculate_interaction_zscores
 # * We are using standard error bars using the same se values as the data now (includes Bessel's correction)
 #    * Plate analysis error bars and some others will be slightly different
 #    * Can be changed back but better to have plots reflect data, no?
+# * Dynamically generate axis limits based on data (if desired)
 #
 # INPUT
 #