Plot tweaks for before QC

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -91,28 +91,29 @@ theme_publication <- function(base_size = 14, base_family = "sans", legend_posit
   
   theme_foundation %+replace%
     theme(
-      plot.title = element_text(face = "bold", size = rel(1.2), hjust = 0.5),
+      plot.title = element_text(face = "bold", size = rel(1.6), hjust = 0.5),
       text = element_text(),
-      panel.background = element_rect(colour = NA),
+      panel.background = element_blank(),
-      plot.background = element_rect(colour = NA),
+      plot.background = element_blank(),
-      panel.border = element_rect(colour = NA),
+      panel.border = element_blank(),
-      axis.title = element_text(face = "bold", size = rel(1)),
+      axis.title = element_text(face = "bold", size = rel(1.4)),
       axis.title.y = element_text(angle = 90, vjust = 2),
-      axis.title.x = element_text(vjust = -0.2),
+      # axis.title.x = element_text(vjust = -0.2), # TODO this causes errors
-      axis.text = element_text(),
+      axis.text = element_text(size = rel(1.2)),
       axis.line = element_line(colour = "black"),
-      axis.ticks = element_line(),
+      # axis.ticks = element_line(),
       panel.grid.major = element_line(colour = "#f0f0f0"),
       panel.grid.minor = element_blank(),
       legend.key = element_rect(colour = NA),
       legend.position = legend_position,
       legend.direction = ifelse(legend_position == "right", "vertical", "horizontal"),
-      legend.key.size = unit(0.5, "cm"),
+      # legend.key.size = unit(0.5, "cm"),
       legend.spacing = unit(0, "cm"),
-      legend.title = element_text(face = "italic"),
+      legend.title = element_text(face = "italic", size = rel(1.3)),
+      legend.text = element_text(size = rel(1.2)),
       plot.margin = unit(c(10, 5, 5, 5), "mm"),
-      strip.background = element_rect(colour = "#f0f0f0", fill = "#f0f0f0"),
+      # strip.background = element_rect(colour = "#f0f0f0", fill = "#f0f0f0"),
-      strip.text = element_text(face = "bold")
+      # strip.text = element_text(face = "bold")
     )
 }
 
@@ -384,39 +385,39 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, grid_layout
     # Create the base plot
     aes_mapping <- if (config$plot_type == "bar") {
       if (!is.null(config$color_var)) {
-        aes(x = .data[[config$x_var]], fill = .data[[config$color_var]], color = .data[[config$color_var]])
+        aes(x = .data[[config$x_var]], fill = as.factor(.data[[config$color_var]]), color = as.factor(.data[[config$color_var]]))
       } else {
         aes(x = .data[[config$x_var]])
       }
     } else if (config$plot_type == "density") {
       if (!is.null(config$color_var)) {
-        aes(x = .data[[config$x_var]], color = .data[[config$color_var]])
+        aes(x = .data[[config$x_var]], color = as.factor(.data[[config$color_var]]))
       } else {
         aes(x = .data[[config$x_var]])
       }
     } else {
       if (!is.null(config$color_var)) {
-        aes(x = .data[[config$x_var]], y = .data[[config$y_var]], color = .data[[config$color_var]])
+        aes(x = .data[[config$x_var]], y = .data[[config$y_var]], color = as.factor(.data[[config$color_var]]))
       } else {
         aes(x = .data[[config$x_var]], y = .data[[config$y_var]])
       }
     }
 
-    plot_base <- ggplot(df, aes_mapping)
+    plot <- ggplot(df, aes_mapping)
-
-    # Use appropriate helper function based on plot type
-    plot <- switch(config$plot_type,
-      "scatter" = generate_scatter_plot(plot_base, config),
-      "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
-    )
 
     # Apply theme_publication with legend_position from config
     legend_position <- if (!is.null(config$legend_position)) config$legend_position else "bottom"
     plot <- plot + theme_publication(legend_position = legend_position)
 
+    # Use appropriate helper function based on plot type
+    plot <- switch(config$plot_type,
+      "scatter" = generate_scatter_plot(plot, config),
+      "box" = generate_box_plot(plot, config),
+      "density" = plot + geom_density(),
+      "bar" = plot + geom_bar(),
+      plot  # default case if no type matches
+    )
+
     # Add title and labels
     if (!is.null(config$title)) {
       plot <- plot + ggtitle(config$title)
@@ -428,6 +429,11 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, grid_layout
       plot <- plot + ylab(config$y_label)
     }
 
