Add pre-calculated error bars to scatter plots
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@@ -560,6 +560,17 @@ generate_scatter_plot <- function(plot, config) {
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# Add error bars if specified
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if (!is.null(config$error_bar) && config$error_bar && !is.null(config$y_var)) {
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if (!is.null(config$error_bar_params)) {
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plot <- plot +
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geom_errorbar(
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aes(
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ymin = config$error_bar_params$ymin,
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ymax = config$error_bar_params$ymax
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),
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alpha = 0.3,
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linewidth = 0.5
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)
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} else {
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y_mean_col <- paste0("mean_", config$y_var)
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y_sd_col <- paste0("sd_", config$y_var)
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@@ -573,6 +584,7 @@ generate_scatter_plot <- function(plot, config) {
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linewidth = 0.5
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)
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}
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}
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# Customize X-axis if specified
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if (!is.null(config$x_breaks) && !is.null(config$x_labels) && !is.null(config$x_label)) {
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@@ -675,9 +687,10 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL, plot_type =
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df_filtered <- df %>%
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mutate(OrfRepCombined = if (plot_type == "reference") paste(OrfRep, Gene, num, sep = "_") else paste(OrfRep, Gene, sep = "_"))
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plots <- list()
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# Separate the plots into two groups: overall variables and delta comparisons
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overall_plots <- list()
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delta_plots <- list()
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# Generate plots for overall variables (L, K, r, AUC)
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for (var in c("L", "K", "r", "AUC")) {
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y_limits <- limits_map[[var]]
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@@ -692,14 +705,12 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL, plot_type =
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error_bar = TRUE,
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x_breaks = unique(df_filtered$conc_num_factor_factor),
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x_labels = as.character(unique(df_filtered$conc_num)),
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grid_layout = list(ncol = 2, nrow = 2),
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position = "jitter",
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smooth = TRUE
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)
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plots <- append(plots, list(config))
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overall_plots <- append(overall_plots, list(config))
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}
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# Generate Delta comparison plots
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unique_groups <- df_filtered %>% select(all_of(group_vars)) %>% distinct()
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for (i in seq_len(nrow(unique_groups))) {
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@@ -752,14 +763,16 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL, plot_type =
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smooth = TRUE,
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x_breaks = unique(group_data$conc_num_factor_factor),
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x_labels = as.character(unique(group_data$conc_num)),
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ylim_vals = y_limits,
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grid_layout = list(ncol = 4, nrow = 3)
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ylim_vals = y_limits
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)
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plots <- append(plots, list(config))
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delta_plots <- append(delta_plots, list(config))
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}
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}
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return(list(grid_layout = list(ncol = 2, nrow = 2), plots = plots))
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return(list(
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overall_plots = list(grid_layout = list(ncol = 2, nrow = 2), plots = overall_plots),
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delta_plots = list(grid_layout = list(ncol = 4, nrow = 3), plots = delta_plots)
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))
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}
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generate_rank_plot_configs <- function(df, variables, is_lm = FALSE, adjust = FALSE, overlap_color = FALSE) {
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@@ -1046,7 +1059,6 @@ main <- function() {
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# Each plots list corresponds to a file
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l_vs_k_plot_configs <- list(
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grid_layout = list(ncol = 1, nrow = 1),
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plots = list(
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list(
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df = df,
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@@ -1063,7 +1075,6 @@ main <- function() {
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)
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frequency_delta_bg_plot_configs <- list(
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grid_layout = list(ncol = 1, nrow = 1),
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plots = list(
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list(
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df = df_stats,
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@@ -1093,7 +1104,6 @@ main <- function() {
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)
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above_threshold_plot_configs <- list(
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grid_layout = list(ncol = 1, nrow = 1),
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plots = list(
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list(
