Add configurable page dimensions

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -20,13 +20,9 @@ suppressPackageStartupMessages({
   library("purrr")
 })
 
+# Turn all warnings into errors for development
 options(warn = 2)
 
-# Constants for configuration
-plot_width <- 14
-plot_height <- 9
-base_size <- 14
-
 parse_arguments <- function() {
   args <- if (interactive()) {
     c(
@@ -515,7 +511,7 @@ calculate_interaction_scores <- function(df, df_bg, group_vars, overlap_threshol
   ))
 }
 
-generate_and_save_plots <- function(out_dir, filename, plot_configs) {
+generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width = 12, page_height = 8) {
   message("Generating ", filename, ".pdf and ", filename, ".html")
 
   # Check if we're dealing with multiple plot groups
@@ -526,7 +522,7 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs) {
   }
 
   # Open the PDF device once for all plots
-  pdf(file.path(out_dir, paste0(filename, ".pdf")), width = 16, height = 9)
+  pdf(file.path(out_dir, paste0(filename, ".pdf")), width = page_width, height = page_height)
 
   # Loop through each plot group
   for (group in plot_groups) {
@@ -1043,7 +1039,7 @@ generate_interaction_plot_configs <- function(df, type) {
   return(list(
     list(grid_layout = list(ncol = 2), plots = stats_plot_configs),
     list(grid_layout = list(ncol = 2), plots = stats_boxplot_configs),
-    list(grid_layout = list(ncol = 4), plots = delta_plot_configs)  # nrow calculated dynamically
+    list(grid_layout = list(ncol = 4), plots = delta_plot_configs[1:12])  # nrow calculated dynamically
   ))
 }
 
@@ -1123,12 +1119,7 @@ generate_rank_plot_configs <- function(df, is_lm = FALSE, adjust = FALSE, overla
     }
   }
 
-  # Calculate dynamic grid layout based on the number of plots
-  grid_ncol <- 3
-  num_plots <- length(plot_configs)
-  grid_nrow <- ceiling(num_plots / grid_ncol)  # Automatically calculate the number of rows
-
-  return(list(grid_layout = list(ncol = grid_ncol, nrow = grid_nrow), plots = plot_configs))
+  return(list(grid_layout = list(ncol = 3), plots = plot_configs))
 }
 
 generate_correlation_plot_configs <- function(df, correlation_stats) {
@@ -1418,29 +1409,34 @@ main <- function() {
 
     plot_configs <- list(
       list(out_dir = out_dir_qc, filename = "L_vs_K_before_quality_control",
-        plot_configs = l_vs_k_plot_configs),
+        plot_configs = l_vs_k_plot_configs, page_width = 12, page_height = 8),
       list(out_dir = out_dir_qc, filename = "frequency_delta_background",
-        plot_configs = frequency_delta_bg_plot_configs),
+        plot_configs = frequency_delta_bg_plot_configs, page_width = 12, page_height = 8),
       list(out_dir = out_dir_qc, filename = "L_vs_K_above_threshold",
-        plot_configs = above_threshold_plot_configs),
+        plot_configs = above_threshold_plot_configs, page_width = 12, page_height = 8),
       list(out_dir = out_dir_qc, filename = "plate_analysis",
-        plot_configs = plate_analysis_plot_configs),
+        plot_configs = plate_analysis_plot_configs, page_width = 14, page_height = 9),
       list(out_dir = out_dir_qc, filename = "plate_analysis_boxplots",
-        plot_configs = plate_analysis_boxplot_configs),
+        plot_configs = plate_analysis_boxplot_configs, page_width = 18, page_height = 9),
       list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros",
-        plot_configs = plate_analysis_no_zeros_plot_configs),
+        plot_configs = plate_analysis_no_zeros_plot_configs, page_width = 12, page_height = 8),
       list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros_boxplots",
-        plot_configs = plate_analysis_no_zeros_boxplot_configs),
+        plot_configs = plate_analysis_no_zeros_boxplot_configs, page_width = 18, page_height = 9),
       list(out_dir = out_dir_qc, filename = "L_vs_K_for_strains_2SD_outside_mean_K",
-        plot_configs = l_outside_2sd_k_plot_configs),
+        plot_configs = l_outside_2sd_k_plot_configs, page_width = 10, page_height = 8),
       list(out_dir = out_dir_qc, filename = "delta_background_vs_K_for_strains_2SD_outside_mean_K",
-        plot_configs = delta_bg_outside_2sd_k_plot_configs)
+        plot_configs = delta_bg_outside_2sd_k_plot_configs, page_width = 10, page_height = 8)
     )
 