+    # Add cartesian coordinates if specified
+    if (!is.null(config$coord_cartesian)) {
+      plot <- plot + coord_cartesian(ylim = config$coord_cartesian)
+    }
+
     # Apply scale_color_discrete(guide = FALSE) when color_var is NULL
     if (is.null(config$color_var)) {
       plot <- plot + scale_color_discrete(guide = "none")
@@ -486,14 +492,17 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, grid_layout
 }
 
 generate_scatter_plot <- function(plot, config) {
+
+  # Define the points
   shape <- if (!is.null(config$shape)) config$shape else 3
-  size <- if (!is.null(config$size)) config$size else 0.1
+  size <- if (!is.null(config$size)) config$size else 1.5
-    position <-
+  position <-
-      if (!is.null(config$position) && config$position == "jitter") {
+    if (!is.null(config$position) && config$position == "jitter") {
-        position_jitter(width = 0.1, height = 0)
+      position_jitter(width = 0.1, height = 0)
-      } else {
+    } else {
-        "identity"
+      "identity"
-      }
+    }
+
   plot <- plot + geom_point(
     shape = shape,
     size = size,
@@ -594,17 +603,12 @@ generate_scatter_plot <- function(plot, config) {
       )
   }
   
-  # Apply coord_cartesian if specified
-  if (!is.null(config$coord_cartesian)) {
-    plot <- plot + coord_cartesian(ylim = config$coord_cartesian)
-  }
-  
   # Set Y-axis limits if specified
   if (!is.null(config$ylim_vals)) {
     plot <- plot + scale_y_continuous(limits = config$ylim_vals)
   }
   
-  # Add Annotations if specified
+  # Add annotations if specified
   if (!is.null(config$annotations)) {
     for (annotation in config$annotations) {
       plot <- plot +
@@ -615,17 +619,12 @@ 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), 4, annotation$size),
+          size = ifelse(is.null(annotation$size), 6, annotation$size),
           color = ifelse(is.null(annotation$color), "black", annotation$color)
         )
     }
   }
   
-  # Add Title if specified
-  if (!is.null(config$title)) {
-    plot <- plot + ggtitle(config$title)
-  }
-  
   return(plot)
 }
 
@@ -640,10 +639,6 @@ generate_box_plot <- function(plot, config) {
     )
   }
 
-  if (!is.null(config$coord_cartesian)) {
-    plot <- plot + coord_cartesian(ylim = config$coord_cartesian)
-  }
-
   return(plot)
 }
 
@@ -680,7 +675,7 @@ generate_plate_analysis_plot_configs <- function(variables, stages = c("before",
         plot_type = plot_type,
         title = paste("Plate analysis by Drug Conc for", var, stage, "quality control"),
         error_bar = error_bar,
-        color_var = "conc_num_factor",
+        color_var = "conc_num",
         position = position
       )
       plots <- append(plots, list(config))
@@ -1126,7 +1121,7 @@ main <- function() {
         plot_type = "scatter",
         delta_bg_point = TRUE,
         title = "Raw L vs K before quality control",
-        color_var = "conc_num_factor",
+        color_var = "conc_num",
         error_bar = FALSE,
         legend_position = "right"
       )
@@ -1138,8 +1133,8 @@ main <- function() {
         x_var = "delta_bg",
         y_var = NULL,
         plot_type = "density",
-        title = "Density plot for Delta Background by Conc All Data",
+        title = "Density plot for Delta Background by [Drug] (All Data)",
-        color_var = "conc_num_factor",
+        color_var = "conc_num",
         x_label = "Delta Background",
         y_label = "Density",
         error_bar = FALSE,
@@ -1149,8 +1144,8 @@ main <- function() {
         x_var = "delta_bg",
         y_var = NULL,
         plot_type = "bar",
-        title = "Bar plot for Delta Background by Conc All Data",
+        title = "Bar plot for Delta Background by [Drug] (All Data)",
-        color_var = "conc_num_factor",
+        color_var = "conc_num",
         x_label = "Delta Background",
         y_label = "Count",
         error_bar = FALSE,
@@ -1165,8 +1160,8 @@ main <- function() {
         plot_type = "scatter",
         delta_bg_point = TRUE,
         title = paste("Raw L vs K for strains above Delta Background threshold of",
-          df_above_tolerance$delta_bg_tolerance[[1]], "or above"),
+          round(df_above_tolerance$delta_bg_tolerance[[1]], 3), "or above"),
-        color_var = "conc_num_factor",
+        color_var = "conc_num",
         position = "jitter",
         annotations = list(
           list(
@@ -1214,7 +1209,7 @@ main <- function() {
         plot_type = "scatter",
         delta_bg_point = TRUE,
         title = "Raw L vs K for strains falling outside 2SD of the K mean at each Conc",
-        color_var = "conc_num_factor",
+        color_var = "conc_num",
         position = "jitter",
         legend_position = "right"
       )
@@ -1228,7 +1223,7 @@ main <- function() {
         plot_type = "scatter",
         gene_point = TRUE,
         title = "Delta Background vs K for strains falling outside 2SD of the K mean at each Conc",
-        color_var = "conc_num_factor",
+        color_var = "conc_num",
         position = "jitter",
         legend_position = "right"
       )
@@ -1453,7 +1448,6 @@ main <- function() {
         adjust = FALSE,
         overlap_color = TRUE
       )
-
       generate_and_save_plots(
         out_dir = out_dir,
         filename = "RankPlots_na_rm",