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df = df_above_tolerance,
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@@ -1145,7 +1155,6 @@ main <- function() {
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)
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l_outside_2sd_k_plot_configs <- list(
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grid_layout = list(ncol = 1, nrow = 1), # Ensures it's compatible with generate_and_save_plots
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plots = list(
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list(
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df = df_na_l_outside_2sd_k_stats,
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@@ -1170,7 +1179,6 @@ main <- function() {
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)
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delta_bg_outside_2sd_k_plot_configs <- list(
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grid_layout = list(ncol = 1, nrow = 1), # Ensures it's compatible with generate_and_save_plots
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plots = list(
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list(
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df = df_na_l_outside_2sd_k_stats,
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@@ -1195,37 +1203,34 @@ main <- function() {
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)
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message("Generating quality control plots in parallel")
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generate_and_save_plots(out_dir_qc, "L_vs_K_before_quality_control", l_vs_k_plot_configs)
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quit()
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# # future::plan(future::multicore, workers = parallel::detectCores())
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# future::plan(future::multisession, workers = 3) # generate 3 plots in parallel
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future::plan(future::multisession, workers = 3) # generate 3 plots in parallel
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# plot_configs <- list(
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# list(out_dir = out_dir_qc, filename = "L_vs_K_before_quality_control",
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# plot_configs = l_vs_k_plot_configs),
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# list(out_dir = out_dir_qc, filename = "frequency_delta_background",
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# plot_configs = frequency_delta_bg_plot_configs),
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# list(out_dir = out_dir_qc, filename = "L_vs_K_above_threshold",
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# plot_configs = above_threshold_plot_configs),
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# list(out_dir = out_dir_qc, filename = "plate_analysis",
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# plot_configs = plate_analysis_plot_configs),
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# list(out_dir = out_dir_qc, filename = "plate_analysis_boxplots",
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# plot_configs = plate_analysis_boxplot_configs),
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# list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros",
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# plot_configs = plate_analysis_no_zeros_plot_configs),
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# list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros_boxplots",
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# plot_configs = plate_analysis_no_zeros_boxplot_configs),
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# list(out_dir = out_dir_qc, filename = "L_vs_K_for_strains_2SD_outside_mean_K",
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# plot_configs = l_outside_2sd_k_plot_configs),
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# list(out_dir = out_dir_qc, filename = "delta_background_vs_K_for_strains_2sd_outside_mean_K",
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# plot_configs = delta_bg_outside_2sd_k_plot_configs)
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# )
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plot_configs <- list(
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list(out_dir = out_dir_qc, filename = "L_vs_K_before_quality_control",
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plot_configs = l_vs_k_plot_configs),
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list(out_dir = out_dir_qc, filename = "frequency_delta_background",
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plot_configs = frequency_delta_bg_plot_configs),
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list(out_dir = out_dir_qc, filename = "L_vs_K_above_threshold",
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plot_configs = above_threshold_plot_configs),
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list(out_dir = out_dir_qc, filename = "plate_analysis",
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plot_configs = plate_analysis_plot_configs),
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list(out_dir = out_dir_qc, filename = "plate_analysis_boxplots",
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plot_configs = plate_analysis_boxplot_configs),
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list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros",
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plot_configs = plate_analysis_no_zeros_plot_configs),
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list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros_boxplots",
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plot_configs = plate_analysis_no_zeros_boxplot_configs),
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list(out_dir = out_dir_qc, filename = "L_vs_K_for_strains_2SD_outside_mean_K",
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plot_configs = l_outside_2sd_k_plot_configs),
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list(out_dir = out_dir_qc, filename = "delta_background_vs_K_for_strains_2sd_outside_mean_K",
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plot_configs = delta_bg_outside_2sd_k_plot_configs)
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)
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# # Generating quality control plots in parallel
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# furrr::future_map(plot_configs, function(config) {
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# generate_and_save_plots(config$out_dir, config$filename, config$plot_configs)
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# }, .options = furrr_options(seed = TRUE))
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# Generating quality control plots in parallel
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furrr::future_map(plot_configs, function(config) {
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generate_and_save_plots(config$out_dir, config$filename, config$plot_configs)
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}, .options = furrr_options(seed = TRUE))
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# Process background strains
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bg_strains <- c("YDL227C")
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