-    # furrr::future_map(plot_configs, function(config) {
-    #   generate_and_save_plots(config$out_dir, config$filename, config$plot_configs)
-    # }, .options = furrr_options(seed = TRUE))
+    # Parallelize background and quality control plot generation
+    furrr::future_map(plot_configs, function(config) {
+      generate_and_save_plots(config$out_dir, config$filename, config$plot_configs,
+        page_width = config$page_width, page_height = config$page_height)
+    }, .options = furrr_options(seed = TRUE))
 
+    # Loop over background strains
+    # TODO currently only tested against one strain, if we want to do multiple strains we'll
+    # have to rename or group the output files by dir or something so they don't get clobbered
     bg_strains <- c("YDL227C")
     lapply(bg_strains, function(strain) {
       message("Processing background strain: ", strain)
@@ -1496,7 +1492,7 @@ main <- function() {
 
       message("Generating reference interaction plots")
       reference_plot_configs <- generate_interaction_plot_configs(df_interactions_reference_joined, "reference")
-      generate_and_save_plots(out_dir, "interaction_plots_reference", reference_plot_configs)
+      generate_and_save_plots(out_dir, "interaction_plots_reference", reference_plot_configs, page_width = 16, page_height = 16)
 
       message("Setting missing deletion values to the highest theoretical value at each drug conc for L")
       df_deletion <- df_na_stats %>% # formerly X2
@@ -1527,7 +1523,7 @@ main <- function() {
 
       message("Generating deletion interaction plots")
       deletion_plot_configs <- generate_interaction_plot_configs(df_interactions_joined, "deletion")
-      generate_and_save_plots(out_dir, "interaction_plots", deletion_plot_configs)
+      generate_and_save_plots(out_dir, "interaction_plots", deletion_plot_configs, page_width = 16, page_height = 16)
 
       message("Writing enhancer/suppressor csv files")
       interaction_threshold <- 2  # TODO add to study config?
@@ -1567,8 +1563,8 @@ main <- function() {
         is_lm = FALSE,
         adjust = TRUE
       )
-      generate_and_save_plots(out_dir = out_dir, filename = "rank_plots",
-        plot_configs = rank_plot_configs)
+      generate_and_save_plots(out_dir, "rank_plots", rank_plot_configs,
+        page_width = 18, page_height = 12)
 
       message("Generating ranked linear model plots")
       rank_lm_plot_configs <- generate_rank_plot_configs(
@@ -1576,8 +1572,8 @@ main <- function() {
         is_lm = TRUE,
         adjust = TRUE
       )
-      generate_and_save_plots(out_dir = out_dir, filename = "rank_plots_lm",
-        plot_configs = rank_lm_plot_configs)
+      generate_and_save_plots(out_dir, "rank_plots_lm", rank_lm_plot_configs,
+        page_width = 18, page_height = 12)
 
       message("Generating filtered ranked plots")
       rank_plot_filtered_configs <- generate_rank_plot_configs(
@@ -1586,10 +1582,8 @@ main <- function() {
         adjust = FALSE,
         overlap_color = TRUE
       )
-      generate_and_save_plots(
-        out_dir = out_dir,
-        filename = "RankPlots_na_rm",
-        plot_configs = rank_plot_filtered_configs)
+      generate_and_save_plots(out_dir, "RankPlots_na_rm", rank_plot_filtered_configs,
+        page_width = 18, page_height = 12)
 
       message("Generating filtered ranked linear model plots")
       rank_plot_lm_filtered_configs <- generate_rank_plot_configs(
@@ -1598,20 +1592,15 @@ main <- function() {
         adjust = FALSE,
         overlap_color = TRUE
       )
-      generate_and_save_plots(
-        out_dir = out_dir,
-        filename = "rank_plots_lm_na_rm",
-        plot_configs = rank_plot_lm_filtered_configs)
+      generate_and_save_plots(out_dir, "rank_plots_lm_na_rm", rank_plot_lm_filtered_configs,
+        page_width = 18, page_height = 12)
 
       message("Generating correlation curve parameter pair plots")
       correlation_plot_configs <- generate_correlation_plot_configs(
         df_interactions_joined
       )
-      generate_and_save_plots(
-        out_dir = out_dir,
-        filename = "correlation_cpps",
-        plot_configs = correlation_plot_configs,
-      )
+      generate_and_save_plots(out_dir, "correlation_cpps", correlation_plot_configs,
+        page_width = 10, page_height = 7)
     })
   })
 }