Rework plotting code, add auto-grid layout

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -370,68 +370,18 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
     config <- plot_configs[[i]]
     df <- config$df
 
-    # Initialize tooltip_text
+    aes_mapping <- if (is.null(config$color_var)) {
-    tooltip_text <- NULL
-
-    # Define aes_mapping based on plot type
-    if (config$plot_type == "scatter") {
-      # Check if y_var is provided
       if (is.null(config$y_var)) {
-        warning(paste("Plot", i, "of type 'scatter' is missing 'y_var'. Skipping this plot."))
+        aes(x = .data[[config$x_var]])
-        next
-      }
-
-      # Construct tooltip_text based on configuration flags
-      if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
-        # Ensure 'delta_bg' exists
-        if (!"delta_bg" %in% names(df)) {
-          warning(paste("Plot", i, "requires 'delta_bg' column for tooltip, but it's missing."))
-          tooltip_text <- paste("OrfRep:", df$OrfRep, "<br>Gene:", df$Gene)
-        } else {
-          tooltip_text <- paste("OrfRep:", df$OrfRep, "<br>Gene:", df$Gene, "<br>delta_bg:", df$delta_bg)
-        }
-      } else if (!is.null(config$gene_point) && config$gene_point) {
-        tooltip_text <- paste("OrfRep:", df$OrfRep, "<br>Gene:", df$Gene)
       } else {
-        tooltip_text <- paste("x:", df[[config$x_var]], "<br>y:", df[[config$y_var]])
+        aes(x = .data[[config$x_var]], y = .data[[config$y_var]])
-      }
-
-      # Define aesthetic mapping with or without color_var
-      aes_mapping <- if (is.null(config$color_var)) {
-        aes(x = .data[[config$x_var]], y = .data[[config$y_var]], text = tooltip_text)
-      } else {
-        aes(x = .data[[config$x_var]], y = .data[[config$y_var]],
-            color = as.factor(.data[[config$color_var]]), text = tooltip_text)
       }
     } else {
-      # Handle other plot types
+      if (is.null(config$y_var)) {
-      # For 'box' plots, y_var is required
+        aes(x = .data[[config$x_var]], color = as.factor(.data[[config$color_var]]))
-      if (config$plot_type == "box") {
-        if (is.null(config$y_var)) {
-          warning(paste("Plot", i, "of type 'box' is missing 'y_var'. Skipping this plot."))
-          next
-        }
-      }
-
-      # Define aes_mapping for non-scatter plots
-      aes_mapping <- if (is.null(config$color_var)) {
-        if (config$plot_type %in% c("density", "bar")) {
-          aes(x = .data[[config$x_var]])
-        } else {
-          aes(x = .data[[config$x_var]], y = .data[[config$y_var]])
-        }
       } else {
-        if (config$plot_type %in% c("density", "bar")) {
+        aes(x = .data[[config$x_var]], y = .data[[config$y_var]], color = as.factor(.data[[config$color_var]]))
-          aes(x = .data[[config$x_var]],
-            color = as.factor(.data[[config$color_var]]))
-        } else {
-          aes(x = .data[[config$x_var]], y = .data[[config$y_var]],
-            color = as.factor(.data[[config$color_var]]))
-        }
       }
-
-      # No tooltip for non-scatter plots
-      tooltip_text <- NULL
     }
 
     # Start building the plot with aes_mapping
@@ -443,10 +393,7 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
       "box" = generate_box_plot(plot_base, config),
       "density" = plot_base + geom_density(),
       "bar" = plot_base + geom_bar(),
-      {
+      plot_base  # default case if no type matches
-        warning(paste("Unknown plot_type:", config$plot_type, "- using base plot"))
-        plot_base
-      }
     )
 
     # Apply additional settings if provided
@@ -465,11 +412,27 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
       plot <- plot + ylab(config$y_label)
     }
 
-    # Convert to plotly object
+    # Apply scale_color_discrete(guide = FALSE) when color_var is NULL
+    if (is.null(config$color_var)) {
+      plot <- plot + scale_color_discrete(guide = FALSE)
+    }
+
+    # Add interactive tooltips for plotly
+    tooltip_vars <- c()
     if (config$plot_type == "scatter") {
-      plotly_plot <- ggplotly(plot, tooltip = "text")
+      if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
+        tooltip_vars <- c(tooltip_vars, "OrfRep", "Gene", "delta_bg")
+      } else if (!is.null(config$gene_point) && config$gene_point) {
+        tooltip_vars <- c(tooltip_vars, "OrfRep", "Gene")
+      } else if (!is.null(config$y_var) && !is.null(config$x_var)) {
+        tooltip_vars <- c(config$x_var, config$y_var)
+      }
+    }
+
+    # Convert to plotly object
+    if (length(tooltip_vars) > 0) {
+      plotly_plot <- ggplotly(plot, tooltip = tooltip_vars)
     } else {
-      # For non-scatter plots, decide if tooltips are needed
       plotly_plot <- ggplotly(plot, tooltip = "none")
     }
 
@@ -489,9 +452,16 @@ generate_and_save_plots <- function(out_dir, file_name, plot_configs, grid_layou
   dev.off()
 
   # Combine and save interactive HTML plots
-  combined_plot <- subplot(plotly_plots,
+  combined_plot <- subplot(
-    nrows = ifelse(is.null(grid_layout$nrow), length(plotly_plots), grid_layout$nrow),
+    plotly_plots,
-    margin = 0.05)
+    nrows = if (!is.null(grid_layout) && !is.null(grid_layout$nrow)) {
+      grid_layout$nrow
+    } else {
+      # Calculate nrow based on the length of plotly_plots (default 1 row if only one plot)
+      ceiling(length(plotly_plots) / ifelse(!is.null(grid_layout) && !is.null(grid_layout$ncol), grid_layout$ncol, 1))
+    },
+    margin = 0.05
+  )
   saveWidget(combined_plot, file = file.path(out_dir, paste0(file_name, ".html")), selfcontained = TRUE)
 }